HLA Fusion Research User Manual v3_0

HLA Fusion Research User Manual v3_0
User Manual
™
HLA Fusion Software Research
HLA Fusion™ Software v. 3.0
2012/03
For Research Use Only. Not For Use In Diagnostic Procedures
Advancing Transplant Diagnostics
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21001 Kittridge Street, Canoga Park, CA 91303-2801
Tel: (818) 702-0042 Fax: (818) 702-6904 www.onelambda.com
One Lambda | User Manual: HLA Fusion™ Research Software 3.0 (FUSREPGRX)
HLA Fusion Research™, ConsenSys™, and Micro SSP™ are Trademarks of One Lambda, Inc.
®
Luminex is a registered Trademark of Luminex Corporation.
®
Windows is a registered Trademark of Microsoft Corporation.
© Copyright 2012, One Lambda, Inc.
All One Lambda software products are designed to assist personnel experienced in HLA
analysis by suggesting typing results. However, any clinical or diagnostic results must be
carefully reviewed by a person qualified in HLA typing to assure correctness. This software may
be used to aid in suggesting results, but should not be used as the sole method for determining
reportable results. This software is meant as a laboratory aid, not as a source of definitive
results. The software design does not mitigate hazards associated with the software. The
laboratory director or technologist trained in histocompatibility testing is required to review all
data to detect any problems with the software.
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Table of Contents
Introduction ............................................................................................................................................................. 12
What is HLA Fusion Research™? ........................................................................................................................... 12
README Files ....................................................................................................................................................... 12
Program Updates ................................................................................................................................................. 12
Limitations of the Program .................................................................................................................................. 13
Technical Support ................................................................................................................................................ 13
Scope of This Manual ........................................................................................................................................... 14
Navigation ................................................................................................................................................................ 15
Logging On To Fusion Research ........................................................................................................................... 15
Retrieving a Forgotten User Name or Password ................................................................................................. 15
Key System Settings ............................................................................................................................................. 16
Screen Resolution ............................................................................................................................................ 16
File Permissions ............................................................................................................................................... 18
Character Length.............................................................................................................................................. 18
User Interface .......................................................................................................................................................... 19
Fusion Research Home Pages .............................................................................................................................. 19
The Navigator....................................................................................................................................................... 20
Navigator Tree ................................................................................................................................................. 21
Results Grouping .................................................................................................................................................. 21
Group by Product ............................................................................................................................................. 21
Group by Catalog ............................................................................................................................................. 22
Group by Test Date .......................................................................................................................................... 23
Group by Session Date ..................................................................................................................................... 23
Accessing HLA Fusion Research™ Software Functions ............................................................................................. 24
Main Menu Options ............................................................................................................................................. 24
Analyze Data .................................................................................................................................................... 24
Reports ............................................................................................................................................................. 24
Data .................................................................................................................................................................. 25
Sample ............................................................................................................................................................. 25
Patient Info ...................................................................................................................................................... 25
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Profile ............................................................................................................................................................... 26
Utilities ............................................................................................................................................................. 26
Help .................................................................................................................................................................. 26
Exit ................................................................................................................................................................... 27
Toolbar Buttons ................................................................................................................................................... 27
Home Button.................................................................................................................................................... 28
Find .................................................................................................................................................................. 28
Print Report...................................................................................................................................................... 28
Preview Report ................................................................................................................................................ 28
Print Screen...................................................................................................................................................... 29
Magnify ............................................................................................................................................................ 29
Reports ............................................................................................................................................................. 29
Show Navigator ................................................................................................................................................ 30
Patient .............................................................................................................................................................. 30
Related Records ............................................................................................................................................... 30
Side-by-Side Analysis ....................................................................................................................................... 31
Product Data Analysis .............................................................................................................................................. 32
Sample Navigation ................................................................................................................................................... 33
ConsenSys Analysis .................................................................................................................................................. 34
Overview: ConsenSys Analysis ............................................................................................................................. 35
Define the File Naming Convention ................................................................................................................. 36
Update Serology Equivalent and Catalog files ................................................................................................. 37
Starting a Combined Analysis Session ............................................................................................................. 38
Adding an Ab1 File ........................................................................................................................................... 40
The ConsenSys Analysis window...................................................................................................................... 40
The EPG Navigator ............................................................................................................................................... 41
Sample Navigator ............................................................................................................................................. 41
Allele Filter ....................................................................................................................................................... 41
Confirm Filter ................................................................................................................................................... 42
Nucleotide Caller.............................................................................................................................................. 42
Electropherogram Navigator ........................................................................................................................... 42
LABType/ConsenSys Selection ......................................................................................................................... 42
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Loci Navigation................................................................................................................................................. 43
Nucleotide position/Mismatch Navigator ....................................................................................................... 43
Reanalyze ......................................................................................................................................................... 43
Comments ........................................................................................................................................................ 43
More Tests ....................................................................................................................................................... 44
Key List ............................................................................................................................................................. 44
Accept Base Call ............................................................................................................................................... 45
Quick Reports................................................................................................................................................... 45
Full Reports ...................................................................................................................................................... 45
Filters ............................................................................................................................................................... 46
Save > > ............................................................................................................................................................ 47
Confirm >> ....................................................................................................................................................... 47
Close................................................................................................................................................................. 48
Exon-Specific Summary Pane ........................................................................................................................... 48
Exon Summary Pane Right-click Options ......................................................................................................... 49
EPG Panel ......................................................................................................................................................... 50
Allele Typing Result Pane ................................................................................................................................. 50
EPG Pane .......................................................................................................................................................... 51
Edit Base Calls .................................................................................................................................................. 51
Navigating the Alignment Screens ................................................................................................................... 51
Sample Alignment ............................................................................................................................................ 52
Sample Base Call Score Alignment................................................................................................................... 52
Allele Pair Alignment........................................................................................................................................ 53
SSO Analysis ............................................................................................................................................................. 54
Starting SSO Analysis ........................................................................................................................................... 54
Opening a SSO Analysis Session ....................................................................................................................... 54
Displaying an SSO Analysis Window .................................................................................................................... 58
Histograms ....................................................................................................................................................... 59
Configuring SSO Data Analysis ............................................................................................................................. 59
P Grouping ....................................................................................................................................................... 59
G Grouping ....................................................................................................................................................... 59
Minimum Positive Control ............................................................................................................................... 60
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Minimum Bead Count ...................................................................................................................................... 60
Set Sure Reaction Bead .................................................................................................................................... 60
SSO Analysis Window Overview .............................................................................................................................. 61
Using the SSO Data Analysis window................................................................................................................... 61
SSO Analysis window - Quadrant 1 ...................................................................................................................... 61
QC Tab.............................................................................................................................................................. 61
Reaction Patterns Tab ...................................................................................................................................... 62
Local QC Tab..................................................................................................................................................... 63
Patient/Sample Results Tab ............................................................................................................................. 63
SSO Analysis window - Quadrant 2 ...................................................................................................................... 64
Bead Profile ...................................................................................................................................................... 64
Raw Data Table ................................................................................................................................................ 65
Bead Info Tab ................................................................................................................................................... 66
SSO Analysis window - Quadrant 3 ...................................................................................................................... 67
Sample Profile .................................................................................................................................................. 67
View Delta ........................................................................................................................................................ 68
Comments ........................................................................................................................................................ 69
SSO Analysis window - Quadrant 4 ...................................................................................................................... 69
SSO Results and Assignment panel .................................................................................................................. 69
Analyze SSO Data ..................................................................................................................................................... 71
Make Typing Assignments in SSO Analysis .......................................................................................................... 72
Typing Assignments ......................................................................................................................................... 72
Flagging a Sample for Further Testing ............................................................................................................. 73
Manual Assignments........................................................................................................................................ 73
SSO Batch Analysis ........................................................................................................................................... 73
Save Assignments ............................................................................................................................................ 74
Confirm Assignments ....................................................................................................................................... 74
Print Screen...................................................................................................................................................... 74
Micro SSP Analysis ................................................................................................................................................... 75
Start Micro SSP Analysis........................................................................................................................................... 76
Configure Micro SSP Data Analysis .......................................................................................................................... 80
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Assign Code ...................................................................................................................................................... 80
Bw4/Bw6 in Serology ....................................................................................................................................... 81
Demographic Information ............................................................................................................................... 81
Using the Micro SSP Analysis Window..................................................................................................................... 82
Test Gel Pane ................................................................................................................................................... 83
View Well Details ............................................................................................................................................. 84
Working with Gel Images ................................................................................................................................. 84
Add Samples .................................................................................................................................................... 86
Rxn (Reaction) Tab ........................................................................................................................................... 87
Number of Allowable False Reactions ............................................................................................................. 89
Force One False Reaction................................................................................................................................. 89
Micro SSP Combined Analysis .................................................................................................................................. 90
Make Typing Assignments in Micro SSP Analysis .................................................................................................... 92
The Pairs Tab .................................................................................................................................................... 93
Assign an Allele Pair from the Suggested List .................................................................................................. 93
The Match Tab ................................................................................................................................................. 94
Manual Allele Pair Assignment ........................................................................................................................ 94
Possible Allele Codes ....................................................................................................................................... 95
Allele Code Assignment ................................................................................................................................... 95
Manual Allele Code Assignment ...................................................................................................................... 96
Unknown Allele Codes ..................................................................................................................................... 96
Other Assignment ............................................................................................................................................ 98
Possible Serology Field..................................................................................................................................... 99
Translate (non-current nomenclature format only) ...................................................................................... 100
Adding Comments to Samples ....................................................................................................................... 100
Flagging a Sample for Further Testing ........................................................................................................... 101
Printing the Current Analysis Window........................................................................................................... 101
Preview or Print Reports ................................................................................................................................ 101
Assign Coded Results ..................................................................................................................................... 102
Save Assignments .......................................................................................................................................... 102
Confirm Assignments ..................................................................................................................................... 102
Micro SSP Session Summary .................................................................................................................................. 103
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Navigator Right-Click Menu Options for Micro SSP ............................................................................................... 105
Session-Level Options ........................................................................................................................................ 105
Reanalyze with New Nomenclature .............................................................................................................. 105
Sample-Level Options ........................................................................................................................................ 106
Related Records ............................................................................................................................................. 106
Side by Side Analysis ...................................................................................................................................... 106
Quantiplex Beads ................................................................................................................................................... 108
Entering and Using Quantiplex Bead Information ................................................................................................. 109
Acquiring Quantiplex Beads Data ...................................................................................................................... 109
Start LABScreen Analysis with Quantiplex Beads .......................................................................................... 111
View SFI Information in LABScreen Analysis.................................................................................................. 111
View MFI Information with Quantiplex Beads............................................................................................... 112
Session Summary and Logs .................................................................................................................................... 114
What is the Session Summary? .......................................................................................................................... 114
Example Session Summary ............................................................................................................................ 114
Creating and Managing Session Logs................................................................................................................. 114
Creating a Session Log ................................................................................................................................... 114
Managing Session Logs .................................................................................................................................. 115
Printing Session Logs...................................................................................................................................... 115
Reports ................................................................................................................................................................... 116
Using the Reports Window ................................................................................................................................ 116
Accessing the Reports Window ..................................................................................................................... 116
Select Report Type ......................................................................................................................................... 117
Refine Report Input........................................................................................................................................ 118
Session/Sample Selection .............................................................................................................................. 119
View, Print or Export Reports ........................................................................................................................ 120
Export Report ................................................................................................................................................. 121
Accessing Reports from the My Favorite Menu ............................................................................................ 122
Removing Reports from My Favorite............................................................................................................. 122
Report Tools ........................................................................................................................................................... 124
Customizing Report Appearance ....................................................................................................................... 124
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Creating Custom Data Export Templates....................................................................................................... 125
Creating Custom Reports ............................................................................................................................... 126
Custom Molecular and Antibody Report Setup ............................................................................................. 127
Sample Summary ........................................................................................................................................... 128
Molecular Typing Sample Summary .............................................................................................................. 128
Antibody Screening Sample Summary ........................................................................................................... 129
View Records ......................................................................................................................................................... 130
Patient Info ........................................................................................................................................................ 131
Audit Trail Report............................................................................................................................................... 132
Report Types .......................................................................................................................................................... 134
Data Management ................................................................................................................................................. 137
Session Management......................................................................................................................................... 138
Manage Session Data Window .......................................................................................................................... 138
Sample Management ............................................................................................................................................. 141
Importing Sample Lists........................................................................................................................................... 142
Information Formats for Sample Lists ................................................................................................................... 143
New packing list format ................................................................................................................................. 143
Packing list: Old Standard ‘X’ samples ........................................................................................................... 143
Old packing list format, '11' for AB/DR samples ............................................................................................ 143
Comma-Delimited Format ............................................................................................................................. 143
Tab-Delimited Format .................................................................................................................................... 144
SDF Format..................................................................................................................................................... 144
Local/Sample/Patient ID Only ........................................................................................................................ 144
Viewing and Editing Sample Information .......................................................................................................... 144
Test Lists................................................................................................................................................................. 146
Creating New Test Lists .................................................................................................................................. 146
Viewing and Editing Existing Test Lists .......................................................................................................... 147
Deleting Existing Test Lists ............................................................................................................................. 147
Exporting Test Lists ........................................................................................................................................ 147
Patient Information ............................................................................................................................................... 148
Importing Patient/Donor Lists ............................................................................................................................... 149
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Managing Patient/Donor Records ......................................................................................................................... 150
Adding New Patient/Donor Records.............................................................................................................. 150
Lookup Patient/Donor Records ..................................................................................................................... 151
Editing Patient/Donor Records ...................................................................................................................... 152
Associating a Patient/Donor ID with Sample ID’s .......................................................................................... 152
Translating Associated Patient/Donor Results to New Allele Code............................................................... 154
Associating Patient and Donor Records......................................................................................................... 154
Associating a Donor with Donor PRA Results ................................................................................................ 155
Printing Patient/Donor Records..................................................................................................................... 156
Exporting Patient/Donor Records .................................................................................................................. 156
Archiving Patient/Donor Records .................................................................................................................. 156
Deleting Patient/Donor Records .................................................................................................................... 157
Creating Patient/Donor Lists.......................................................................................................................... 157
Patient Antibody Tracking...................................................................................................................................... 159
Profile Management .............................................................................................................................................. 163
User Management ............................................................................................................................................. 164
Viewing the User List ..................................................................................................................................... 165
Adding New Users .......................................................................................................................................... 165
Editing User Profiles ....................................................................................................................................... 165
Changing Passwords ...................................................................................................................................... 166
Resetting Passwords ...................................................................................................................................... 166
Changing User Privileges ................................................................................................................................ 166
Inactivating Users........................................................................................................................................... 167
Lab Profile .............................................................................................................................................................. 168
Editing the Lab Profile .................................................................................................................................... 168
Managing Lab Codes ...................................................................................................................................... 169
Utilities ................................................................................................................................................................... 170
Managing Catalog Reference Files..................................................................................................................... 171
Updating Catalog Files from a Local or Network Drive .................................................................................. 171
Updating Catalog Files from the One Lambda Download Site ...................................................................... 174
Updating Molecular Typing Reference Files .................................................................................................. 175
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Updating NMDP Codes from a Local or Network drive ................................................................................. 175
Updating NMDP Files from the NMDP Website ............................................................................................ 176
Creating a Local Code File .............................................................................................................................. 176
Updating the Local Code File ......................................................................................................................... 177
Updating P Group and G Group Files from the One Lambda Website .......................................................... 177
Updating Serology Equivalent File from One Lambda Website..................................................................... 178
Catalog Management and Information ............................................................................................................. 180
Archive Catalogs............................................................................................................................................. 180
Un-Archive Files ............................................................................................................................................. 181
Viewing Catalog File Information................................................................................................................... 181
Deleting Catalog File Information .................................................................................................................. 182
Reporting Catalog File Information................................................................................................................ 182
Associating Product Catalog Files and Luminex Templates ........................................................................... 182
Importing Allele Frequency Files (Demographic Frequency)......................................................................... 183
Updating Allele Frequency Files (Demographic Frequency) .......................................................................... 185
Managing CREG List Information ................................................................................................................... 186
Changing Product Configuration Settings .............................................................................................................. 187
Changing Molecular Product Configuration ...................................................................................................... 188
P and G Code Configuration for LABType ...................................................................................................... 189
Changing Antibody Product Configuration .................................................................................................... 190
Creating a Combined LABScreen Session Catalog ......................................................................................... 191
Changing LABScreen Default Negative Serum Control Value ........................................................................ 192
Changing the LABScreen Mixed Product Configuration ................................................................................ 192
Importing NS Files .......................................................................................................................................... 193
Choosing General Settings ..................................................................................................................................... 194
Printer Defaults .................................................................................................................................................. 194
Setting HLA Fusion Default URLs and Directory Paths....................................................................................... 195
Activating Products ............................................................................................................................................ 196
Software Validation ............................................................................................................................................... 197
IQ (Installation Qualification)............................................................................................................................. 197
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Introduction
What is HLA Fusion Research™?
HLA Fusion Research is a companion to One Lambda’s ConsenSys™, SSO, and Micro SSP™ products.
This software runs in both stand-alone, (on a single computer) and in network environments.
The features of this software allow you to do the following:
•
Import raw data
•
Manually enter reaction patterns
•
Analyze the raw data and review the results in graphical form
•
Easily update product information (new product and lot information)
•
Search for specific data and create standard or custom reports
•
Compare results to One Lambda quality control (QC) data
README Files
A README file is provided with each software update.
This file provides a list of significant changes to the software and also critical information that is not
included in the user’s manual.
Program Updates
Note: For best results, always make sure you are using the latest version of HLA Fusion™ Research
software.
You may obtain updates of HLA Fusion™ Research by request. Please contact your One Lambda, Inc.
representative for a copy of the software or see the Technical Support section for more contact
information. Product information updates, (catalog files, etc.) for HLA Fusion™ Research are available
through your One Lambda Inc. representative, or from the One Lambda website:
http://download.onelambda.com
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Limitations of the Program
All One Lambda software products are designed to assist personnel experienced in HLA analysis by
suggesting typing results. However, results must be carefully reviewed by a person qualified in HLA
typing to assure correctness. This software may be used to aid in suggesting results, but should not be
used as the sole method for determining reportable results. This software is meant as a laboratory aid,
not as a source of definitive results.
For the reliability of patient information stored in the database, users must ensure that the identifier
for each patient is unique and that each sample identifier is unique.
The storage capability of HLA Fusion™ Research is limited by the Microsoft SQL Server Desktop
Engine or SQL Server 2008. (The user must manually archive data.)
HLA Fusion™ Research assumes that data for each required input is in a standard format that has not
been modified.
The HLA Fusion™ Research analyzes a data file in one of the following formats:
.ab1 file for ConsenSys
.csv file for SSO
.csv file for Micro SSP
The data file name, (also known as a Session ID) can be up to 100 characters long and includes the .csv
extension.
The data is generated based on original, unmodified templates provided by One Lambda, Inc.
The user is responsible for final assignments and must review all suggested results.
Technical Support
For technical support or to report software problems, contact your One Lambda representative.
From the United States, call 800-822-8824, or from the Greater Los Angeles Area, call 818-702-0042.
Contact us by e-mail at: [email protected]
For system requirements, see the HLA Fusion Research Installation Guide.
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Scope of This Manual
This manual provides information on how to import raw data and then analyze it, making adjustments
in cut-off values as necessary. It is very important to recognize that the QC, (Quality Control) data used
with this program and the defaults set in this program are based on One Lambda’s experience with the
product in a tightly-controlled research and development environment. Thus, a laboratory performing
HLA typing in another environment may need to reset cutoff values to meet specific laboratory
requirements.
From the Main Menu of HLA Fusion™ Research, you can access the three major components of
the program:
•
Analyze Data
•
Manage Records
•
Manage Samples
In addition, you may also access the following features:
•
Patient Information
•
Utilities
•
Help
This manual helps you start using One Lambda’s HLA Fusion™ Research. It includes an overview of
the system and then quickly takes you into the process of analyzing data.
See the HLA Fusion Research Installation Guide for installation instructions.
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Navigation
This section describes the various ways to access the HLA Fusion™ Research software functions, as
well as how to use the Navigator tool to access and move between sessions and samples.
Logging On To Fusion Research
Double-click the HLA Fusion Research icon on your computer desktop.
You can also open the program by clicking Start > All Programs > One Lambda > HLA Fusion
Research.
The Security Login dialog box is displayed.
1. Enter your User Name and Password.
2. Click the Log In
button to open the program.
Note: The Database field displays the database to which you are currently connected.
Retrieving a Forgotten User Name or Password
If you forget your HLA Fusion Research password, click the Forgot Password link, and answer the two
security questions you were asked when you set up your user profile. The password is displayed when
the questions are answered correctly.
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If you forget your user name, click the Forgot UserName link,
enter your first and last name, and select your lab role,
(supervisor or technician).
The system displays the user name matching the data you
provide.
Key System Settings
Screen Resolution
HLA Fusion software requires a screen resolution of 1280 x 960. The software displays a message if
your current resolution is less than the expected settings.
Minimum Screen Resolution
Note:
You can choose to suppress this message through the Edit link on the General
Configurations section of the Home page.
You can select Yes to have the system attempt to make the adjustment. It will continue to start the
application even if it could not adjust the resolution. Or, you can select No and adjust it manually.
In addition, if your computer is running the Microsoft® Windows 7® operating system, the text display
setting must be set to Smaller - 100% (default).
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Take these steps if you need to adjust the screen text display size:
Right-click on the computer desktop. Select the Screen Resolution option.
Windows 7 Screen Resolution window
The Screen Resolution window displays.
Select the Make text and other items larger or
smaller.
1. Select Smaller sized text.
Windows - selecting smaller sized text
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File Permissions
All HLA Fusion Research users must have read and write permissions to the following directories and
files:
•
•
•
OneLambda.Fusion.Interface.exe.config
ReportMap.xml
C:\OLI Fusion\
…and all the sub directories and the files in these directories.
Character Length
If you are using SQL Server 2000 and encounter a report or results that require more than 8000
characters of data, you must update to SQL Server 2005.
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User Interface
Fusion Research Home Pages
Opens the Catalog
Management window
Opens the
Reference File
Opens the Analysis
Product Selection window
Notification that
new or updated
catalogs, NMDP
and Serology
equivalent files
are available.
Opens the
User List
window
Opens the
Navigator
Search
Criteria
The Fusion
Explorer: click
any button to
open the
corresponding
product
Status
Opens the
printer setup
window
Opens the Fusion
setup window for
general, printer,
URL’s and directory
path setup.
Green if
Audit
Logging is on,
Red if it’s off
Note: If the current page does not show updated information upon modification or downloads, go
back to the main Home page, and then return to the product home page to see the changes.
This interface is the default when you first log in to HLA Fusion Research, but you can change it.
On the HLA Fusion Research Menu Bar, click
Utilities > General Settings and select the
General Setting tab.
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To go to home page for one of the products listed in the bottom left area of the page, (the Fusion
Research Explorer) click the appropriate button in this area, as in this example for SSO:
Or, click the KIR/SSO button on the Toolbar as shown here.
Or, click the ConsenSys Home Page button in the Fusion Research Explorer.
You can also click the ConsenSys (aka: SBT)
Toolbar at the top of the screen.
button which is located on the HLA Fusion Research
Note: Migrated and upgraded databases also use this same interface.
The Navigator
If the Navigator tab is not already displayed on the right of the application window, click the Show
Navigator
toolbar button to activate the Navigator function.
Otherwise, move your cursor over the Navigator tab on the right border of the application window to
slide the Navigator into view.
The Fusion Navigator
When the top of the Navigator window is Blue, it will remain open
until you click any button or control, or on various other active areas
of the main screen.
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Navigator Tree
Using the Navigator tree, you can easily move between analysis sessions and samples.
Note: Double click on a session, or click the + sign to the left of the catalog, date or product module
to display the list of sessions.
Results Grouping
The sessions and samples displayed though the Navigator tool can be sorted by various criteria:
•
•
•
•
Product type
Catalog (Session Name)
Test Date
Session Date
The default is to group by Product. See the next few sections for details about these different display
options.
Group by Product
The Navigator displays imported sessions for each product type based on the date range and other
criteria set in the Find option.
To set or adjust the default search settings for HLA Fusion Research, do the following:
1. Click the Find
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This will open the Search Criteria screen.
Whatever search settings you set here become the default search settings for HLA Fusion Research.
So, if you’re already in the analysis mode with a certain product, only the sessions that fit the Find
Criteria you’ve set for that product will display.
You can choose to search by Patient ID, Sample ID, Session ID, or Other.
Other allows you to provide multiple search criteria: Test Date range, Session Date range,
Session status, and Catalog Type.
The Find dialog box also allows you to modify the Navigator session sort and display criteria.
Note: The date range set here, in the Session Date field, is used as the default date range
throughout the software, such as in the Navigator and Reports windows. Each time you change it,
and click Find, the default changes for the rest of the application.
Group by Catalog
Navigator: Product List
When you select the Catalog option, sessions are displayed in
alphanumeric order by catalog name.
Click the  sign next to the product type you’re interested in to display
its individual sessions.
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The sessions displayed in blue are the ones that have not yet been
reviewed. Once you review a session, its color on the Navigator list
changes to black.
Otherwise, the use of this tool is the same as described above in Group
by Product.
Group by Test Date
When you select the Test Date group option, sessions are displayed in
chronological order by their test dates.
Otherwise, the use of this tool is the same as described previously in Group
by Catalog or Group by Product.
Group by Session Date
When you select the Session Date option, sessions are displayed in order
of their creation dates.
Click a session name to display the samples within this session and a session
summary.
Otherwise, the use of this tool is the same as described above in Group by
Product, Catalog, or Test Date.
If a session sample is listed in red, this means the sample failed in batch
analysis.
Click a sample name to display it in an analysis window.
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Accessing HLA Fusion Research™ Software Functions
Main Menu Options
You can access HLA Fusion Research functionality at any time from the Menu Bar, which is
displayed at the top of all HLA Fusion Research application windows.
See the following sections for a list of the options available under each main menu item.
Analyze Data
Each option under this menu item is a molecular product for which you can import CSV files, or
manually enter reactions and analyze data.
Any of these analysis programs can also be opened by clicking on their Toolbar Icons or the tiles for
each program at the bottom left of the screen in the Fusion Explorer.
For details, see the individual product analysis sections in this user manual.
Reports
When you select this menu item, the Reports page is displayed, allowing you to create reports of your
analysis data.
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Data
When you select this menu item, a Data window is displayed that allows you to manage, (delete,
archive, activate and move) sessions and samples, map session alleles to the new NMDP nomenclature,
and view/print log files of session data.
Sample
Options under this menu item pertain to importing, creating, managing, and exporting sample
information. This is also the menu to use for managing Luminex test lists and for creating sample work
lists and plate designs.
Patient Info
Options under this menu item pertain to importing patient and/or donor lists, and managing
individual patient and/or donor information.
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Profile
There are options under this menu item for creating and managing your own user profile, lists of
system users and privileges, and lab information.
There is also an option for switching between the home page options, depending on your system
navigation preferences.
Utilities
The options under this menu item pertain to importing catalog, code and serology files, configuring the
molecular and products you analyze, setting up your HLA Fusion Research system, and system
validation.
Help
This menu item allows you to access the following HLA Fusion Research Software information:
•
•
Online help, which provides guidance in using HLA Fusion Research Software.
•
Dynamically updated Frequently Asked Questions (FAQs) about the HLA Fusion Research
software.
•
The build and version number of the HLA Fusion Research Software application you are
currently using.
Notification of updates and a description of new features in the latest HLA Fusion Research
software.
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Note: The online help can be accessed from anywhere within the HLA Fusion Research application
when you press the F1 key.
Occasionally, updates are made to the online help between releases of the HLA Fusion Research. To
ensure you have the most current help file, you can either check the OLI download site,
download.onelambda.com - /pub/tray_info/Windows/HLA_Fusion_Catalogs/Document/, or you
can enable the auto-download feature from the Fusion Research default home page.
Exit
When you select this menu item, a dialog box displays that allows you either to select
Yes to exit and close the HLA Fusion Research application, or select No to keep the
current session open.
Toolbar Buttons
HLA Fusion Research provides a toolbar, displayed just below the Menu Bar, with access to commonly
used functions.
•
Note that some icons may not be available or enabled unless you’re on an analysis screen.
•
Some icons are only enabled in HLA Fusion Research while other icons are not enabled in the
research version.
The table on the next page describes each toolbar button.
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Button
Name or Function
Home
Find
Home Button
Wherever you are in Fusion, clicking the Home
returns you to the Fusion Home Page.
button
Print Report
Preview Report
Print Screen
Magnify
Reports
Find
Clicking the Find button opens the Search Screen where you
can search by Patient ID, Sample ID, Session ID, or by
Other criteria.
The Search Screen also allows you to modify the Navigator
session sort and display criteria.
Show Navigator
Patient Information
Print Report
Related Records
From any analysis window, you can click the Print Report
button to display a list of the reports that you can print. The
reports you see listed are specific to the product you are
currently analyzing.
Side-by-Side Analysis
SBT/ConsenSys
If you have set a default printer for your system, (configured
through Utilities > Printer Setup) the selected report is sent
directly to the specified printer.
SSO/KIR
Otherwise, a dialog box is displayed from which you can select a
printer.
Micro SSP
Preview Report
From any Analysis Screen, click the Preview Report
button to display a list of reports you can
investigate before printing. The reports listed are specific to the product you’re currently analyzing.
The reports are displayed in a preview window.


and Export
buttons in the preview window to output the report in
Use the Print
the selected format.
Click the Close button at the upper right of the screen to exit the preview window.
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Print Screen
From any Analysis Screen, click the Print Screen
screen shot of the entire Fusion screen display.
Click the Print
button to open a new window containing a
button, (top, left corner)to send the screen shot directly to the printer.
To close this window, click the Exit
button or the Close
button.
Magnify
From any analysis window, click the Magnify
any section of the window.
button to activate the magnifying glass and enlarge

Use the arrow keys on your computer keyboard to
increase or decrease the height and width of the
magnified area.

Click anywhere on the screen to deactivate the
magnifying glass.
Reports
From any screen, click the Reports
You can also click the Reports
the screen.
button on the Fusion Toolbar to open the Reports Screen.
button located in the Fusion Explorer at the bottom, left of
The type of available reports listed will
depend on the product and nature of
analysis you’re conducting.
Please see the section on Reports for
detailed information.
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Show Navigator
Click the Show Navigator
button if the Navigator tab, normally
displayed on the upper right side of the application window, is not
visible.
Once the Navigator tab is displayed, you can move your cursor over it to
slide the Navigator panel open. When the top of the Navigator window
is Blue, it will remain open until you click any button or control, or on
various other active areas of the main screen.
Patient
From any analysis window, click the Patient button to display the Patient/Donor Information
Screen where you can enter or edit information related to a patient or donor and associate it with the
current sample.
Patient/Donor Information Screen
Related Records
A related record is a sample that is associated in some way with the
current sample or patient.
From any analysis window, click the Related Records
button to
load all records related to the current sample into the drop-down list
in the Sample ID field. Use the sample navigation arrows to display
the analysis of each related record one-by-one.
To exit from the related records mode, click the <<Summary link
next to the Sample ID field near the top, center of the screen.
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Note: This function can also be accessed by right-clicking a sample in the Navigator. See the
product-specific sections of this manual for more information about using this feature.
Side-by-Side Analysis
From any analysis window, click the Side-by-Side Analysis button to compare the current sample
analysis with previous analysis sessions for the same Sample ID.
Select a previous sample analysis from the displayed list to compare to the current one. The two
analysis windows are then displayed together in a comparison window.
Each window can be resized and moved by dragging and dropping. Click again on the Side-by-Side
Analysis button to cancel the comparison display.
Current
Analysis
Previous
Analysis
Note: This function can also be accessed by right-clicking a sample in the Navigator.
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Product Data Analysis
Click any of the Product Data Analysis buttons to display the product home page, import a session
file, manually enter a session, or select from the Navigator list of already imported sessions for that
product.
Remember that you can also access any product by clicking on it in the HLA Fusion Explorer at the
bottom, right of the screen, or by clicking on Analyze Data on the Fusion Menu Bar.
Fusion Explorer
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Sample Navigation
The Sample Navigation tools, (only accessible from the analysis windows) give you access to all the
samples in the current session.
You can select a different sample within the same session either by selecting from the drop-down list in
the Sample ID field, or by clicking the forward/back arrow buttons to the right.
Sample ID
First
Sample
Previous
Sample
Next
Sample
Last
Sample
Current
Sample
Clicking on the drop-down
arrow displays the samples within the current session.
Selecting a sample from this list in the Sample ID field makes the selected sample active in the analysis
window.
Alternatively, you can use the Forward and Back Arrow
samples.
buttons to select different
At the top of the main analysis window, click the word <<Summary to return to the Summary Screen
for the current session.
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ConsenSys Analysis
HLA Fusion™ Research ConsenSys Analysis uses sequence-based typing techniques, (SBT) to analyze
sequence data and to determine an HLA typing. The software aligns sequence data generated by an
ABI sequencer with IMGT/HLA data and assigns allele typing based on sequence similarity. The
software also normalizes the electropherogram (EPG) so peaks are uniform in height, this enables the
quick and clear detection of polymorphic SNPs and the correct HLA type is automatically identified in
most cases. Through the sequence navigator, the end user is guided through all sequence mismatches
which require auditing. Auditing each nucleotide mismatch will refine the final assigned allele typing.
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Overview: ConsenSys Analysis
HLA Fusion™ Research analysis uses sequence-based-typing techniques, (SBT) to analyze sequence
data and determine an HLA typing.
To begin a ConsenSys™ analysis session, you build a session using Sample IDs or Ab1 files. This
information can be saved as a Plate Record for later use. You can also analyze Ab1 files directly.
Base mismatches or close base calls are flagged by the software and must be resolved by the user.
From the Analysis window you can:

View the electropherogram, (EPG) results

Add sample comments

Flag a sample for more testing

Accept, edit or audit base calls

Compare sequence data against IMGT/HLA reference sequences and the EPG interpretation
algorithm to automatically assign HLA alleles that match your data.

Utilize tools to audit, manually edit, compare, and report HLA allele assignments.

Improve SSO results significantly with the combined analysis feature using SBT data.
Analysis Objectives:

Audit all polymorphic bases and confirm all base assignments.

Audit and edit all mismatches and heterozygous bases to obtain the best-matched sequences
for heterozygous alleles.

Evaluate and confirm final allele assignments.
Note: Before beginning, make sure you have the most up-to-date serology. On the Fusion Research
Menu Bar, click Utilities > Update Reference > Update Reference File. Select Update Serology
Equivalent and click the Import Serology button. Also make sure you have updated the ConsenSys
reference files.
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Define the File Naming Convention
With HLA Fusion™ Research, you can define and specify the file naming rules to be used with
ConsenSys:
1. On the Fusion Research Menu Bar, click Utilities > Molecular Product Configuration >
Ab1 Filename Configuration.
The Ab1 Filename Configuration screen opens:
When defining the Ab1 and Locus file naming configurations, remember that the Sample ID name
must match between LABType and SBT sessions for combined analysis.
For example:
“SampleName_BLocus_2F”
Or…
“SampleName_HLA-B_2F”
Another Example:
TEF401
in a LABType session
TEF401_DRB1_2F
in a ConsenSys session
Remember to only use an underscore “_” in sample names. No spaces or other special characters
should be used.
2. As you make changes to the Ab1 file configuration, Fusion
displays an example of what a Sample ID might look like
using the new configuration:
3. Click the Save
selections.
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Update Serology Equivalent and Catalog files
To analyze SBT data, first make sure that you have the most up to date serology and ConsenSys™
catalog files.
To update serology files:
1. Click: Utilities > Update References > Update Reference File
2. Select the Serology equivalent radio button.
3. Choose the appropriate Sero_equivalent file from the list on the right side of the screen.
a. If a serology file does not appear in the window, navigate to it by using the directory tree
on the left.
4. Select the appropriate serology file
button.
5. Click the Import Serology
After successful serology file importation, you should see this
message:
6. Click the OK
7. Click the Close
button to close the confirmation message.
button when you’re done.
To update ConsenSys™ file catalogs:
1. Go to Utilities > Update References > Update Reference File >
2. Select the ConsenSys radio button.
3. If the ConsenSys™ catalog file(s) are not listed, navigate to it by using the directory tree on the
left.
4. Select the ConsenSys™ catalog files to import.
button.
5. Select Import ConsenSys
After the catalog files have been successfully imported you
should see the following message:
6. Click the OK
7. Click the Close
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Starting a Combined Analysis Session
Note: If analyzing LabType™ data in combination with ConsenSys™ data, make sure that the database
linked to HLA Fusion™ Research matches the database used to analyze SSO data in HLA Fusion™. If
the database names are different you will not be able to link SSO and SBT data. Nomenclature
updates between SSO and SBT analysis must also match.
1. Click the ConsenSys home page button…
…or the ConsenSys Toolbar
button to open the ConsenSys Home Page.
ConsenSys Home Page
The ConsenSys Home Page displays important information concerning your ConsenSys products and
reference files, and the Ab1 File Name Format being used.
2. Next, click the Manual Entry button located at the top, left
corner of the screen.
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When the dialog box for starting a ConsenSys Manual Entry session displays, you’ll notice that Fusion
has already assigned a session name.

The Analysis Session Name: You can rename the session if you prefer. Remember that the
Session Name must be unique within Fusion Research.
Start Manual Entry ConsenSys Analysis

The Test Date: You may accept the current Test Date, or select a different test date by
clicking the Down Arrow and selecting another date from the pop-up calendar.
3. You have the choice of creating a new session/tray or open existing sequencing samples.
To create a New Session/Tray:
Click the Create New Session/Tray
button.
A new window is displayed to allow for subsequent session/tray information.
4. Enter all required information in the fields at the top of the window.
5. Click the Start Analysis button at the bottom of this screen.
Session Tray/Information Window
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The ConsenSys analysis window is displayed.
Adding an Ab1 File
1. From the Session/Tray information window, click the Add Ab1 File button at the bottom. The
file import window is displayed.
2. Browse to the folder on your computer containing the Ab1 data file(s) you want, select the file,
and click Open. The imported Ab1 data file(s) will be displayed on the right side of the
Analysis window.
Note: You can select and import more than one file at a time by holding down the CTRL key.
3. Click the Start Analysis button to analyze the Ab1 files.
The ConsenSys Analysis window
The main ConsenSys screen is divided into four general areas:
1. The EPG Navigator, (moveable)
2. An exon-specific summary
3. The EPG panel
4. Allele Typing Result Pane
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The EPG Navigator
Nucleotide Caller
Deactivate
Click to
and undo
Insert
all edits
Click arrows to made to comments
for a sample
navigate through
E PG
the EPG
Accept
base call
Generate a
quick report
with EPG
peaks
Save audit
and typing
Select/
navigate
between
samples
Add or
remove
SSO
assigned
alleles
Click to
Nucleotide
Select/
Display
position
navigate navigate
or hide
and
confirmed between between
LabType and mismatch
loci
allele pairs
ConsenSys
navigator
in the
result pane
Marks sample
for more tests
Opens
Click to
the
display a list
of shortcut Reports
Menu
key
combinations
Close the
window
Sample Navigator
If several samples have been imported, click the drop-down arrow to select a specific sample for
analysis.
Allele Filter
For combined analysis: if checked it will filter alleles based on SSO typing. Unchecked, it will give only
SBT results.
When the check mark is in place, the Allele Filter will retest the sample against the filtered allele list.
Remember that inserting a check mark will re-analyze the sample and all the edits that you’ve made
will be deleted.
For your protection, Fusion Research will display a message asking you to
reconfirm your decision to use the Allele Filter with the sample.
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Confirm Filter
The Confirm Filter will either display or hide the confirmed allele pairs in the result pane.
Nucleotide Caller
Use the Nucleotide Caller to audit sequences that need modification by selecting the appropriate
nucleotide.
button to place an insertion marker

Click the Plus

Click the Minus
button to insert a deletion marker
Electropherogram Navigator
Move to the
beginning of
the sample.
Move to the
previous
nucleotide.
Move to the
end of the
sample.
Move to the
next
nucleotide.
LABType/ConsenSys Selection
Use this drop-down control to switch between LABType and ConsenSys
analysis.
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Loci Navigation
Click the drop-down arrow to navigate between different loci including, IMGT/A, IMGT/B, IMGT/C
and IMGT/Cw.
Nucleotide position/Mismatch Navigator
The number displayed indicates the currently-selected nucleotide as displayed on the
electropherogram, (EPG) pane. Use the drop-down to navigate to a critical mismatch with a
highlighted allele pair.
Reanalyze
Clicking the Reanalyze button will perform a new analysis on the sample, but it will deactivate and
undo any edits you’ve made to the EPG for this sample.
Fusion Research will ask you to reconfirm the new analysis before proceeding.
Comments
Clicking the Comments button will open the “Comments and Warnings” window. Any comments you
add here will be saved with the sample.
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Note that the Comments and Warnings window becomes read only after the session is saved and the
button is pressed.
Confirmed
More Tests
A check mark placed here indicates that you recommend that additional tests be performed on the
sample. The More Tests column for a sample on the Session Summary Screen will indicate True if a
check mark is placed here.
Key List
After you click the Key List button, a pop-up window appears which displays a list of shortcut keys
and key combinations which can speed up and simplify editing, analysis and display navigation. The
following chart lists some of these keys.
Shortcut
TAB
A
A+Shift key
A+Ctrl key
C
C+Shift key
G
G+Shift key
T
T+Shift key
B
D
H
Description
Confirm the current IUB code call and
move to the next unconfirmed position
Set the current IUB code to A
Show/hide the A trace
Toggle the amino acid translation view
Set the current IUB code to C
Show/hide the C trace
Set the current IUB code to G
Show/hide the G trace
Set the current IUB code to G
Show/hide the T trace
Set the current IUB code to B
Set the current IUB code to D
Set the current IUB code to H
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Description
K
Set the current IUB code to K
M
R
S
V
W
X
Y
+
F
I
[
Set the current IUB code to M
Set the current IUB code to R
Set the current IUB code to S
Set the current IUB code to V
Set the current IUB code to W
Set the current IUB code to X
Set the current IUB code to Y
Add an insertion marker at the current position
Insert deletion marker at current position
Open the sequence find dialog
Show/hide trace information
Step back through the sequence primer layers
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Accept Base Call
You can individually accept the close base calls determined by HLA Fusion™
Research. After you accept a base call, you are moved to the next marked base
position.
From the Analysis window:

Click Accept Base button to accept the computer-suggested base call and move to the next base.
When you click the Accept Base button, Fusion Research highlights the mismatch in green on the
EPG.
Quick Reports
Unlike a Full Report which opens a secondary Reports Menu, a Quick Report, (see sample) generates
a more minimal report with sample name, date, EPG peaks and basic allele typing results.
Click the down arrows to select the Locus and Exon region(s) to be covered by the quick report and
click the OK button. Place a check mark in the EPG check box if you want the EPG peaks included.
Full Reports
Clicking the Full Report button
opens the Reports Menu.
The Reports Menu allows you considerable flexibility in
sorting, summarizing and filtering the presentation of
report data.
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Filters
Sample - Filter genotyping for all samples or for a specific sample.
Locus – Display genotyping for all samples, or for specific loci, (i.e.; IMGT/A, IMGT/B,
IMGT/C or IMGT/Cw.

Sort by
Sample Name – Present genotyping results in alphabetical order by Sample Name.
OR
Locus - Genotyping results will be ordered by locus.

Summary Options
NMDP – The Default Setting
Brief – Does not include the Summary or exons
Differences – Includes exon information

Audit Options
Save – Was the analysis saved?
Confirm – Need info here

Mismatch Limits
Here, you can set the allowable mismatch limits from zero to “Best Only,” “Best +1,” or “Best
+2,” etc.

Sample List or Table format
Here, you can specify if you want the report formatted as a sample list, or as a table – with or
without alleles listed.
Sample: Full Report as a text file
Output Format
Text – Creates a file saved in a text,
“(.txt”) format.
Excel – Outputs the full report as a
spreadsheet in the “.xls” format.
XML – Formats the report in the
Extensible Markup Language, known
more simply as XML.
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Page Breaks – Inserts page breaks to separate report data over many pages.

Full Report Section
Sample – For either of these two data options, your choices are to leave the sample section
empty, match the sample to the Summary and auditing.
Layers – This section allow you to select up to four fields with the following data: The
electropherogram list, by sequences, Edit List and Mismatch List.

Additional Information
These extra fields located at the bottom, left of the Report Menu allow you to insert
supplementary information about the analysis.
After making your selections:
1. Click the Report
button.
The Select File window opens.
2. Select a directory or folder location to save the report file.
3. In the File Name field at the bottom, left of the screen, give the report a unique file name.
4. Click the Save
button.
The previous Reports Menu screen opens.
5. Click the Done
button to close.
Click the Update
button at the bottom of the Reports Menu and Fusion Research will
remember the format and criteria selections you’ve made for use in future reports.
Save > >
Clicking the Save >> button stores the results of your analysis to the database.
Confirm >>
The Confirm >> button becomes visible only after you’ve clicked the Save>> button.
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Close
Clicking the Close button exits you from ConsenSys application, but not from Fusion Research.
Exon-Specific Summary Pane
Magenta color
indicates a mismatch
Exon sites
Left arrow
direction
indicates a
reverse
sequence
E PG
positioEnPG
Indpiocsaittoiorn
indicator

Numbers located at the top left corner indicate each exon site.

A right pointing arrow indicates a forward sequence.

The length of the line indicates the coverage of the sequence.
Right arrow direction
indicates a forward sequence

A left-pointing arrow indicates a reverse sequence and its length indicates the coverage of that
sequence.

The short, magenta-colored vertical bars indicate positions that require auditing. These are
polymorphic nucleotides sites that could change the final allele pair assignment.

The long vertical bar indicates your current position within the EPG pane.
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Exon Summary Pane Right-click Options
Set Start Base: Ignore all bases left (in the 5’ direction) from the current
cursor position, (this is effective only for the exon where the cursor is
placed). This function is used to trim bases that are not interpretable. All
unique sequence polymorphism that exists will also be ignored and
possibly result in more alleles assigned.
Set End Base: Ignore all bases right (in the 3’ direction) from the current
cursor position, (this is effective only for the exon where the cursor is
placed). This function is used to trim bases that are not interpretable. All
unique sequence polymorphism that exists will also be ignored and
possibly results in more alleles assigned.
Less Sensitivity: Forces a reanalysis of an EPG after reducing the detection limit.
This function is very effective for improving the base call accuracy of data with
high background.
More Sensitivity: Forces a reanalysis of an EPG after increasing the detection limit.
This function is very effective for improving base call accuracy of data with low
signal.
Reanalyze EPG: Re-analze EPG and discard all edits made.
Deactivate EPG: Remove the EPG from the analysis completely. Useful to ignore poor
quality extension data.
The Reference Sequence displays a magenta highlight around bases that differ between the
reference and consensus sequences.
These bases need to be individually viewed and accepted or edited.

Blue highlights between the reference and consensus sequences indicate the location of
manually-edited bases.
The ConsenSys Sequence is the combined consensus between both the forward and reverse primers. It
displays any manually edited bases.
 A Green highlight on a base in the Consensus Sequence indicates an accepted base.
 Hold down the Shift
Key and use the Up
change the size of the electropherogram.
and down arrow keys on your keyboard to
 Right-click an electropherogram to display a pop-out menu with more options.
Note: Press the letter “Z” while viewing the EPG to magnify the area where the position indicator is
located.
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EPG Panel
Click and drag
to scroll quickly
Sample name
Nucleotide
position
Combined forward
& reverse sequence
Nucleotide signal
intensity
(>> indicates forward)
Reference
sequence
for loci
Forward
sequence
read
Reverse
sequence
read
Nucleotide
average signal
intensity
Sample name
(<< indicates reverse)
E PG
E PG
Allele Typing Result Pane
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EPG Pane
The EPG pane is the visual representation of the sequencing reaction. Here you can view the base call
and edit any mismatched base calls in the EPG navigator.
Click and
drag to scroll
up and
down the
Allele Pairs
List.
Edit Base Calls
Any base call can be edited. The base assignment button is
highlighted for the currently selected base. More than one base
can be selected at a time and the corresponding base code is
displayed. If no bases are highlighted, an asterisk (*) is
displayed in the consensus sequence.

Assignment Buttons
Select a base and click one or more of the assignment buttons to change the base assignment.
Navigating the Alignment Screens
The alignment screens were designed to give the end user all the tools necessary to:




Analyze sequence data between samples
Ascertain quality
Check against IMGT/HLA reference sequences for allele pairs
Check against all IMGT/HLA alleles for the loci of interest.
Use the Ctrl key plus a Bracket key, (
1.
2.
3.
4.
+ [ or
+ ]) to navigate between the various alignments:
Sample alignment
Sample Base Call Score alignment
Allele pair alignment
Reference allele alignment
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Sample Alignment
Four samples were imported into this
session.
This sample alignment displays four
sequences which correspond to the four
different samples.
On this screen, use
+ [ or
display nucleotide vs. dots.
+ ] to
Sample Base Call Score Alignment
Generally the first 20-50 bp of a sequence read will be poor, the next 200-400 bases will have an
improved quality sequence before gradually deteriorating again at the opposite end.
This figure shows an example of poor quality data at 5’ and 3’ end with improved quality data in the
center.
Four samples were imported into this
session. This alignment reflects the integrity
of the peak shape, the background and the
separation from neighboring peaks.
White = High BCS value/good quality
Red = Low BCS value/poor quality
+ [ or
+ ] to switch between
Use
nucleotide and dots.
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Allele Pair Alignment
The Allele Pair Alignment Window displays the alignment for the allele pairs that correspond to
the sample being analyzed. This window will aid the end user when auditing sequence data. In this
window the end user can narrow down which allele of the allele pairs is positive for the nucleotide that
was sequenced. You can view the sequence of both allele pairs together or individually by turning Allele
1 or Allele 2 on and off.
If an allele header is highlighted green then the allele is being aligned in the EPG window. If you click
on Allele1 or Allele2 you will be turning off the sequence and the header will change color from green
to red. Use
+ [ or
+ ] to switch between nucleotide and dots.
1. Reference Allele Alignment
The sequence of each allele is aligned in the Allele Alignment Window. This window is useful when
+ [ or
you’re specifically looking to cross reference sequence data with an individual allele. Use
+ ] to switch between nucleotide and dots.
Analysis Workflow
After you successfully imported your data:
1. Audit the assigned nucleotides at every position making sure to audit the mismatched sites for
the quality of sequence data, ambiguity and polymorphism.
If changes are required, use the nucleotide auditor to edit and accept audits. (Clicking the
Tab button on the keyboard automatically accepts the base call.)
2. After all base calls are audited click the Save>>
button. Click the Confirm
button to save your sequence typing.
This will change the red box next to the sample name from red to green to indicate that the
sample has been typed.
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SSO Analysis
The SSO Genotyping analysis feature of HLA Fusion Research analyzes three Luminex .CSV output
files as a new session and can continue the analysis of a previously unfinished session.
Starting SSO Analysis
SSO analysis results are based on catalog specifications that are provided with the software. You can
analyze samples one at a time in order to view, adjust and assign results for each one.
Opening a SSO Analysis Session

Select the SSO Home page
button or the SSO
toolbar button.
The SSO Home page is displayed.
Note: Open worksheets and probe/primer sheets to verify the accuracy of revision numbers, (these
documents do not contain a revision number in their filename).
Opens the Catalog
Management window
Opens the Update
Reference File window
Notification that new or updated
catalogs, NMDP and Serology
equivalent files may be available.
Click here to
open the
Navigator
Click to open
the KIR Analysis
Configuration
Screen.
Click the blue
links to display
the selected
catalog, worksheet
or probe/primer
documents.
Fusion
Explorer
The SSO Home Page
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Note: HLA Fusion Research converts Luminex-generated CSV file data, such as date and time, to the
local regional code if a regional code is specified in the CSV file. (A regional code cannot be
specified for CSV files created with Luminex software version 2.2 or earlier.) If the first date field
is highlighted yellow, it indicates a regional code mismatch. In this case, it is recommended that
you use the drop-down selector in the second date field to choose the appropriate date, taking into
consideration regional date format differences.
To begin an SSO session, do the following:
1. Select a file from the list of CSV files to import, or click the folder icon above the list to browse
to SSO session files(s) on your system/network.
If samples in a session have a positive control value below the minimum
setting, they are flagged so you can easily select and delete them from
the session.
Previously imported CSV session files have a tan or light brown
background.
2. Place a check mark next to the CSV session file you want to open.
The SSO Session Import Screen opens.
Lists
previously
Imported
CSV files
Catalog ID
Date may be highlighted
in yellow if regional settings
do not match between
the current CSV file and
Fusion Research.
Session ID
Click to open the
Import Patient Screen
Luminex
CSV
Session
files
Sets the
Patient ID
to be the
same as the
Sample ID.
Lists the
Double-click Place a check
mark here
Positive
here to open
to allow auto Control (PC)
the Select
Sample screen. analysis of all values for
session
each
Sample ID’s
samples
sample.
can be edited.
upon import.
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here to see
the current
patient list.
Click to assign patient type
to corresponding Patient ID
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The system assigns a Session ID, (the CSV filename) automatically. Optionally, you can change the
ID. The ID can be alphanumeric, (containing letters and numbers) and will be listed alphabetically
with any other SSO session files in your database.
If a sample is already associated with a patient, the Patient ID and any existing, related patient
information is displayed.
To add patient information, do one of the following:

To add data from the system, double-click in the Patient ID column of the Sample/Patient
Details table or click the Patient
button on the toolbar.
The Import Patient window is displayed, allowing you to import the patient information file.

To manually add patient data, type data directly into the patient-related fields of the table.

You can assign the Sample ID to empty Patient ID fields by selecting the check box for Set
empty patient ID to Sample.
3. Select a catalog file. Your catalog file selection method varies, depending on the CSV file and
the catalog files you have previously imported for LABType.
If you need to import more catalogs, click the [Download] link on the LABtype home page to
add new catalog files to the database.
Note: The catalog drop-down list may not be immediately updated if you downloaded the catalogs
during the current import session. You may need to click the Home button and then click the
button again to return to the import process.
LABType
If the CSV file specifies a template name, (only applies to CSV files from Luminex 2.2 and later) and
one of the available catalog files is associated with that template, then that catalog file is automatically
selected.
Note: You can also select a different catalog file from the one the system has selected by using the
drop-down list in the Catalog ID field and selecting any catalog file listed.
If there is no template match, the system then considers the closest bead match between the session
and all available catalog files. If only one catalog file is a close match, it is automatically selected.
If there is more than one match, a Catalog Validation screen is displayed with the best bead
matches.
4. Clicking the
Close
button also
means that you
confirm the
selection of this
catalog.
Or, you can double-click a catalog file name on the list of other Suggested Catalogs, listed below.
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Click the Detail
button and Fusion Research will display information about bead mismatches
between the selected catalog and the CSV file.
Following catalog file validation, the system may ask you if you would like to associate that template
name with the specified catalog file. If you click Yes to associate the two, the system automatically
selects this catalog file for all future imports of any CSV files that reference this template.
Select the check box if you don’t want
Fusion to continue asking if you want
to associate templates and catalogs.
If you change your mind, go to
Utilities > Catalog Template
Association and place a check mark
in the bottom, left corner next to
Enable During CSV Import.
5. On the Sample/Patient Details Table, check to see if there are any samples that have been
flagged as having a low positive control (PC); the rows of low PC samples are highlighted gray.
Take the following steps if you want to delete any of these samples:
Click in the border to the left of the Well position column to highlight the entire row for the sample.
Press the Delete
key on your computer keyboard to delete the sample and prevent it from being
imported as part of the session.
6. When session and sample information has been verified, click the Import
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The newly imported session is displayed in the Navigator tree, at the
top of the list.
If you had selected the Auto Analysis check box, the session is
imported as well as analyzed when you clicked the Import
button; it is now displayed on the Navigator as an analyzed session.
You can continue importing Luminex session files, or you can click a session on the Navigator to start a
batch analysis.
Note: Once a CSV file has been imported, it no longer displays on the Luminex session import list
unless you select the Include Imported CSV check box at the top, left of the screen.
Displaying an SSO Analysis Window
1. Open a SSO session.
2. Click on a sample to display its analysis in the Analysis Window.
The SSO Analysis window is divided into four quadrants:
SSO Analysis Screen
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Select a sample from this list to make the sample active in the Analysis window. Alternatively, you
can use the arrow buttons to navigate between the samples.
Sample Navigation buttons

Click any column header among the sample list to sort the table by that column.

Click the arrow buttons to display the samples according to the sorting criteria.
Histograms
Double click on a sample histogram in quadrant 2 to make that sample active. The color of the selected
sample histogram in quadrant 2 will change to red and the selected sample profile will be displayed in
quadrant 3.
Configuring SSO Data Analysis
The Configuration Menu allows you to define certain parameters for the analysis. Click on the Set
button, (or anywhere in the gray area to the left of the button) to display the pop-out
Config
Configuration Menu.
SSO Configuration Menu
P Grouping
Codes allele strings in P Grouping as published by IMGT.
G Grouping
Codes allele strings in G Grouping as published by IMGT.
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Minimum Positive Control
The default Minimum Positive Control value assigned by the system is 1000. If desired, you can enter a
new value into the Minimum Positive Control Value field.
If the positive control bead count for a sample is lower than the entered value, a warning is displayed.
In sample analysis, each sample is processed individually. Results can be viewed, adjusted and final
typing assignments made.
Using batch analysis, all samples are processed at once and no assignments or changes can be made
during analysis. You can continue the session to make adjustments and assignments.
Minimum Bead Count
The default Minimum Bead Count Value assigned by the system is 100. If desired, you can enter a
new value in the Minimum Bead Count Value field. A warning is displayed if the count for any bead in
a test falls below the Minimum Bead Count threshold.
Set Sure Reaction Bead
Selecting the Set Sure Reaction Bead option in the configuration menu displays a new window, as
shown below. In this window, you can force positive or negative bead ID values by typing in the box.
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SSO Analysis Window Overview
From the SSO Analysis window you can:

View sample analysis results

Change histogram scaling

Add comments and mark samples for more testing

Print analysis information and reports
For each sample in the current session, you can view the test data, adjust the cut-off and assign a
typing.
HLA Fusion™ Research analyzes a sample when you move to view that sample. Any unviewed samples
do not have analysis results when the session is saved. To analyze an entire session, all samples in the
session must be viewed and typings assigned by the user.
Using the SSO Data Analysis window
The Sample Analysis Screen provides detailed analysis information for each sample in the session.
You can review the typing assignments suggested by the program and to modify and accept the
assignments. HLA Fusion™ Research suggests possible typing results, but the final assignment is
made by the user. Cut-off adjustments made in the Analysis window are sample-specific and affect
only individual samples.
SSO Analysis window - Quadrant 1
QC Tab
Quadrant 1 displays the QC data histogram for the currently selected bead in the QC tab. Each bar
represents a QC sample and its height represents the normalized reaction value for the selected bead in
that sample.
Hover your cursor over any sample to display
the sample details, as shown here.
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To change the histogram scale, click inside the Max Scale
box, type in new limits, and press the Enter
key on
your keyboard.
This changes the maximum scale for the histograms in
quadrants 1 and 2. You can change the scale back to a new
value the same way.
Reaction Patterns Tab
In the Analysis window of Quadrant 1, click on the Rxn tab to display the Reaction Pattern Table.
Reaction
Table Tab
The Find
Allele button
Click to reset table to its
original configuration
The
maximize/
minimize
button
Type
Allele
here
Type all or part of an allele into the text box and click the Find Allele
reaction pattern, or patterns, beginning in the first row of the table.
button to display that
To Sort beads by reactivity for the allele, click on the gray area on the left of the allele name. The
button to reset
positive reactions will be moved to the left of the table. Click on the Rxn Reset
the table to the original configuration.
Double-click either in the light blue area between the Find Allele and Maximize/Minimize button,
or click the Max/Min
button and the reaction table will be expanded.
To bring the table back to its original size, double-click either area or button again.
Click on any column header to Sort the table by well position. Positive reactions are listed above
the blue line, and negative reactions below.
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Local QC Tab
The Local QC tab displays a histogram of the reaction profile for the current bead against all samples
this user has ever run for the same product, (same lot/revision) and over a specified date range.
One Lambda
cut-off line
Local QC Tab
Each Green bar represents a QC sample and its height represents the normalized reaction value. This
serves as a user-created QC graph.

Hover your cursor over any sample, and the sample details are displayed.

The graph is continually updated as you analyze the product over time.

The cut-off line represents the One Lambda default cut-off value.
Patient/Sample Results Tab
The Patient/Sample Results tab details all of the results for all
the tests done on a Sample ID or Patient ID. As results are saved for
each locus, either the serology result or the allele code for each loci
appears in this all-loci section.
Click on any of the labeled Gray tabs along the top of the grid to sort
the results in either ascending or descending order. The direction of
the small triangles  indicate how the results have been sorted.
Hover your mouse over any Possible Allele Code to see the entire
allele code.
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You can use your mouse to widen the grid, or double-click between
the tabs to automatically increase the column width to
accommodate all the data presented.
Patient/Sample Results tab
SSO Analysis window - Quadrant 2
Bead Profile
The Bead profile tab displays the histogram for the currently selected bead. Each bar represents a
sample and its height represents the normalized reaction value for the selected bead in that sample.
The red bar represents the currently selected sample.
Click the arrow buttons to navigate between beads and display the profile of the selected bead in
Quadrant 2.
Bead Profile
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Alternatively, you can select the bead from the Bead drop-down choices.
Hover your cursor over any
sample.
The sample details are displayed,
as shown here.
If you wish to exclude a bead from analysis, you can select
the check box for Exclude.
Click on the Reset button to reset the changed values back to default. The following options are
displayed to choose from.
Raw Data Table
Select the Raw Tab and the Raw Data Table displays all raw data and test details for the current
sample.
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To change the threshold value, enter a new value in the Threshold field
and press the Enter
key on your keyboard.
Normalized bead values that fall within the specified threshold range of the cutoff for that bead are
highlighted in yellow.
Click the Maximize
button to expand the Raw Data Table. Click the button again to minimize it,
(or double-click anywhere in the light blue area between the threshold box and the
Maximize/Minimize button to expand the table).
Clicking on any column header will sort the raw data table by that column.
The RAW table
after double-clicking
on the header for
the Rxn column.
Bead Info Tab
From the Analysis window in Quadrant 2, click the
Bead Info tab to display the allele specificity of the
selected bead.
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SSO Analysis window - Quadrant 3
Sample Profile
The Sample Profile displays each bead in the currently selected sample. Each bar represents a bead in
the sample sorted by bead number and its height represents the normalized reaction value for the
selected bead in that sample.
Quad 3 – Sample Profile
Red = A positive reaction; Blue = A negative reaction; Green = The selected bead in quadrant 2.
•
The gray diamonds inside the histograms indicate the current cut-off position. Arrowheads
identify the direction and position of cut off changes made to a bead.
•
Click arrow buttons on the toolbar to select a sample bar and display the selected sample in
Quadrant 3.
•
Alternatively, you can also select a sample from under the Sample drop-down list in the
toolbar. You can also select a sample by double-clicking on a sample bar in the Bead Profile
histogram, (Quad 2).
The Magenta and the white, (or non-colored bar on the right) represent the raw data values for the
positive and negative control beads of a LABType assay:
•
X-axis: Beads in numeric order.
•
Y-axis: Raw data value, (trimmed mean).
•
Data points: Bars represent the raw data value of a bead vs. the sample reaction.
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Bar colors/display:

Positive control = Magenta

Negative control = White
R aw
Data
Value
Magenta
Positive
Control
White
Negative
Control
B e ad s
Hover your mouse pointer over any sample.
The sample’s details are displayed, as shown
here.
You can expand the histogram by double-clicking anywhere in the light blue area between the View
Delta
button and the Maximize
button.
To resize the histogram to its original size, double-click on the light blue panel again, or click the
Minimize
button.
View Delta
To view the Delta data, (the difference between the signal generated and the cutoff
point for each bead) click the View Delta button.
Quadrant 3: Delta View
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To go back to the normalized view, click the same button which now says View Normal
.
Would you prefer to make View Delta the default view so that it automatically displays each time you
bring up a sample for analysis?

Save the layout while this quadrant is in the View Delta mode by clicking
button.
the Save Layout
After you exit Fusion and log in again, your SSO sessions will display in Quadrant 3 in View Delta
mode.
Comments
You can add comments to the sample by typing in the Comment field at the bottom. Double-clicking
in this text box invokes a new window to type comments in.
Double-click
in the User
Comments
field here…
…to open
a larger
Comments
screen here.
SSO Analysis window - Quadrant 4
SSO Results and Assignment panel
Quadrant 4 displays the possible typing assignments for the current sample.
The left side, (the Summary) shows possible allele pair assignments suggested by the
software.
The alleles highlighted in yellow are a positive match.
The red ones are mismatches.
The un-highlighted ones are negative.
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You must make assignments manually.
The right side shows possible coded assignments.
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Analyze SSO Data
From the Analysis window you can:

View raw data

View reaction patterns

View bead and sample details

View results and make typing assignments
The raw data table can be used to easily review raw data, normalized data and cut-off values. The
reaction pattern table can be used to compare reaction patterns.
Reaction-specific pop-ups display the probe details and reaction data for the selected sample and
probe.
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Make Typing Assignments in SSO Analysis
HLA Fusion™ Research provides computer suggested assignments. Final typing assignments can only
be made by the user. You can save multiple SSO Typing assignments. From the Analysis window you
can assign typings and make manual assignments.
Typing Assignments
The SSO results are displayed in Quadrant 4 of the Analysis window. This quadrant is divided into
three sections. The Summary section displays the system suggested results for the SSO locus groups,
where the alleles highlighted in yellow are positive match, red highlighted are a mismatch, and the
remaining un-highlighted ones are negative.
To make a manual assignment, please follow the steps below. The Allele Assignment panel lists the
possible allele pair results for the selected SSO locus groups.
Assign All
Assign
Selected
Remove
Select an allele, (or several alleles by holding down the Ctrl Key on your keyboard) from the
Summary, and click the Assign button to assign the SSO locus group in the Final Assignment panel.
To assign allele pairs, select one or more pair results from the allele assignment panel and click
Assign.
Click the Assign All button to assign all Positive SSO locus groups. The selected allele(s) are displayed
under the Final Assignment.
To remove any or all alleles from Final Assignment sections, select them and click the Remove (X)
button.
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Flagging a Sample for Further Testing
This option flags a sample for further testing in the current analysis session and in reports created in
HLA Fusion™ Research. The More testing required flag is saved with the analysis.
In the Analysis window, select the More Test check box below the
Assignments area.
Manual Assignments
Manual assignments must be entered in standard format with each allele separated by two spaces.
Click to move
allele into the
final assignment
box above.
Type allele
name here in
the manual
assignment field.
Type the allele name in the text box below the Final Assignment section and click the Up Arrow
button.
The newly entered allele is moved into the Final Assignment field.
SSO Batch Analysis
Batch analysis is carried out from the Session Summary screen.
When the session summary for a new session is activated, a batch analysis is automatically run. Batch
analysis allows you to quickly analyze a session and save it for later review and final assignments. You
can graphically view samples during batch analysis, but no final typing assignments are made.
From the Session Summary you can:
•
Run a Batch analysis for a session
•
View the Batch Analysis Summary Chart
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Save Assignments
Lab Technicians and Supervisors can save analysis results for further review and approval. Until
approved, samples are marked as Ready.
In the Analysis window, click the Save>>
button to save analysis results and move to the next
sample. Prior to confirming, a sample can be re-saved, if needed.
Confirm Assignments
When an analysis has been saved, Lab Supervisors can review and confirm the analysis results.
Confirmed samples are marked as Approved.
The Confirm button is grayed-out
when you view a saved but as yet un-confirmed sample.
when you view a sample which has been confirmed by the
The Confirm button becomes purple
Lab Supervisor. Samples may be reconfirmed.
From the Analysis window, click Confirm>> to confirm analysis results and move to the next
sample.
Note: The application records two levels of analysis reviews - Save and Confirm. For re-saved and
reconfirmed analysis, only the last user to save or confirm is recorded.
Print Screen
Print Screen prints the entire, currently displayed analysis screen.
From the Analysis window Menu Bar, click the Print Screen
button. A print preview screen is
displayed in a new window if you wish to examine the image before sending it to the printer.
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Micro SSP Analysis
The Micro SSP analysis feature of HLA Fusion™ Research analyzes manually input reaction patterns
as a new analysis session and can also continue the analysis of a previously unfinished session. Each
session consists of as many samples as you wish to analyze with the same catalog information. It can
also accept data from eGene and new samples can be added to an existing session.
Analysis results are based on catalog specifications, NMDP code, and serology code references that are
provided with the software. Micro SSP analysis uses NMDP cross codes. Fusion Research suggests the
allele pair assignments, but the final assignment has to be made by the user. The results can be saved
in the database for further review by Lab Technicians and for final approval by the Lab Supervisor(s).
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Start Micro SSP Analysis
1. Click the Micro SSP
button on the Fusion Explorer, the Micro SSP
on the Fusion Toolbar, or select Analyze Data > Micro SSP.
icon
The Micro SSP Home page is displayed.
Click to open the Catalog Management screen.
Click to open
the Update
Reference Files
screen.
Click to open
the Available
Reference
Updates screen.
(catalogs display
nomenclature dates
and revision notes)
Click to edit
the MicroSSP
global settings.
Click any link
to display the
selected catalog,
worksheet or
probe/primer
worksheets.
Note:
Open worksheets and probe/primer sheets to verify the accuracy of revision numbers,
(these documents do not contain a revision number in their filename).
Click the Batch Entry button at the top, left side of the screen.
Place a check mark next to Include Imported if you also want to bring in
batches which have previously been imported.
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The Micro SSP Batch Entry window is displayed.
Sample Name field
Select locus to filter catalog list
Browse for
MicroSSP files
Patient ID Field
Start a new batch
Save the current
batch information
Go to the
analysis screen
Fusion assigns a Batch Name automatically. But you can change it.
Note:
A batch must be unique to the Fusion database for each product type. If it already
exists, the software prompts you to rename the batch. It is highly recommended that
you do not use any special characters in this field since they may serve a specific
purpose as field separators.
Use the Browse
button at the bottom of the window to search for and import one or more Micro
SSP files (.csv), or follow the steps below.
1. Use the drop-down menu in the Locus Filter field to select a locus by which to filter the
catalog listing. This will limit the catalog list in the next field to only those catalogs that include
the selected locus.
2. Use the drop-down menu in the Catalog field to select a catalog file.
Note:
If you need to import more catalogs, click the Download link on the Micro SSP Home
Page for instructions on how to add new catalog files to the database.
The catalog drop-down list may not be immediately updated if you downloaded the
button
catalogs during the same import session. You may need to click the Home
and then open Micro SSP again to return to the import process.
3. Accept the session name in the Session field, or modify it.
4. Enter a name in the Sample Name field.
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If this is an existing sample name, other fields such as the Patient ID and Ethnicity, are populated
with existing data. You can also double-click in the Sample Name field to display the Select
Sample window from which you can select a sample.
5. Click the drop-down arrow in the Sample Date field and select a date. The analysis window
for this session is displayed.
6. Enter an ID in the Patient ID field. If this is an existing patient/donor ID, other fields such as
the First Name, Last Name and Ethnicity are pre-populated with existing data. You can also
double-click in the Patient ID field to display the Select Patient window from which you can
search for and select a Patient ID.
7. If they are not already filled-in, you can enter the First Name and Last Name for the patient
or donor in the appropriate fields.
8. Click the drop-down arrows in the Ethnicity and Patient/Donor fields to choose ethnicity
for either Patient, Donor or Both.
9. If you want to associate a gel image with the sample, double-click in the Gel Image field and
browse to the location of the image you want to attach to the sample.
Note:
Fusion supports the BMP, JPG, BMP, GIF, PNG and TIF image formats. However,
certain versions of the TIF format may not be supported by the Windows version used
on your computer.
Select Gel Image Browser
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Repeat the above steps until you complete the batch information, or until you want to save and
complete the batch later.
Each Micro SSP batch session can consist of as many samples as you wish to analyze with the same, or
with different catalog information.
Take one of the following actions once you are ready to stop creating the batch:


Click the Next>
Click the Save


to begin creation of an additional batch.
Click New Batch
Click Close
to exit the Batch Entry window.
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button to open the Micro SSP analysis window.
button to save the current batch information and return to it later.
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Configure Micro SSP Data Analysis
The Global defaults for Micro SSP product configurations can be set at one of two places:

The Micro SSP Home Page

The Utilities menu on the main HLA Fusion home screen.
In addition, configurations can also be set from within the analysis window for the current Micro
SSP sample by right-clicking anywhere on the Micro SSP analysis window and a pop-up list of
configuration options will appear at the upper, left corner of the analysis screen.
After an analysis has begun, you’ll need to right-click in the light blue area just to the right of the
Find Allele
button to open the Micro SSP Configuration Menu.
Micro SSP Sample-Level Configuration Menu
Assign Code
By default, the system assigns NMDP codes to the alleles. However, the user can optionally change
these codes to one of the following options:

No Code - The results, allele pairs assembled into a string with no formatted code, are
simply condensed without applying a coded format.

P Grouping - Codes allele strings in P Grouping as published by IMGT.

G Grouping - Codes allele strings in G Grouping as published by IMGT.

Local Code - assigns user-defined code definitions, (code used by your Lab) for
suggested code results.

Cross Code - allows allele combinations that cross serological groups (e.g., EAPW =
DRB1*04:03:01 DRB1*04:03:03). By default, cross coding is turned off so that allele
pairs are condensed only within the same allele groups.

Bw4/Bw6 in Serology - Bw4/Bw6 is added to the serology results.
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Bw4/Bw6 in Serology
Serology has identified many pairs of HLA-B alleles which appear to
differ only at the Bw4/Bw6 region - the two mutually exclusive
serological epitopes.
If you select this option, Bw4/Bw6 is added to the serology results.
Demographic Information
The Demographic Information option allows you to
organize alleles based on their frequency.
Based on the demographic selection you make, HLA Fusion displays as many as three allele groups
in the allele pairs list:
Note:

Group 1: Frequent on both alleles

Group 2: Frequent on one or the other of the alleles only

Group 3: Frequent on neither allele
If the Demographic Information option is not active, it means you need to import an
allele frequency input file. See the topic: “Importing Allele Frequency Files,” which
is located in the section, “Updating Allele Frequency files.”
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Using the Micro SSP Analysis Window
The analysis window displays detailed analysis information for each sample in the session. You can
review the allele assignments suggested by the program, modify and accept the assignments.
HLA Fusion suggests possible typing results, but you must make the final assignment. Any
adjustments made in the analysis window are sample-specific and affect only the current sample.
From the Analysis Window you can do the following:

Use the test gel pane to change reactions and sample row positions.

Change the allowable number of false reactions.

Force one false reaction.

View and print sample analysis results.

Add comments and mark for more testing.
You can return to a session summary from the analysis window
any time by clicking the <<Summary link from the HLA Fusion
toolbar next to the Sample ID.
Micro SSP Analysis screen
Input and
analysis
tables
Displays
allele
pairs
Click here
to view
or add a
gel image.
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The
reaction
pattern
table.
Groups and
Condenses
pairs with
the same
reaction
pattern.
The Results
area
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Test Gel Pane
The pane on the left side of the window displays each well of the
test in rows that are intended to duplicate the test gel. Each
well is shown with a reaction button.
When clicked or entered from the keyboard, you can modify the
reaction for the selected well between the following settings:

8 = positive reaction

1 = negative reaction

0 = no clear amplification, (wells with a “0” will be
excluded from analysis)
If you right-click in the black area of the test gel pane, you can select a different
order for the reactions when you click on a well: 0->1->8, or 8->1->0, etc.
Note:

After you analyze a tray, you can no longer add any
more sample information to that tray.

If the sample has not been analyzed, the right most
button on the bottom of this pane is labeled Analyze.
If an analysis already exists for the sample, then the
button is labeled Re-Analyze.

This button is only enabled when a Sample ID has
been entered. If a Sample ID has not been entered
when this button is clicked, the Sample ID field is
flagged with "!" as being empty and no analysis is performed.

If other than the first well reaction (1H) is set to zero (0), a message displays, allowing
you to see system-suggested reaction information to help you decide if you want to
analyze the non-amp well with a positive or a negative score. If more than one well is set
to zero, the message does not display, but the suggested reaction information can still
be viewed.
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To see the possible reactions if the well was positive or
negative, click Yes and scroll down the Possible Allele
Pairs list to the headings, Neg Reaction and Pos
Reaction.
If neither type of result can be suggested, the heading is No
Solution and it will not be followed by any results.
Headings to look
for when viewing
possible non-amp
well results.
View Well Details
You can view comprehensive details about the current sample by hovering your cursor over a well
in the test gel area of the analysis window.
View Well Details (with your mouse over a well)
Working with Gel Images

If you have a gel image already linked to the current sample, you can view it, or unlink
it.
OR

You can search for and link another gel image to the current sample.
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Here’s how you can link a gel image to the current sample:
1. Click the View Gel
button at the bottom,
left of the gel image screen. If no image is
currently linked to this sample, you’ll see this
message: “Gel Image does not Exist. Click Yes to
Browse for an Image.”
2. Click the Yes button and Fusion opens the
Select Gel Image screen.
3. Browse and select a new gel image. Click the
Open
button.
4. Fusion opens the Gel Image window and
displays the gel image you’ve selected. The
window can be resized if needed.
Gel Image Viewer
If you want to link this image to this sample,
click the Link Image
button.

To zoom in, click the  button.

To zoom out, click the
- button.
 To turn the image, click the Rotate
button.
Click to
close the
Gel Viewer
Zoom In
Zoom Out
Click to rotate
the gel image
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To link the image to
the current sample.
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To Unlink an image already associated with the current sample:
1. Click the View Gel
button.
2. When the image is displayed in the Gel Image viewer, click the Unlink
(which now replaces the Link button).
button,
Add Samples
There are two methods that samples can be added and analyzed in a session:
1. Click the Add New Sample
button.
2. Type a new Sample ID, or Sample Name, in the Sample ID field, (above the gel image).
3. Select the Sample Date by clicking the Down
Arrow  in the Date field to the right of the
Sample ID field.
4. And click the Analyze
button.
OR
Here’s an alternate method to add existing
samples for analysis in Micro SSP:
1. Click the Sample Selection button to the right of the
Sample ID field.
2. Select an existing
sample from the list of
Available Samples.

You can use the text box
at the top as a search
tool.
3. Click the OK button at
the bottom of this
window to move the sample from the list of Available
Samples to the Sample ID text box above the gel
image viewer. You may use the existing Sample Name,
or create a new one.
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4. Select/create a Sample Date.
5. Click the Analyze
button.
6. When finished, click the Close
viewer.
button, or click the Exit
button to close the gel
Modify the Session Start Position
For multi-test trays, you can skip tray positions to match your gel photos by clicking the Add New
Sample button until the correct test start position is displayed.
Rxn (Reaction) Tab
The reaction pattern table displays the positive reactions for each well, or bead, if combined with
LABType, (x-axis) versus every allele (y-axis) defined in the current catalog.
The Reaction Pattern Table is displayed in the right pane of the Micro SSP analysis window.
Search by Allele
The Max
button
expands the
reaction table.
Double-click anywhere in this
area to expand the table
to half the analysis window.
Click to sort
the table
by the
selected
well
reactions.
Search by
reaction
pattern
Default configuration:
Bead ID’s for LabType tests used in combined
analysis with the current Micro SSP sample.

Wells, (beads if it’s a combined analysis with LABType) are sorted by sample reaction.

The Well ID depends on the row and location of the sample in the test gel pane.

The current sample appears in a Blue font, just below the cross loci row.

Positive alleles are listed below the sample row and are highlighted

Cross loci wells are identified with the pound sign (#).

Salmon background shading indicates a false positive.

Green background shading indicates a false negative.
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Working with the Reaction (Rxn) Tab
Positive reactions are displayed as an “X” on the table, (blue for the current sample and
black for the remainder). PC, NC and excluded beads are displayed as “0” on the table.
If you want to expand the table to full window size, click the
click the
button.
button. To minimize it again,
Double-click in the gray and light blue area just above the table, (see graphic) between the
Find Allele and Max buttons to expand the table to half the analysis window. To size the
table back to its original size, double-click in the same area again.
Type an allele into the Search by Allele field, (top left corner of the Rxn Table) and click the
Find Allele
button to search and display the allele and its reaction pattern in the first
row.
Double click on an allele name to bring that allele to the top of the table. You can bring all of a
certain allele group to the top by entering an allele group (i.e., DRB1*07).
Click on a gray tile to the left of an allele name, to move all the beads with that reaction to the
left. Click the Rxn Reset
button, (just above the Max button) to reset the table to its
original configuration.
When a column header, (along the top of the table) is clicked, the table is sorted by reaction
criteria for that well or bead, (if combined with LABType). The first click sorts in ascending
order from top to bottom, the second click sorts in descending order.
If you use the Analyze Combined
button from the analysis window to analyze
a LABType test and a Micro SSP test, the Bead IDs from the LABType test are displayed in the
Well ID row on the Rxn table. These are recognizable by the bead ID followed by an
underscore and a 0.
Rxn Table column headers
Click on a gray tile to the left of an
allele name to move all the beads
with that reaction to the left.
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Number of Allowable False Reactions
If HLA Fusion cannot determine any results that exactly match the reaction pattern entered, it
analyzes the reaction assuming that there is one false reaction in the sample.
If a solution still cannot be found, the system continues to search through additional false reactions
until the number of allowable false reactions has been reached, or a solution is found.
The false reaction setting allows you to set the number of allowable false reactions:
Minimum setting = 0
Maximum setting = 4

Note:
In the # False Rxn field, click the up or down
arrow to change the number of allowable false
reactions.
Regardless of the maximum false reactions set here, sample analysis stops at the first
false reaction found.
Force One False Reaction
When a sample has a result with no false reactions, (exact match result) the Force 1 feature forces
HLA Fusion to re-analyze the reaction to allow for one possible false reaction in any well. This
feature is used to search for results for which one additional reaction can change the results.
1. From the analysis window, click the Force 1
button to force Fusion to analyze the
sample with one false reaction.
Click the Reanalyze
button to reset the analysis to the original results.
Click the Rxn Reset
button to return the Rxn Pattern table to the default settings.
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Micro SSP Combined Analysis
The HLA Fusion software supports a combined analysis feature. In a combined analysis, the
reactions from two tests of the same sample are combined together in a single analysis. The
previous test must either have the same Sample ID or be associated with the same Patient ID.
To combine results for a sample, you need to start or continue a Micro SSP allele-specific test and
have a previously saved Micro SSP or LABType session to combine with it. After combining
sessions, the possible typing assignments are displayed, and the reaction pattern table changes to
reflect the reaction pattern of both tests.
1. In the analysis window, click on the Analyze Combined button below the reaction
pattern table.
The Combined Analysis window displays a list of previous sessions that have used the
current sample and share the same Sample ID.
2. Select the desired previous session(s) by selecting the associated Combine check box on the
far left.
3. Click the Analyze
Note:
button at the bottom of the pop-up window.
If you combine one sample in the previous nomenclature format with a sample in the
newer nomenclature format, the possible and assigned allele pairs and code will be
displayed in the new format. If the sample with the previous nomenclature format
contains an allele that is not included in the new nomenclature, that older allele is
dropped.
To rerun the combined analysis, click the Reanalyze Combined

button.
If the nomenclature dates between the current one and the one(s) being combined with it
conflict, then the session(s) you selected is highlighted Red.
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If you click the Analyze
button and there is a conflict on nomenclature dates, a warning
message is displayed that gives you the option of continuing or canceling the combined analysis.
The nomenclature of the sample test you selected to combine with the current one will be used if
you continue.
Note: Notice that the Analyze Combined button in the analysis window changes to Reanalyze
Combined button. This is an indication that the selected sessions have been combined.
If sessions are combined, a note is added to the system comments box.
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Make Typing Assignments in Micro SSP Analysis
HLA Fusion provides computer-suggested allele pairs and coded assignments. Final typing
assignments can only be made by you, or your supervisor.
From the analysis window you can do the following:

Switch between code formats

Apply Bw4/Bw6 to serology results

Apply frequency filters

Assign non-coded allele pairs

Assign a coded allele pair

Assign serology equivalents

Make manual assignments

Remove assignments

Save and confirm assignments
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The Pairs Tab
The Pairs Tab displays the possible allele pairs results that match the reaction pattern for the
sample. The pairs are suggested by the software.

The list identifies the pairs and groups them by either full-match pairs, (no false
reactions) or the number of false reactions. Results with false reactions are listed with
the false reacting bead/well identified.

The results display one allele pair per row.

Possible homozygous pairs are flagged in the Comment field.
Assign an Allele Pair from the Suggested List
1. Double-click on an allele pair under the Possible Allele Pairs to assign it to the final pairs
assignment area.
Alternatively, you can click to highlight an allele pair on the list under the Pairs tab, and
click the V (assign) button next to the Assigned Allele Pairs title to add it to the final
assignment area.
To remove an assignment, select the assignment on the Assigned Allele Pairs list and click the X
(remove) button.
Double-click
a pair to
assign them
The Final
Assignment
area
The Manual
Entry Box
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Select an allele pair,
(or pairs) and click
this button to send
them to the final
assignment area.
Click the “X”
button to
remove allele
pairs.
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The Match Tab
This data grid displays the coded format of the actual allele pairings for the sample. A Matched
Reaction Pair is a pair of alleles, (or group of alleles) with a reaction pattern that completely
matches the reaction pattern of the current sample.
Hove your
mouse pointer
over an allele
to see its code
definition.

This result differs from the Possible Allele Code results. The Possible Allele Code
condenses the results into a single code, where possible.

Hovering your cursor over a coded allele format displays its code definition.
Manual Allele Pair Assignment
1. Make sure you type the assignment in the correct allele code format:

New nomenclature format: X*##:##(####) X*##:##(####), where X = locus type and #
= code number.

Previous nomenclature format: X*#### X*####, where X = locus type and # = code
number.
A manually
entered
assignment.
Type an assignment into the text box directly below the Assigned Allele Pairs list.
Press the Enter
key on your keyboard to move the typed allele upwards and into the Assigned
Allele Pairs text box.
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Possible Allele Codes
The Possible Allele Code field displays the possible coded results for all results that fully match the
sample. The type of code used is dependent on your configuration selection: NMDP code, (default)
local code, (user-defined) or no code.
Possible
allele code
Allele code
definition
Assigned
allele code

The possible coded result is listed at the top section of the field. The code definition is listed
below it.

If there are no codes for a particular suggestion, then the suggestion is listed with XX,
meaning the code is undefined. For multiple XX suggestions, each suggestion is numbered
as XX1, XX2, etc., to distinguish one from the other.

The allele codes displayed in the Possible Allele Code field are condensed by Fusion
based on suggestions from the list of possible allele pairs displayed under the Pairs tab.

The allele code is based on the current NMDP code, or local code installed in the system. By
default, the system assigns the NMDP codes to the alleles. You can optionally change these
codes to either No Code, Local Code or Cross Code.

No Solution is listed if there are no results that match the sample’s reactions within the
allowable number of false reactions.
Allele Code Assignment
1. Double-click the possible allele code, or select the suggested code and click the V (assign)
button.
Select an allele code and click the X (remove) button to remove an allele code assignment.
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Manual Allele Code Assignment
1. Type an assignment into the text field just below Assigned Allele Code. Make sure you
type the assignment in correct allele code format:

New nomenclature format: X*##:##(####) X*##:##(####), where X = locus type and # =
code number.

Previous nomenclature format: X*#### X*####, where X = locus type and # = code
number.
Otherwise, the system does not accept it, and prompts you to make corrections.
Note:
If you click on the Translate button to display alleles in the new nomenclature
format, you cannot enter a manual allele code unless you reanalyze the sample and
alleles are again displaying in the previous nomenclature format.
Press the Enter
Note:
key to move the allele code you typed in to the Assigned Allele Code field.
If you have a homozygous result, the assigned code can be edited in the Manual Allele
Code field to show the homozygous-coded results once.
Unknown Allele Codes
Unknown allele codes are marked with XX followed by a sequential number. The numbers are reset
to 1 for each sample and locus. When you see unknown codes, you should first make certain you
have imported the latest NMDP file.
If you have the latest code file, and are still seeing XX codes, you can store these unknowns for later
submission to the NMDP in a .txt file named nmdp_code_report.txt. By default the text file is
stored in C:\OLI Fusion\data\NMDPExport, but the location can be changed by modifying the
Interface path (see the section: Setting HLA Fusion Default URLs and Directory Paths). Code
information is appended to the end of this text file as it is added; the newest additions are at the
bottom.
1. From the Possible Allele Code area, select the XX code to enable the NMDP Code
Report
button at the bottom of the screen.
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Select XX
code here…
…to enable
the NMDP
report
button here.
Click the
“X” button
to cancel.
2. Right-click the Report
button and choose one of the following:
To send the unknown code information to NMDP, select
Direct Request NMDP.

To add the unknown code information to a text file,
(default location is C:\OLI
Fusion\data\NMDPExport), select Save in text
file.

To add the unknown code information to an Excel file,
(default location is C:\OLI
Fusion\data\export\NMDPExport), select Save in
Excel File, or simply left-click the mouse button.
3. When you’re done, click the
Note:
button to remove the buttons from display.
The Rpt+ button retains the last selection you made, (direct, text or Excel) so it can
be used as a shortcut; unless you want to change your selection, the next time you
report XX code simply click the Rpt+ button.
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The following shows examples of each result:
Direct to NMDP
XX code saved
as a spreadsheet
(.csv) file.
XX code saved as
a text, (.txt) file.
Other Assignment
The Other Assignment field can be used to make a sample assignment that is not restricted to
any format. In addition, you can highlight and add serology or allele pair or code assignments and
add them to the field for modification.
You can make other code assignments one of two ways:

Type an allele pair, or allele code into the Other Assignment field.

Click the Assign V button and select one of two options:
1. To assign just the possible allele code, select Assign Possible Allele Code.
2. Choose Assign All to bring the Possible Allele Code, Serology or Assigned Allele Pairs
assignment(s) into the Other Assignment field.
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You can then choose to modify any of the copied code if desired.

The entered allele is assigned and is included in reports that are run that include this sample.

It is not listed in any final assignment fields for this sample.
Possible Serology Field
The serology equivalent field displays all serology equivalent suggestions for the sample based on
the possible allele pairs. When you select a displayed serology equivalent, the allele pairs associated
with it are displayed in the field below.
Note:
Make sure you have imported the current serology equivalent file through the Utilities
menu. If a zero (0) appears in the serology assignments, this means you need to
import the current serology equivalent file.

Only one serology equivalent assignment for the sample can be made at a time. Therefore, a
current serology assignment is replaced if you select and assign a different one.
If this is a multi-loci test, more than one locus can be assigned. However, for single
locus tests, only one locus can be assigned.
Note:
Serology
Equivalent
Related
Allele
pairs
Serological
assignments
Assign
button
Remove
button
1. Double-click a serology suggestion, or highlight it and click the V (assign) button to copy it
to the Assigned Serology field.

Select the a serology equivalent and click the X (remove) button to remove it. Or, select and
assign a different one to replace it.
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Translate (non-current nomenclature format only)
The Translate
button is displayed if your alleles format is displayed with older
nomenclature. Clicking the button does the following:

Displays all assigned, (except from the Other Assignment field) and possible allele
code/pairs in the latest nomenclature format. If a matching allele in the new format cannot
be found, the allele remains displayed in the old format.

You can view and print this display, but results cannot be saved or reported in this new
nomenclature format.

To go back to the older allele format, you can navigate to another sample, and then return
to this sample.
Adding Comments to Samples
Comments you, or Fusion adds to the Comments fields are displayed with the sample results in
the current analysis session, data look up and reporting functions in HLA Fusion.
1. In the analysis window, type sample comments into the Sample Comments field,
(located just below the Assignments area).
Or, double-click in the User Comments field to open a larger writing space.
Your own
Comments
(255 characters
maximum)
Comments
entered by
HLA Fusion
Comments are only saved after you click the Save
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Flagging a Sample for Further Testing
You can indicate the need for further testing of a sample by selecting the More Tests check box
button. The More Tests indication is displayed in results,
followed by clicking the Save >>
data look up and reports for the sample.

In the analysis window, click the More Tests check box, located
below the Assignments area.
Printing the Current Analysis Window
The Print Screen button prints the currently displayed analysis window.

From the analysis window, click the Print Screen
current analysis screen.
button on the toolbar to print the
Preview or Print Reports
You can view/preview a Micro SSP report for the current sample by using the Preview Report
and/or Print Report buttons on the HLA Fusion toolbar.
In the analysis window, click the Preview Report button or
the Print Report button
to display a list of reports you can
preview or print for the current sample.
The drop-down report menus are identical whether you are
previewing or printing a report.
Note:
You cannot create a new Molecular Custom report directly from the analysis screen.
The only custom reports available from the analysis window are ones you previously
created through the reports window.
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Assign Coded Results
Use the Assign
button to designate and save all unambiguous possible coded results, (those
results for which there is only one coded result).
Save Assignments
Lab Technicians and Supervisors can save analysis results for further review and approval. Saved
samples are available for confirmation by a lab supervisor only.

From the analysis window, click the Save
button, located in the bottom right corner
of the analysis window to save the analysis results.

Fusion will automatically move to the next sample.

Samples must be saved in order to associate any user-created comments in the database or
reports. For confirmation, a supervisor needs to access the sample for which you saved the
assignments.
Confirm Assignments
Lab Supervisors can confirm analysis results. Samples are marked as Confirmed.

From the analysis window, click the Confirm
button, located in the bottom right
corner of the analysis window, to confirm all analysis results.
You automatically move to the next sample to continue confirming results.
When you first return to a confirmed sample, you see that the Confirm
shaded purple to let you know it has been previously confirmed.
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Micro SSP Session Summary
The summary table can be launched by clicking on a session in the Navigation Tree on the far
right of the screen. It lists each sample in the session and any saved analysis results.
After opening a session:

Double-click a sample in the Summary Table to go directly to the analysis screen for that
sample.

Click on the Field Chooser
Chooser.
button to the left of the table headings to display the Field
The Field
Chooser
button
In this window you can select or clear the check boxes next to column headings to include or
exclude those columns from the Summary Table.
Selecting or clearing check boxes in this window instantly updates the Summary Table.
Note:
If you do not see a particular field available through the field chooser, and you are
sure it should be there, go to: C:\HLA Fusion\temp and delete the file named
SSP_Layout.xml.

Click on any column header of the Summary Table to sort the
table by that column. The small Up  or Down arrow in the
column header indicates the sorting order: up for Ascending and
down for Descending.

You can also click on a header and drag and drop it to change the
column order.
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
You can save any modifications you’ve made to the layout by
clicking the Yes button in the message box when it appears.
Your changes are saved for all future Micro SSP session summaries
on this same computer until further modifications are made and
saved.

Click the Export button, (located at the bottom of the screen) to save the Summary Table
on your computer or network, (default location is C:\OLI FUSION\data\report). The
file will be saved in the Excel spreadsheet (.XLS) format.

Click the Print button to create a hard copy of the Summary Table.

Click the Preview button to view and/or resize the Summary Table before printing.
In the print preview window, the page view slider on the left displays icons for each page of the
report.

Click on a page representation, (left side) to display that page in the preview window on the
right.
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Navigator Right-Click Menu Options for Micro SSP
HLA Fusion provides special menu options which are available when you right click on either a
session, or a sample, in the Fusion Research Navigator.
Session-Level Options
There is a special session-level menu that displays if you right-click on an active session in the
Navigator, (select the session first with a left-click) which allows you to reanalyze with new
nomenclature:
Reanalyze with New Nomenclature
This feature allows the session to be reanalyzed using a new or
updated catalog.
1. After right-clicking on a session, the Select New Product screen opens.
2. Rename the session.
3. Click the drop-down arrow
the list of available catalogs.
4. Click the Analysis
in the New Catalog ID field and select a new catalog from
button.
The session on which you right-clicked is now re-analyzed with the catalog you’ve selected.
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Sample-Level Options
Two menu options are displayed if you right-click on an active
sample in the Navigator, (remember to select the sample first
with a left-click).
Related Records
A Related Record is a record that is associated with the current sample by Patient ID or Sample ID.
Note:

This option is also available when you use the Related Records toolbar button
Right click a sample from the Navigator and select Related Records to load all records
related to the current sample into the Sample drop-down list, (at the top, center of the
screen).
Sample ID’s

.
Navigation buttons
Use the sample navigation buttons to display the analysis of each related record one-by-one.
To go back to viewing the samples in the current sessions, click the <<Summary link at the top of
the window.
Side by Side Analysis
Use this option to compare the current sample analysis with one previously conducted.
Note:
This option is also available when you use the Side-By-Side Analysis toolbar button
.
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1. Right-click the sample, and select Side-by-Side Analysis.
2. Select a previous sample analysis from the displayed list to compare it to the current one.
The two analysis windows are then displayed in a comparison window.
Side-by-Side analysis display
Current
Analysis
Previous
Analysis

Each window can be resized and moved by dragging and dropping.

Click the Side-By-Side Analysis toolbar button again to cancel the comparison display.
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Quantiplex Beads
Quantiplex Beads™ data can be imported and used during LABScreen Analysis. When imported with
LABScreen sessions you can view SFI values in bead pop-ups and raw data tables in the LABScreen
analysis window.
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Entering and Using Quantiplex Bead Information
You can select different Quantiplex Beads Sessions for use in LABScreen analysis. Quantiplex Beads
Sessions cannot be changed after they have been imported.
From the Main Menu you can:

Enter Quantiplex Beads sessions

Select a Quantiplex Beads session for use in LABScreen Analysis

View Quantiplex Beads SFI values in LABScreen Analysis
Acquiring Quantiplex Beads Data
1. Select the Quantiplex Beads
Beads button on the Fusion toolbar.
button from the home page panel, or the Quantiplex
The Quantiplex Beads Home page is displayed.
Click to open the
Catalog Manager
Click links to
display selected
catalog,
worksheet, or
probe/primer
documents.
Note:
Click to open the Update
Reference file window
Click to open the
Available Update
Reference window
If you are not using the default Fusion user interface, the data and links shown on the
right side of the window are not displayed.
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2. If Luminex CSV files have not already been loaded into Fusion,
click the small folder
icon located at the at the top, left.
Note:
Open worksheets and probe/primer sheets to verify the accuracy of revision numbers
(these documents do not contain a revision number in their filename).
Select Luminex session(s) from the Select CSV
Files List.
3. Click the Open
button.
The Quantiplex Beads Session Import screen
displays.
Session
Catalog
Nomenclature /
IMGT version
Date will be highlighted
yellow if regional settings do
not match between the
current CSV file and Fusion.
Click to
browse
for
CSV
files
Luminex
CSV
session
files
Quantiplex Beads
Home Page button
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Note:
A Session ID must be unique to the Fusion database. If the Session ID already exists, the
software prompts you to rename the session. It is also highly recommended that you do
not use any special characters in this field since they may serve a specific purpose as
field separators.
4. On the Session Import Screen, select a catalog file from the drop-down list in the Catalog ID
field.
Note:
If you need to import more catalogs, click the [Download] link on the Quantiplex Beads
Home Page. The catalog drop-down list may not be immediately updated if you
downloaded the catalogs during the current import session. In this case, you may need
button again to
to click the Home button and then click the Quantiplex Beads
continue the import process.
5. Place a check mark in the Select Quantiplex check box
for all samples you want to import.
6. Click the Import
button.
The sample(s) are imported for use in LABScreen analysis sessions.
Start LABScreen Analysis with Quantiplex Beads
Quantiplex Beads values can be viewed only with LABScreen Sessions started after the Quantiplex
Beads Session has been entered.
Start the import process for a LABScreen session with which you want to use Quantiplex Beads.
1. From the LABScreen import window, select a Quantiplex Beads sample from the Quantiplex
Beads drop-down list.
2. Once you click Import for the LABScreen session, the selected Quantiplex Beads sample is
imported as well.
View SFI Information in LABScreen Analysis
You can view Quantiplex Beads SFI values for each bead in the bead information pop-up or the raw
data table of a LABScreen session.
1. Place your cursor over a bead reaction bar on the LABScreen Analysis Window to view the bead
pop-up with SFI values.
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Click the Raw
values.
button on the LABScreen analysis window to display the Raw Data table with SFI
View MFI Information with Quantiplex Beads
The Trimmed Mean Fluorescent Intensities, (MFI) of test samples can be converted into Standard
Fluorescent Intensity (SFI) units by using the linear standard curve obtained for the Quantiplex Beads
read in parallel on the same machine.
1. If Luminex CSV files have not already been loaded into Fusion, click the small folder
located at the at the top, left.
icon
2. Select Luminex session(s) from the Select CSV Files List.
3. Click the Open
button.
The Quantiplex Beads Session Import window displays.
1. Place a check mark in the Select Quantiplex check box.
2. Click the Quantiplex SFI
button.
The Quantiplex MFI screen opens.
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HLA Fusion plots the linear standard Curve of
Quantiplex Beads using SFI (y axis) vs. Trimmed Mean
(x axis), both plotted on a log scale.
If you select more than one sample, Fusion plots the
average values.
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Session Summary and Logs
What is the Session Summary?
The session summary table presents a pre-analysis of the results. It lists each sample in the session
and their saved analysis results. This option allows you to quickly analyze a session in HLA Fusion™
Research, and save it for later review and final assignments. You can graphically view samples during
batch analysis, but no final typing assignments are made. The summary table can simply be launched
by clicking on a session in the Navigation tree.
Note: You can return to a session summary from the Analysis Window any time by clicking the
<<Summary link at the top of the HLA Fusion™ Research toolbar next to the Sample/Session ID.
Example Session Summary
The figure below displays the session summary displayed by clicking on a session. The summary table
displays the analysis results for each sample in the selected session.
Session ID
Session Summary Screen (ConsenSys)
Creating and Managing Session Logs
With HLA Fusion™ Research, you can create log files of your analysis sessions which you can then
print or archive.
Creating a Session Log
1. On the HLA Fusion™ Research Menu Bar, click Data.
The Data Management Screen opens.
2. Provide all necessary session input information by using the drop-down menus and search
buttons on the left side of the Data window.
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The Data Management Screen
3. Once a session is selected, its information is displayed on the right side of the window where
you can add information.
4. Once you have all information you want to include in the log, click Save.
Managing Session Logs
1. On the HLA Fusion™ Research Menu Bar, click Data.
The Data Management Screen opens.
1. Provide all necessary session input information by using the drop-down menus and search
buttons on the left side of the Data window in order to bring up the session you want.
2. Once you’ve displayed the session log you want, use the Archive
Unarchive
buttons at the bottom of the window to manage the Session Log.
and Delete
Printing Session Logs
1. On the HLA Fusion™ Research Menu Bar, click Data.
The Data Management Screen opens.
1. Provide all necessary session input information by using the drop-down menus and search
buttons on the left side of the Data window in order to bring up the session you want.
2. Once you have displayed the session log you want, use the Print Session Log
button at the bottom of the window to print a copy of the Session Log.
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Reports

HLA Fusion™ Research provides different report formats in which to output your analysis data
and results.
From the Reports menu you can do the following:

Create, print and export reports for analysis data for all supported products

Create custom reports for which you determine content type

Create reports for electronic submission, such as NMDP HML reports

Store as many as 18 reports in a “My Favorites” list for convenient access

Modify the appearance of any report, such as fonts, formatting, and background colors
(supervisors only)
Note: To view reports, your computer must have some form of printer driver installed. If you do not
have a printer driver installed, you can download a free copy of PDF Distiller from Adobe.com, or
the Microsoft Office Document Image Writer from Microsoft.com.
In addition, you can print and export these reports directly from an analysis or batch summary screen.
Using the Reports Window
The following sections describe how to create, save and print a report containing your analysis data.
Here are the main steps you should take to create a report from this window:
1. Select a report type.
2. As needed, select criteria to refine the report data, such as the date range.
3. Select the sessions or samples to include in the report.
4. Select the View Report or the Export Report button.
Accessing the Reports Window
Access the Reports window in one of two ways:

On the home page, click the Reports

Or click
button in the Fusion Explorer.
on the Fusion menu bar.
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The Reports window is displayed, with a list of any sessions that fall within the date range, based on
the session date range set in the Find dialog box. If no session are displayed, try modifying the date
range.
Report
types
Set the
order and
sort criteria
for report
columns.
Create a
Shortcuts
separate
to other
Fusion
To close Report
menu
the reports for each
options.
window sample
Date range
for
displayed
sessions
Click to
filter
sessions by
selected
criteria
You can
pair a
Catalog ID
and alleles,
(that match
alleles in
the allele
pair or
assigned
allele field.)
View,
customize,
export or
email a
report.
Report
title
List of
sessions
Filtered
by report
type and
input
criteria.
Criteria to
refine report
data (filters
the displayed
sessions)
Select a tab
to view either
by session
or sample.
Select Report Type

Select a report from the report type menu options displayed at the top of the Reports window.
The list of sessions in the right pane of the Reports window is filtered to display only the ones
related to the selected report type.
Report Types
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Refine Report Input
If needed, use the left panel of the Reports window, to further filter the sessions you want to include
in your report. There are a number of criteria you can set:
1. Enter a Patient ID, Session or Sample ID
fields, or browse for the information using
the Browse
button.
2. Adjust the date range. Use the drop-down
calendars in the Session Date fields to
select a different start and end date.
Click to filter sessions
by selected criteria.
3. Enter or browse for specific sample or
session characteristics or status (see
below).
4. Once you set criteria and click the Find
button on the left panel of the Reports
window, the session list in the right panel
of the window filters accordingly.
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Session/Sample Selection

In the Samples/Sessions list, click the  sign next to any session to expand the display to
show its samples.
View by Sessions
or by Samples
A session with
some, but not all
samples selected
A session with all
samples selected
Sessions
Samples
1. Select the check boxes next to each sample you want to include in a report. Select the check
box next to a session ID to include all of its samples. (Deselect the check box of any sample or
session you do not want to include in the report.)
2. If at least one sample has been selected for a session, the Include cell for that session is
highlighted with grey. If all samples for a session are selected, there is a check box in the
Include In cell.
3. (Optional) To view all the samples available, or to view only the samples you have selected so
far, click the Samples tab and select or deselect the check box for Show selected samples.
4. Alternatively, you can right-click on a session or sample and apply one of the following:

Select All: select all sessions and samples for inclusion in the report.

Deselect All: deselect all sessions and samples from inclusion in the report.

Analysis Select: specify the analysis product report type (Micro SSP, KIR, ConsenSys,
Quantiples Beads, etc.)
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To create a separate report for each selected sample, select the
check box next to 1 Sample per Report.
View, Print or Export Reports

Once you have the report type and all the samples selected, click View Report. The report is
displayed in a separate window, the Report Viewer.
Example of a report viewed in the Report Viewer
The Report Viewer contains
various toolbar buttons to
allow you to export, print and
navigate through your report.
The functionality of these
buttons is described in the
following table.
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Report Viewer Toolbar
Toolbar Button
What it Does
Export Report: Exports reports in one of several available
formats including, Crystal Reports, PDF and Microsoft Word.
Print Report: Sends the current report directly to the printer.
Toggle Group Tree: Opens a tree panel on the left side of
the Report Viewer window which lists all the samples
included in the current report.
Report Page Navigator: If the report has multiple pages,
these buttons allow you to move to the first page, the next
page, the previous page or the last page.
Find Text: Clicking this button opens a text box which allows
you to search and find text throughout the report.
Zoom: Click the down arrow on this button to choose a zoom
setting, view an entire report page, or view by the report
page’s width.
 To close the Report Viewer window, click the Close button
viewer.
in upper right corner of the
Export Report
1. Click the Export Report button
when you want to export a report in one of several
standard formats. The Select Output Directory and Save Type dialog box is displayed.
Exported report destination/file save as type screen
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1. Enter a name for the current exported report, or browse for a report file to export.
2. Select a format from the Save as type drop-down list, (Excel, Acrobat, Word, or Rich Text
format).
3. Click the OK button. By default, the file is saved in C:\OLI Fusion\data\report.
4. You can also export a report by clicking the Export Report
Reports page.
button on the main
Accessing Reports from the My Favorite Menu
The My Favorite menu is a convenient way for you to access and generate the reports you use most
often. You can make as many as 18 report types available from the My Favorite drop-down, including
custom reports. Adding to or deleting from the list is easy.
Adding Reports to My Favorite
Make sure you have selected the report you want to add to My Favorite (verify that its name is
displayed in the Report Options section of the Reports window).

Select My Favorite > Add to My Favorite.
Add a new report to the My Favorites menu.
The current report name is added to your My Favorite menu. When you want to generate this report,
just click on its name from the bottom portion of the My Favorite menu.
Saved reports are
listed below this line
and can be accessed
at any time.
Removing Reports from My Favorite
1. Select My Favorite, and select the report you want to remove from the list of reports at the
bottom of the menu.
The My Favorite menu closes.
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2. Select My Favorite > Remove from My
Favorite.
The report you selected in step 1 is no longer displayed at the bottom of the My Favorite menu.
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Report Tools
Customizing Report Appearance
Note:
You must be a supervisor-level user in HLA Fusion and have Crystal Report Designer
software installed on your computer to use this feature.
This feature allows you to format the appearance of HLA Fusion reports to meet your specific needs.
For example, you can change font style, size and color as well as the location of text and data fields on
the report.

HLA Fusion automatically launches the report designer if it is installed in the default directory
(C:\Program Files\Business Objects\BusinessObjects Enterprise
12.0\win32_x86\crw32.exe).

Use Notepad to open the OneLambda.Fusion.Interface.exe file, located in C:\Program
Files\One Lambda\HLAFusion\IVD. Make sure that Crystal Report Designer path name is
entered on the following line of this file (see figure below): <add key="ReportDesigner"
value="C:\Program Files\Business Objects\BusinessObjects Enterprise
12.0\win32_x86\crw32.exe"/>
Editing
OneLambda.Fusion.Interface.exe
Please note that all the report files used in HLA Fusion are installed in the directory C:\OLI
Fusion\rpt, and they all have the extension of .rpt. These files can be moved anywhere for
central access, but to do so, you must update the OneLambda.Fusion.Interface.exe file
to reflect the new location (see figure above).
 When you open a report to customize it, a backup copy is automatically created with the
timestamp as the suffix of the report name. This allows you to retrieve the original report
format, if needed.
1. Select Reports > Tools > Customize Report.

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Use the Crystal Report Designer tools to modify the appearance of your report.
Once you have made changes to the report format, save it. Make sure you do not change the name of
the report file. Next time you run this report in HLA Fusion, the report will have the appearance you
last saved in Crystal Report Designer.
Creating Custom Data Export Templates
1. Select Tools > Setup Data Export to customize report data export by setting up templates
that determine the type of report data (session, sample, patient, results, etc.) is exported when
you select that template.
The Export Data Setup dialog box is displayed, allowing you to
select the name of the export template, the fields to be included, and
the field order you want for the template. Select check boxes on the
left to select category and fields. On the right side of the dialog box,
drag and drop the fields, or hold the CTRL key down and press the
Up/Down arrow keys to change the order.
2. When you are done, click the Save
button.
The new template is added to available export templates from the Tools > Export Data menu.
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Export Data – Select template
3. When you are ready to export data, first select all the
sessions you want to include from the available list.
Then, select Tools > Export Data, and select one of the
templates. The Export Data dialog box is displayed.
Export Data – file save location
4. Select the format for the exported data—XML, CSV or Text. The exported data file is saved by
default in C:\OLI Fusion\data\export.
5. Click the Save
button.
Creating Custom Reports
Certain report types allow you to customize the types of fields which are included or excluded.
Note:
For Molecular Custom reports, you must make sure the Free 3 of 9 Extended font is
installed on your computer—otherwise, the barcode will not be recognized. If needed,
you can download this font for free at http://www.free-barcode-font.com/.
1. To create a custom report, select a report type containing the word “Custom” in its name, (for
example, Molecular Custom, under the Generic Typing report type menu).
2. Click the Setup button in the Report Option section of the window.
The Custom Query Report Setup window is displayed, allowing you to customize report content by
selecting from various categories and fields.
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Molecular Custom report setup screen
Custom Molecular and Antibody Report Setup
1. Enter a name or select one from the drop-down list.
2. Select the check box next to each field you want to include in this report.
Note:
To include all related fields, you can click the Check All button to select all the fields in
the category.
3. Click the Save
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Sample Summary
The Sample Summary feature lists multiple samples and their typing results.

Select samples using the Reports window.

Click the Sample Summary button. The Sample Summary window is displayed; it
contains two tabs— Molecular and Antibody.
Sample Summary window
Molecular Typing Sample Summary
Selected antigen typing records are displayed on the Molecular tab of the Sample Summary screen.
You can view typing information in a condensed format, as well as display more details for any
sample.
1. Select samples using the Reports window.
2. Click the Sample Summary button. The default tab is
Molecular.
3. Select an option from the Select Type of Data to Display
drop-down list.
(The window displayed depends on the option selected.)
Reports – Sample Summary Screen
4. Click the Export
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
Or, click the DNA
button to export molecular specificities as an Excel file.
button at the upper right corner of the window to close and return to the
5. Click the Close
Reports window.
Antibody Screening Sample Summary
Any selected antibody screening records are displayed on the Antibody tab of the Sample Summary
screen. You can view screening information in a condensed format, as well as display more details for
any sample.
1. Select samples using the Reports window.
2. Click the Sample Summary
button.
3. Click the Antibody tab.
Antibody Sample Summary Window
4. Click the Export
button to export the displayed data as an Excel file.
5. Click the Close
button at the upper-right of the window to close and return to the main
Reports window.
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View Records
The View Records feature presents typing results and analysis details for each sample selected.
Sample information is shown for one sample at a time. From the View Records menu, you can view
screening and typing records individually.
1. Select data records using the Reports window.
2. Click the View Records
button.
3. The Data Display screen opens. Use the Arrow
samples.
buttons to navigate through
Reports – View Records Screen
4. Use the arrow buttons to navigate through samples.
5. Click the View Analysis
sample.
button to open the analysis window for the current
The analysis window can be resized.
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View Analysis
Display
Click the Close
button to close the window and return to the main Reports window.
Patient Info
You can view patient records associated with selected samples by clicking on the Patient Info tab.
Patient information can also be viewed by Patient ID using the Patient look up function of the Patient
Management menu. From the Patient Info menu, you can view Patient/Donor records.
To view patient information, you must select a sample(s). You can view, but not edit the displayed
information.
1. Select sessions or samples from the Reports window that have an associated Patient/Donor
ID.
2. Click the Patient Info
button.
The Patient/Donor information screen is displayed.
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Patient Information Screen
3. Click the Test Info tab to see the information for the current patient/donor. If more than one
information card is displayed, use the arrow buttons to navigate through the patient records.
4. Click the Close
window.
button in the upper right corner to close and return to the Reports
Audit Trail Report
You can view and print a report of user activity for the current database. This data is only available if
you have done the following:

Set up and connect to an Audit Trail Log/database, (see the: HLA Fusion Database Utility User
Manual).

Enabled Audit Logging from the HLA Fusion default home page.
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Once you have completed the above and wish to view audit log data, take the following steps:

On the home page, click the Reports
tab in the Fusion Explorer,
Or...

Select Reports on the Fusion Menu Bar at the top of the screen.

At the Reports screen, select Miscellaneous > Audit Trail Log.
The Audit Trail Log dialog box displays.
Audit Trail Log Screen

Use the drop-down arrow to select the User for whom you want to see database actions.

Select the date range and options you want the report to include.
Click the List
the Export
button to see the report. If you want to export the Audit Trail Report to Excel, click
button.
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Report Types
There are several report types available. Although most report types are listed in this section, please
note that because new reports are sometimes added between updates to this user manual, you may see
more reports listed in the software.
Patient - (all patients in the Fusion database)

Patient Summary - (summary of both typing and antibody testing results associated with a
Patient ID)

Patient Typing for Batch - (typing summary report over different loci for a set of samples,
based on a selected session)

Patient Custom - (you select the type of patient data to include for the selected samples)
Generic Typing - (typing data from analyzed LABType and Micro SSP samples)

Molecular Custom - (you select the type of molecular data to include for a set of samples)

Custom Typing Results by Sample - (you select the type of molecular data to include for
selected samples)

Allele Summary - (typing report of possible allele pairs and assigned allele code results for a
set of samples)

Allele Code - (typing report of possible allele codes and assigned allele code results for a set
of samples)

Molecular Typing Summary - (typing report of the possible allele code, assigned allele
code, assigned allele pairs, assigned serology, and other assignments for a set of samples)

Combined Sample – Generic Typing - (Combines samples from other sessions into one
report)
Micro SSP - (data from analyzed Micro SSP samples)

Custom SSP Report – (User-selectable data fields based on Micro SSP analysis)

SSP Report - (detailed typing report for Micro SSP™ tests that may be customized)
SSO - (data from analyzed SSO samples)

KIR Summary Table
Generic Antibody - (antibody data from analyzed LABScreen, FlowPRA, LAT or LCT samples)

Antibody Custom - (User may customize a report for antibody data for a set of samples)

Antibody Screening/ID - (antibody data report that is fixed in format)

Antibody Screening Results - (summary table for a selected set of samples which includes
the overall final results made, %PRA, other assignments, and comments)
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Specialty - (reports created for a specialized purpose for specific users)

Antibody Reaction - (summary table of computer specificity assignments based on reaction
scores)

LBSW

LBSW v3

HML V0.2

HML V0.3

SCORE

BmT – ABDR
 Reaction Assignment Report - (export report including Sample ID and reaction string)
 Thai Export
 Thai Export v3
 Thai Export - LABScreen
 UMC-Utrecht Report
 KIR HML: v.3 Report
 BML
 NMDP Code Report
 ABMDR
 CMDP
 Manzen – LABType
 Manzen - LABScreen
 LABScreen SA MFI
 LABScreen – Australia MFI (Summary and detailed reports)
 LABType – Australia
 Raw Data Export
 Maastricht Export
 NIH Export
 KIR Export
 LAT Export
 NKR Report
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Statistical - (statistical or aggregate data for trending, measurement, monitoring, etc.)

Allele Group Frequency (displays the frequency of allele groups based on the first two
digits of an allele assignment for selected sessions or the database)

Allele Group Frequency Extended - (displays the frequency of allele groups based on NMDP
code results or allelic level assignment for selected sessions or the database)

Bead Exclusion Report (Bead numbers excluded from an analysis)

Cut-off Adjustment Summary (summary of all cut-off changes made for selected sessions
or based on a specific catalog file)

LABType Control Value (Control values by exon for a given catalog)

Catalog Statistics (Number of samples analyzed using a specific catalog)
Miscellaneous - (reports that do not fall into one of the above categories)

Database Information (describes the usage of the current database)

Batch Data File Summary (a log of the status of all the sessions run in the system)

NMDP Code (list of NMDP codes and their allele definition)

Serological Equivalent (list of alleles and their serological equivalent definitions)

Typing Query (database search report that lists the samples found for a selected allele)

NMDP Report + Export

Audit Trail Log (a log with all specified activity for a selected users in the current Fusion
database)
My Favorite - (any of the above reports saved in a favorites list)

(Reports listed depend on what you have stored under this menu.)
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Data Management
When you select Data on the Fusion menu bar, a window is displayed that allows you to manage
session files, as well as create log files of session data. From this menu, you can delete, archive,
activate, and move sessions to a different database. You can also map the alleles in a session to the new
nomenclature format.
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Session Management
To manage your data at the session level, use the Data option from the HLA Fusion main menu.
When you select the Data main menu, the Manage Data window is displayed.
Select patient records
to archive or delete.
Sort/Select display options
View
Session
data and
add
comments.
S et
Search
Criteria
Exit the
Manage
Data
window.
Copy patient
data to
another
database
Move
sessions
to a
different
database.
Translate
session
alleles
to the
new format
Prints details
about which
tests were
done, by
whom, etc.
Archive Restore an Delete
archived selected
the
selected session and record
make it
session.
available
for use.
Manage Session Data Window

When you click the Translate Alleles
button, all final allele pairs and code for the
selected sessions are converted to the new nomenclature format and stored in the database.

When you click Move Sessions
the selected sessions are moved to.

Clicking the Copy Patient
button, opens the Select Patient screen.
, you can select another Fusion database into which
1. Select a patient from the list
displayed on the Select Patient
screen.
2. Click the OK button.
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The Copy Patients table opens.
3. Select the patients from the list that you wish to copy by placing a check mark next to the
Patient’s ID in the Select column.
4. Click the Browse
button at the bottom of the screen to select the Target database
where the patient record(s) will be copied.
If necessary, click the Back
5. Click
button to return to the previous screen.
to make a copy of the patient’s records in the target database.
Note that copying a patient’s records to another database leaves a copy of those records in the source
database.
Moving a record deletes the specified record(s) in the source database and adds them to the Target
database.
HLA Fusion allows you to create session log files of your selected analysis sessions, which you can then
print or archive.
1. Provide all necessary session input information by using the drop-down menus and search
buttons on the left side of the Data window.
Once a session is selected, its information is displayed on the right side of the window, the Session
Info pane, where you can add information.
2. Once you have all information you want to include in the log, click Save.
Once you have displayed the session log you want, use the Print Session Log, Archive, Active and
Delete buttons at the bottom of the window to manage the log.
Note:
Samples can also be deleted individually, without the need to delete an entire session.
The only exception are LABType or Micro SSP samples that have been combined.
HLA Fusion allows you to move patient records.
1. Select Patient ID as the Sorted Select Level, (top center of the main, Manage Data Menu).
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2. Click the Move Sessions
button at the bottom
of the screen.
The Database Login screen appears.
3. Login using your Login Name and Password.
The Move Sessions screen opens.
The database which is listed is the database you are currently using.
To move session data to another database, click the drop-down arrow
on the right side of the Database Name field and select the Target, or
destination database name.
4. Click the OK button and Fusion begins the
data transfer.
After the session(s) have been successfully transferred
to the target database, Fusion will display this message.
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Sample Management
In HLA Fusion, sample lists are an easy way to input a large list of Sample IDs and other sample
information into the database for use in analysis sessions. Sample lists may be in .XLS, CSV or .TXT
file format. From the Sample List Import menu, you can import sample lists or edit sample lists prior
to importation.
Note:
Please verify all data you import as HLA Fusion performs minimal data validation upon
import.
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Importing Sample Lists
Sample lists are an easy way to input an extended list of Sample ID’s and other sample information
into the database for use in analysis sessions.
1. From the Main Menu, select Sample > Import Sample List.
The Import Sample List window displays.
Import Sample List Screen
2. Click the Search Sample List
button.
3. Browse for the sample list to be imported and click the Open
button.
4. Type a name in the List ID field, and, if necessary, select a Lab code or Contact ID from the
drop-down list.
5. Confirm sample information and edit if needed.

This symbol
indicates that the Patient ID already exists in the Fusion database.
6. Click to clear the check boxes of any samples you do not want to import.
7. Click the Import List
button to import the selected sample lists.
8. Click Close to return to the Main Menu.
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Information Formats for Sample Lists
The information inside a sample list that you import in to HLA Fusion must be in one of the following
formats.
New packing list format
This file gives the fields (in this order):
ShipmentLoc(1 – 13),SampleIDName(0198-0398-0),SampleType(AB, DR or AB/DR),
TurnaroundTime(14, 21 or 14AB/21DR),DCN (3 digit).
Example line:
1 - 13,0198-0398-0,AB/DR,14AB/21DR,074
Packing list: Old Standard ‘X’ samples
This file gives the fields (in this order):
ShipmentLoc,SampleIDName,SampleType (1, 2, 3..., and an 'X' for AB/DR samples),DCN
Example line:
1 - 12,0287-7867-8,X,074
Old packing list format, '11' for AB/DR samples
This file lists (in this order):
ShipmentLoc, SampleIDName, SampleType (1, 2, 3..., and an '11' for AB/DR samples),
DCN
Example line:
1 - 15,0287-0779-2,11,074
Comma-Delimited Format
Each field is separated by commas. The use of quotes around a field is optional, and is required only if
the contents of the field use a comma, which could confuse field separation. This file lists (in this
order):
ShipmentLoc, SampleIDName, SampleType (AB, DR or AB/DR), TurnaroundTime (14, 21 or
14AB/21DR), DCN
Example line:
"1","12","0287-7867-8","AB/DR","14AB/21DR","074"
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Tab-Delimited Format
Each field is separated by a tab. This file lists (in this order):
ShipmentLoc, SampleIDName, SampleType (AB, DR or AB/DR), TurnaroundTime (14, 21 or
14AB/21DR), DCN
Example line:
1
12
0287-7867-8
AB/DR
14AB/21DR
074
SDF Format
Each field is separated by commas. This file lists (in this order):
BoxSlot, DonarID, SampleType (AB, DR or AB/DR), TurnaroundTime (14, 21 or 14AB/21DR),
DonarCenter
Example line:
1120287-7867-8AB,DR14,21074
Local/Sample/Patient ID Only
This file is a Microsoft Excel file. This file lists (in this order):
Row 1:
Column
Column
Column
Column
Column Title “Local” and “Sample” and “Patient”
A: LocalID
B: SampleIDName (required)
C: PatientIDName
D: Date
Example:
Viewing and Editing Sample Information
Sample information can be edited, but associated Patient IDs cannot—only new Patient IDs can be
added.
1. On the Main Menu, select Sample > Manage Sample Info.
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Manage Sample Window
2. Use the filters to find samples and click the View Sample
Note:
button.
Wildcards can be used in the Sample ID field to widen the results.
3. Edit sample information.

Note:
Double-click on a Patient ID to open the Patient/Donor Information screen and
edit information for that patient/donor.
You can rename a sample by modifying the name in the Sample ID field. Sample ID’s are
listed alphanumerically, with all ID’s beginning with numbers listed first.
4. Click Save to save. Or, click Delete to delete the sample.
5. Click Close to return to the Main Menu.
Note:
You cannot delete a sample which is part of a session that has already been analyzed.
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Test Lists
A Test List is a list of Sample IDs that can be used repeatedly to automatically write the Sample IDs
into a session analysis that can be read by Luminex®. It is a useful tool when you have a group of
samples to be run on multiple tests.
With the Test List menu you can:

Create new Test Lists

View and edit existing Test Lists

Delete Test Lists

Export Test Lists to a .txt file
Creating New Test Lists
Test Lists must be created in the order in which the samples are to be analyzed.
1. From the Main Menu, select Samples > Manage Test List.
Manage Test List Screen
2. Type in a name for the new test list, (or select a previously created test list) and press the Enter
key on your keyboard.
3. Search for samples to add to the test list using the search fields, and click the Search
button to view the search results.
4. Highlight samples, and click the Add
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5. Click the Save
6. Click the Close
button to save the new test list.
button exit this screen and return to the Main Menu.
Viewing and Editing Existing Test Lists
Test Lists can be viewed or edited at any time.
1. From the Main Menu, select Manage Samples > Manage Test List.
2. Use the drop-down list to select a test list, and click Continue>>.
3. Click Delete List to permanently delete the selected test list.
4. Click Close to return to the Main Menu.
Deleting Existing Test Lists
Deleting a test list removes the list from the database, but the Sample IDs are not removed or changed
in the database.
1. From the Main Menu, select Manage Samples > Manage Test List.
2. Use the pull-down menu to select a test list, and click Continue>>.
3. Add, remove or move samples as desired.
4. Click Save to save the new test list.
5. Click Close to return to the Main Menu.
Exporting Test Lists
Test lists can be exported for use outside of HLA Fusion only as a .txt files.
1. From the Main Menu, select Manage Samples > Manage Test List.
2. Use the pull-down menu to select a test list, and click Continue>>.
3. Click the Export button to export test list details to a .txt file.
4. If prompted to save the test list before export, click Yes to save and continue.
5. Select a location to save the test list and enter a file name for it.
6. Click Save.
7. When prompted to create a Luminex Patient List input, click No.
8. Click Close to close and return to the Main Menu.
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Patient Information
HLA Fusion™ can store patient information and associate Sample IDs with patients and donors. You
can store all typing and screening information in one location for each patient.
Note:
Please verify all data you import as HLA Fusion performs minimal data validation upon
import.
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Importing Patient/Donor Lists
After creating a Patient/Donor List, you can import the information into HLA Fusion.
1. From the Main Menu, select Patient Info > Import Patient List.
The Import Patient window displays.
Import Patient Window
2. If needed, click the Browse
button to locate the patient list.
3. Select the check box in the Import column for each patient you want to
import. You may also click Select All
to import an entire patient
to remove all check marks from from the
list, or Deselect All
Import column.
4. Click the Import
5. Click the Close
Note:
button to import the selected patients.
button to return to the main menu.
The HLA Fusion system checks the patient/donor lists you attempt to import to verify
that all characters contained in the data are supported by Fusion. If your list contains
unsupported characters, a message is displayed to let you know, and the list is not
imported. Newly imported patient records display alleles in the new nomenclature
format. Existing patient records display alleles with the existing allele format.
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Managing Patient/Donor Records
The Patient/Donor Management menu allows you to manage one record at a time.
From the Patient/Donor Management menu you can:







Add new patient/donor records
Search existing patient/donor records
Edit patient/donor records
Associate patient/donor IDs with Sample IDs
Associate patient and donor records
Assign a donor to the Donor PRA
Print, export and archive patient records
Adding New Patient/Donor Records
You can add patient information using the Patient/Donor Information menu. This is the best option
for adding a small number of patient records.
1. From the Main Menu, select Patient Info >> Manage Patient.
Click to display a list of patients/donors in the Fusion database
which you can search through by using numerous criteria.
After selecting
a patient or
donor, place
a check mark
here to edit
the information
fields.
Tools to manage patient
and donor information.
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2. Enter an ID in the Patient/Donor field. The ID can be alphanumeric, (contain letters
and/or numbers).

button which opens the Patient/Donor List from which
Or click the Browse
you can search and select a patient/donor.
3. Enter patient/donor information as needed.
Fields with an asterisk (*) are required.
4. Click the Add New
to the Fusion database.
5. Click the Close
button to save the data and add the patient/donor information
button to close and return to the main menu.
Lookup Patient/Donor Records
This option allows you to browse through records or search for specific ones.
If you know the Patient or Donor ID:
1. Enter the Patient/Donor ID in the Patient or Donor ID field.
2. Click the Enter
keyboard.
key on your
If you know only part of a patient or donor’s information, (first name, last name, etc.):
1. From the Main Menu, select Patient Info > Manage Patient.
2. Click the Browse
button which opens the Patient/Donor List.
3. Enter your search criteria, (i.e., patient or donor, last name, etc.) and click the Search
button.
4. If the patient/donor is located, place a check mark in the box next to the patient/donor.
5. Click the Close
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Editing Patient/Donor Records
Note:
You must be a Supervisor in order to edit a patient/donor record.
All patient/donor information, (except patient/donor ID) can be edited.
1. From the Main Menu, select Patient Info > Manage Patient.
2. Enter a Patient or Donor ID, or search by using the steps outlined above.
3. Place a check mark in the Edit/Update check box at the bottom,
left of the screen.
4. Edit patient/donor information on either of the three
tabbed forms which are part of this screen.
(Fields marked with an asterisk (*) are required.)
5. Click the Save
6. Click the Close
button to store your changes.
button to return to the previous screen.
Associating a Patient/Donor ID with Sample ID’s
A Sample ID cannot be associated with more than one patient or donor record, but a patient or donor
record can have more than one Sample ID associated with it.
From the HLA Fusion Main Menu, select Patient Info > Manage Patient.
1. Select a Patient or Donor ID from the drop-down ID box on the main Patient/Donor
Information screen.

2.
Or, click the Search Patient/Donor
button to locate the correct
Patient or Donor ID.
Click the HLA Tests tab at the top of the window.
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The HLA Tests screen opens:
Patient/Donor Information Screen – HLA Tests Tab
3. Place a check mark next to Edit at the top of the screen to allow changes to be made to the
record(s).
4. Select a Patient or Donor ID.
5. Click the Associate Sample IDs button.
6. In the Patient/Donor Sample Association window, highlight a Sample ID and click the
to remove a
arrow
button to add it to the Patient/Donor Sample List. (Click
highlighted Sample ID from the list.)
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7. Click OK to associate the Sample ID’s and return to the patient record
8. Click the Close
menu.
button, or the Exit
.
button to return to the previous HLA Fusion
Translating Associated Patient/Donor Results to New Allele Code
Patient or Donor results can be translated to update the allele code names to the new NMDP allele
code format.
The new format will affect allele code and allele pairs assigned to the selected patient/donor, and will
be stored in the Fusion database in the new format.
1. On the HLA Fusion menu bar, select Patient Info > Manage Patient.
2. Select a patient/donor record.
3. Click the Translate Alleles
button.
4. Click the Save
button to save your data.
5. Click the Close
button, or the Exit
button to return to the previous window.
Associating Patient and Donor Records
A Patient ID can be associated with more than one donor record, and a donor ID can have more than
one patient record associated with it.
1. From the Main Menu, select Patient Info > Manage Patient.
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2. Select a patient/donor record.
3. Click/Select the HLA Tests tab.
4. Place a check mark next to Edit at the top of the screen to allow changes to be made to the
record(s).
5. Click the Associate Donor IDs
button.
6. In the Patient/Donor Sample
Association window which
opens, highlight a Donor ID and
to add it to the
click
Patient/Donor Sample List.
to remove a
(Click
highlighted Donor ID from the
list.)
7. Click Save to store the data.
8. Click OK to return to patient
record.
9. Click Close to return to the
previous menu.
Associating a Donor with Donor PRA Results
A Donor ID can be included in the calculation for Donor PRA percentage for the antigen products.
1. From the Main Menu, select Patient Info > Manage Patient.
2. Select a donor, or create a new one.
3. Make sure the Patient/Donor field is set to Donor.
Located at the bottom, right of the Patient/Donor Information screen is the Donor Info
section.
4. Select the Include in Donor PRA check box.
5. Select the Donor Type from the drop-down selection.
6. Click the Browse Button
to open the
Donor Group Selection screen and choose the
appropriate donor group(s).
button to return to the
7. Click the OK
Patient/Donor Information screen.
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Printing Patient/Donor Records
HLA Fusion prints both Record Management tabs regardless of which tab is currently being viewed.
1. From the Main Menu, select Patient Info > Manage Patient.
2. Select a patient/donor record.
3. Click Print to print.
4. Click Close to return to the Main Menu.
Exporting Patient/Donor Records
Patient/donor records can be exported individually to a CSV file. The file has the same format as a
Patient List.
1. From the Main Menu, select Patient Info > Manage Patient.
2. Select a patient/donor record.
3. Click Export to export.
4. Select a location to save the CSV file to and enter a file name.
5. Click Save.
6. Click Close to return to the Main Menu.
Archiving Patient/Donor Records
Archived patient/donor records are not available for reporting or associating. You can still view
archived records and reactivate them by clearing the archive check box.
1. From the HLA Fusion Menu bar, select Patient Info > Manage Patient.
2. Click the General Info tab.
3. Select a patient/donor record.
4. From the Patient/Donor List window, select Archive from the drop-down Active/Archive
list.
5. Click Save to save.
6. Click Close to return to the Main Menu.
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Deleting Patient/Donor Records
Patient/donor records can be deleted through the Manage Patient menu option.
1. From the Main Menu, select Patient Info > Manage Patient.
2. Click the General Info tab.
3. Select a patient/donor record.
4. Click Delete to delete the patient/donor record from the Fusion database.
5. Click Save.
Creating Patient/Donor Lists
The following is an example of a patient list that can be created and the guidelines for doing so. The
patient list must be formatted for import via a program like Excel or Notepad and saved as a
Windows compatible CSV file.
The first field/section must contain the names of the patient list fields, each separated by commas.
Note:
Creating a new patient list can be made easier by first exporting an existing list into CSV
format, and using the fields in that to build your new list.
Patient List Field Names and
Format
PatientIDName,CategoryGrp,FamilyID,FirstName,MiddleName,LastName,Ssn,Dob,Gender,Ethni
city,Address,City,State,Region,Country,ZipCode,Email,Phone,WkPhone,Cellular,Fax,Emplo
yer,SpouseName,SpouseBloodType,EmergencyContact,EmrgncyTel,DCN,HospitalName,Division,
BloodType,Disease,RhBloodType,PatientDonorFlg,Associated SampleIDs,Associated
DonorIDs,HLA1_A,HLA2_A,HLA1_B,HLA2_B,HLA1_BW,HLA2_BW,HLA1_C,HLA2_C,HLA1_DRB1,HLA2_DRB
1,HLA1_DRB3,HLA2_DRB3,HLA1_DRB4,HLA2_DRB4,HLA1_DRB5,HLA2_DRB5,HLA1_DQB1,HLA2_DQB1,HLA
1_DQA1,HLA2_DQA1,HLA1_DPB1,HLA2_DPB1,HLA3,HLA1_DRB4,HLA2_DRB4,HLA1_DRB5,HLA2_DRB5,HLA
1_DQB1,HLA2_DQB1,HLA1_DQA1,HLA2_DQA1,HLA1_DPB1,HLA2_DPB1,HLA1_DPA1,HLA2_DPA1,HLA1_MIC
A,HLA2_MICA,HLA1_MICB,HLA2_MICB,HLA_KIR,ClassI_AbSpec,ClassII_AbSpec,MIC_AbSpec,Unacc
eptableAntigens,AcceptableAntigens,Notes,SHLA1_A,SHLA2_A,SHLA1_B,SHLA2_B,SHLA1_Cw,SHL
A2_Cw,SHLA1_DR,SHLA2_DR,SHLA1_DR345,SHLA2_DR345,SHLA1_DQ,SHLA2_DQ,SHLA1_DP,SHLA2_DP,D
onorType,IncludeInDonorPRA
Subsequent lines must list the actual patient information, alphanumerically, (can be letters and/or
numbers) separated by commas. If there is no information for the patient in a particular field, that
field still requires a comma as a placeholder.
Note:
For all manual serology entries, the locus must precede the value. For example, for an
A locus of value 23, you must enter A23.
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Example Patient/Donor List
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Patient Antibody Tracking
You can track antibody strength for each patient over a period of time. The information tracked is
taken from the typing data stored in their Patient/Donor Info card and the antibody data in their
analysis samples (LABScreen Single Antigen and LABScreen Singles) for the specified date range. Take
the following steps to display graphs and data that track a patient’s antibody data.
Make sure you have patient and donor information entered into HLA Fusion. If not, you can import it
from a patient list and/or manually enter the data on the Test Info tab of the Patient/Donor Info
card. Patient and donor records must be associated.
1. Select Patient Info > Ab Tracking.
The Patient Antibody Tracking window is displayed.
Clicking the Save
button here saves
any samples listed
in this area for
future analysis as
samples within the
chosen date range.
Patient Antibody Tracking window
2. Click the drop down arrow next to the Patient ID field to select from a list of patients stored
in your Fusion database. Or click Search and search by Patient ID, First or Last name, etc.
3. The Molecular and Serological Typing fields are automatically filled with available data for the
specified patient.
4. Select the start and end date range from which you want to view sample antigen data for this
patient, (click the drop down arrows in the date fields to display a calendar).
5. You can select Secondary Ab (IgG, IgM, C1Q, All) or enter one of your own. This is a way to
filter samples and it means that samples you want to bring up must have this secondary Ab.
Otherwise, they will not be available when Find is clicked.

(Optional) You can display the percentage of PRA from available donors in the system or
from selected donor groups who match the computer-assigned antibodies for the current
sample.
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6. Click the Donor PRA button to bring up the following dialog box from which you can select
donor groups or All Donors.
The Donor PRA calculation is displayed next to the Donor PRA button.
Donor Group Selection
7. Click the Find button to display a list of samples for this patient that are within the specified
date range.
Find Patient List
Note:
To add final assignments to a sample, double-click in the Final Assignment column for
the sample to display the analysis window and add the assignment. Also, only samples
with a date can be included in this tracking. If the Sample Date column is empty for a
sample, click on the empty Sample Date cell and use the pull-down date-finder to add a
date.
8. Select the check box in the Include column for the sample(s) you want to include in the Ab
tracking graphs and data.
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The graphs are displayed, (to display a specific type of graph, click on the associated tab).
9. Select the check box for the antigen(s) you want to include in the tracking.
Molecular
Sero
Date
Samples
Examples
of the
graphs
that can be
displayed
with Ab
Tracking
Options
available
if you
right-click
on a graph.
Include Antigen List
10. Select the formula to use for the graphs by clicking the drop down arrow in the Formula
field, (Default versus Raw). The formula can also be changed after the graphs are displayed if
you want to compare the tracking with different formulas.
You can double-click on a graph to expand it, and there are right-click options available from each
graph, (see graphic above). You can also use the expand/contract buttons
at the upper right
corners to expand the graphs.

(Optional) You can add donor data, if desired, by using the drop-down arrow next to the
Donor ID field to select from a list of donors associated with the selected patient. You can also
create a new donor on the fly by typing a unique name into the Donor ID field and filling in
the molecular and sero typing.

(Optional) Enter a numeric value in the User-defined cut-off field. If you want to track the
antibody signal strength with or without the cut-off applied, select or deselect the check box
next to User-defined cut-off.
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
(Optional) Select the check box next to Track DSA to track donor specific antigens. If this is
selected and there are donor-specific antigens that are not tested with OLI product kits, these
are listed.
Various other Ab tracking graphs are available by clicking any of these tabs:
Donor ID drop-down list.
Select to
include
Class II
tracking.
Select to track
donor-specific
antigens.
List antigens
not tested
with OLI
test kits.
Donor Antibody Information

(Optional) Select the DQA/DPA check box to include these in Class II tracking.

(Optional) Manually enter the donor typing in the Sero Typing field.
11. Click the Data Table button to display a raw data table CSV file with the patient antigen
signal over a period of time. The table can be printed or exported.
Patient Antigen Signal Data table
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Profile Management
HLA Fusion™ tracks all changes to analysis data made by users and allows added data security with a
two level analysis result confirmation (Save and Confirm). HLA Fusion also stores general laboratory
information to be used on reports including multiple contract lab codes.
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User Management
From the Profile main menu you can:

Add new users

Edit existing user profiles

Change passwords

Reset passwords

Archive users
HLA Fusion uses two user levels for added security and control of typing and screening results.
A Supervisor can...
A Lab Technician can...
Modify all product configuration settings
Modify all product configuration settings—except to
enable Auto Accept All and Computer Generated
Serology for LABType and Micro SSP products
Save and Confirm analysis results
Analyze data and save analysis results
Update reference files, such as catalogs
and NMDP codes
(Only if authorized by the supervisor) - Update reference
files, such as catalogs and NMDP codes
Archive catalogs
Archive catalogs
Modify and delete session and sample
data
(Only if authorized by the supervisor) - Modify and delete
session and sample data
Modify own & other user accounts
Modify own account only
Change the Lab Profile
Manage sample and patient information
Types of User Privileges
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Viewing the User List
The List User option displays a list of all users currently in the database, both active and retired. You
can look up and select user profiles.
1. From the Main Menu, select Profile > List User.
2. Type in a name and click Search to search for current users.
3. Double-click to the left of a user entry to view the profile.
4. Click Close to return to the main menu.
Adding New Users
Supervisors can add new supervisor or technician level users. Technicians cannot add new users.
Fields marked with an (*) are required.
1. From the Main Menu, select Profile > List User.
2. Click Add User to add a new user.
3. Enter new user information.
4. Select the Active check box under the Role field to activate the user account.
Note:
If this is a lab tech profile and you want to allow reference file update and/or data
management privileges for this user, select the appropriate check boxes.
5. Click Save to save the new user information and return to the main menu, or click Close to
discard changes and return to the main menu without saving.
Editing User Profiles
Supervisors can edit the user profile of any user. Technicians can only edit their own profiles. Fields
marked with an asterisk (*) are required.
1. To edit your own profile, select Profile > My Profile.
2. To select from a list of users to edit, select Profile > List User and double-click to the left of a
user to select that profile.
3. Edit user information.
4. Click Save to save user information and return to the Main Menu.
or
5. Click Close to discard changes and return to the Main Menu without saving.
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Changing Passwords
Supervisors can change passwords for any user, but they must have the user’s old password.
Technicians can change only their own passwords.
1. From the Main Menu, select Profile > My Profile.
2. In the user profile, click the Change Password button.
3. Enter the current and new passwords.
4. Click the Save Password button to change the password. Or, click Close to close and return
to the main menu without changing the password.
Resetting Passwords
If a user loses or forgets their password, HLA Fusion can reset the password. The new password is the
same as the user’s user name. Only Supervisors can reset a user’s password.
1. From the Main Menu, select Profile> List User and select a user.
2. In the user profile, click the Reset Password button.
3. Click Close to return to the main menu.
Changing User Privileges
Only Supervisors can modify a user’s privilege level.
1. From the main menu, select Profile> List User
2. Double-click to the left of a user to open their profile.
3. In the user profile, select the check box next to either Manage Data or Update Reference
Files, or both, to give the selected user privileges for those activities within the Fusion
application.
4. Place a check mark next to Can Email Report if you want to give a user that privilege. (You
will need to supply an email address.)
5. Click Close to return to the Main Menu.
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Inactivating Users
Supervisors can inactivate users who are no longer using HLA Fusion. User information is still stored
in the database, but the user is not able to log into the program.
1. From the Main Menu, select Profiles > List User and select a user to edit.
2. Clear the Active check box to deactivate the user.
3. Click Save to save user information and return to the main menu, or click Close to discard
changes and return to the Main Menu without saving.
Note:
If a User ID is still associated with analysis records, the User ID cannot be deleted.
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Lab Profile
The Lab Profile menu displays the contact information for your lab, network information used by HLA
Fusion, and NMDP contract lab codes. Most of this information is entered during installation, but can
be updated at any time. Only supervisors can change the Lab Profile.
From the Lab Profile menu you can:

Edit the Lab Profile

Add, edit and remove Lab Codes

Change the Network Path

Change the Email Server Name
Lab Profile Information Screen
Editing the Lab Profile
Laboratory information displays on most reports, and includes contact information for your lab. This
information is initially entered during installation, and can be edited any time from the Lab Profile
menu. Fields marked with an asterisk () are required.
1. From the main menu, select Profile > Lab Profile.
2. Edit lab profile information.
3. Click Save to save changes and return to the main menu, or click Cancel to return to the main
menu without saving any changes.
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Managing Lab Codes
Lab codes are used on NMDP reports to identify contract labs. Multiple lab codes may be entered and
stored in HLA Fusion. You can select the lab code you wish to use when creating an NMDP report.
Only the first three digits of a lab Code are used on NMDP reports; lab code descriptions are not
included on reports.
1. From the main menu, select Profile > Lab Profile.
To add, edit or delete Lab codes:

Click Add Lab Code to add a new lab code. Enter information into the new row.

Highlight a lab code to be edited. Click Edit Lab Code to edit the lab code.
2. Edit lab code information.
3. Highlight a lab code to be deleted.
4. Click Delete Lab Code to delete the lab code.
5. Click Save to save changes and return to the main menu, or click Cancel to discard changes
and return to the main menu without saving.
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Utilities
HLA Fusion™ uses a variety of reference files for data analysis that need to be updated for new
products, lots and revisions. You can also change many global product settings to customize analysis
for your lab, and you can modify default system settings to reflect your personal or network file
system.
Warning:
Always use the latest reference files for analysis. Otherwise, analysis results may not be accurate.
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Managing Catalog Reference Files
Catalog reference files contain all of the reaction-specific information needed for analysis, including
the following:

Bead and well specificities

QC information

Cut-off values

Bead and primer information
Each new lot or revision of a product needs its own catalog file for analysis results to be accurate.
Updating Catalog Files from a Local or Network Drive
Lab supervisors can input new catalog files for use in analysis when new products, lots, or updates
become available. Catalog files are also available on the One Lambda download site.
1. From the main or any of the product home pages, click the [Download] link, or from the
main menu, select Utilities > Update Reference > Update Reference File.
The Update Reference File dialog box displays.
File
directory
tr e e
Catalogs
Catalog
Options
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If your serology information is outdated, or you have not imported it yet, a message like the one
shown below is displayed. If you do not see this type of message, go to the next step. If you see the
message, click the OK button to open the Serology Import dialog box.
Serology equivalent file notice
2. Make sure the Catalog option button is selected.
3. Click the Auto Update
button, (only enabled if you’re connected to the Internet).
The Reference File Manager screen opens.
The number
of catalogs
currently in
your Fusion
database.
Updated &
revised
catalogs
available for
download.
Lists all
available catalogs
Available catalogs which are
not in your Fusion database.
In the Show these products section, (bottom left) use
the radio buttons to easily determine which catalog
reference files have been updated and decide which ones
you’d like to import into your HLA Fusion database.
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The Latest Lot or Revision
drop-down is only enabled if you select the
Updates/Revisions radio button in this section.

Fusion updates the number of available recent catalog reference files for products when you
select either by Latest Lot, Latest Revision, or the default listing of Latest Lot or
Revision, (which includes both).

Clicking the Select All
product reference files.

Clicking the Deselect All

Click the Get Docs
button to download all associated documents including
worksheets, probe/primer sheets and data sheets.
button places a check mark in the Select Column for all
button clears all reference file selections.
4. Using the file directory tree on the left, choose the catalog files to be imported, or click Select
All to indicate all files that are listed.
Note:
To determine which catalog is the most recent one available, HLA Fusion looks first at
the lot number and then the revision number. A updated lot number gets flagged as the
most recent version of a catalog, even if there is also an update to the revision number
of the previous lot since you last downloaded catalogs.
5. Click the Import
Note:
button.
If you select Yes or Yes All, the software will translate the old allele format into the
latest format. For the Molecular products (LABType or Micro SSP), the software will
drop the old format allele completely if it does not find a matching allele in the new
format list. For Antibody products, if the software does not find a matching allele in the
new format, it keeps the old format allele, but adds a colon.
If you select a catalog to import that is in the old allele format, you are notified with a
message. Select the translation option you want to use before going to the next step.
Translate alleles Option
6. Click Yes, or Yes All to translate the selected catalog files.
Note:
Catalog importation takes a bit longer when alleles are also translated.
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The results of your reference catalog update are
noted by Fusion at the bottom, left of the
Reference File Manager window.
6. Click the Close
Note:
button to return to the previous Update Reference window.
Imported catalog files can be used without restarting Fusion.
Updating Catalog Files from the One Lambda Download Site
Product catalog files are available on the One Lambda download site
(http://download.onelambda.com).
1. From the main or any of the product home pages, click the Download link, or from the main
menu, select Utilities > Update Reference > Update Reference File. The Update
Reference File dialog box displays.
to open the One Lambda Catalog Updates Selection
2. Click Auto Update
window.
3. Select the check box next to the files you want to import. Click the plus or minus signs on the
file directory tree, to locate the catalog files for each product. You can also click Select All or
Deselect All to select or clear all the check boxes at once.
4. Click the Import
button to import the selected catalog files.
Reference File import progress
5. When the confirmation dialog box displays the importation results, click OK.
6. Click the Close
button.
Imported catalog files can be used without restarting Fusion.
Note:
You can also click Go to OLI, click the links for the products and catalog files you want to
import, and follow the download instructions.
If Auto Update does not respond, verify your network connectivity and that the URL you
set for One Lambda in Utilities > URLs & Paths is correct.
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Updating Molecular Typing Reference Files
Reference files contain allele code and serology equivalent information used in analysis. It is
important to update them regularly for accurate allele code and serology assignments.
From the Update Reference menu you can download the necessary files:

NMDP codes

Local codes

Serology Equivalent files
Updating NMDP Codes from a Local or Network drive
The National Marrow Donor Program (NMDP) provides a list of allele codes that can be used in
molecular typing analysis. If you have a current list stored on your local or network drive, use this
procedure to import it so HLA Fusion can access it. The most current NMDP code file is available on
the NMDP download site.
1. From the main or any of the product home pages, click the Download link, or from the main
menu, select Utilities > Update Reference > Update Reference File.
The Update Reference File dialog box displays.
Folder/
Directory tree
2. Select the NMDP option.
NMDP Code
option
Information
on last
download
and update
Updating NMDP Code
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3. Navigate to the NMDP file on a local or network drive, using the Import Directory tree.
4. Click the Import NMDP
5. Click the Close
button to import the selected file.
button to return to the Update Reference menu.
Updating NMDP Files from the NMDP Website
Follow this procedure to import the NMDP list from the NMDP website:
1. Click the [Download] link, or from the main menu, select Utilities > Update Reference >
Update Reference File.
2. The Update Reference File dialog box displays.
3. Select the NMDP option.
4. Click Auto Update, which automatically imports the current NMDP file for use with HLA
Fusion.
Or, click Go to NMDP and follow the instructions for downloading an NMDP file from the
website.
Note:
If Auto Update does not respond, verify your network connectivity and that the URL you
set for NMDP in Utilities > URLs & Paths is correct.
Creating a Local Code File
Local code files are created by individual labs; local codes are created to make ambiguous typing
assignments easier to store and read. For example, ambiguities, such as B*1501/1501N/1502, can be
condensed with a code to B*15AB for simpler record keeping.
1. Copy the local code template from the HLA Fusion CD to a local drive.
2. Use a text editor to edit the template and add code definitions.
3. Follow the example format, using a Tab to separate each field and a slash ( / )to separate
multiple values within a field: letter code <tab> numeric allele extension to which the code
applies
4. Save the file as local_code.txt
See the next section, Updating the Local Code File, to import the file.
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Updating the Local Code File
After a Local Code file has been created, it must to be updated in HLA Fusion.
1. From the main or any of the product home pages, click the Download link, or from the main
menu, select Utilities > Update Reference > Update Reference File.
The Update Reference File dialog box displays.
Update Reference File: Local Code
Directory/
Folder tree
Local Code
Option
2. Select the Local Code option as shown above.
3. Use the import Directory Tree to locate and select the Local code file to be imported.
4. Click Import Local Code
to import the selected file(s).
5. Click Close to return to the Update Reference menu.
Updating P Group and G Group Files from the One Lambda Website
The P Group and G Group files, (as published by IMGT) can be downloaded from the One Lambda
download site:
download.onelambda.com/pub/tray_info/Windows/HLA_Fusion_Catalogs/P_and_G_Group/
1. From the main or any of the product home pages, click the [Download] link, or from the main
menu, select Utilities > Update Reference > Update Reference File.
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The Update Reference File dialog box displays.
Update Reference File: P/G Grouping
Directory/
Folder tree
P Group &
G Group
options
2. Click the Import P Group
buttons.
button, or the Import G Group
Updating Serology Equivalent File from One Lambda Website
The Serology Equivalent file can be auto updated from the One Lambda download site
(http://download.onelambda.com).
3. From the main or any of the product home pages, click the Download link, or from the main
menu, select Utilities > Update Reference > Update Reference File.
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The Update Reference File dialog box displays.
Update Reference file: Serology Equivalent
Directory/
Folder Tree
Serology
Equivalent
option
4. Select the Serology Equivalent option.
5. Click Auto Update
window.
to open the One Lambda Catalog Updates Selection
6. Select the check box next to all files you want to import.
7. Click Import Serology
without restarting HLA Fusion.
to import the selected files. Catalog files are ready for use
8. After the confirmation dialog box displays import results, click Ok.
9. Click the Close
Note:
button.
If Auto Update does not respond, verify your network connectivity and that the URL you
set for Serological in Utilities > URLs & Paths is correct.
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Catalog Management and Information
Archive Catalogs
You can archive catalog files that are no longer used. The catalog information still exists in the
database, but is not included in the list of available catalog files for analysis. Catalog files can also be
restored for use in analysis.
1. From the Main Menu, select Utilities > Update Reference > Catalog
Information/Management.
Archive Catalog
2. Select the S (select) check box for the catalog files you want to archive, and click the Archive
button.
3. When a pop-up message displays Data Saved, click OK.
4. Click Close to return to the main menu.
Note:
When you import a new version of a catalog file, the system auto-archives the previous
version.
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Un-Archive Files
Archived catalog files display an A in the Status column when you view the catalog list and the check
box for Show Archived Catalogs is selected.
Archived Catalogs check box
Archive and unarchive catalog files
Place a check mark here and
click the Unarchive button
to unarchive the catalog.
Place a check mark here and
click the Archive button
to archive the catalog.

The letter “A”
indicates that
the catalog
has been
archived.
In the Archive Catalog window, select the check boxes next to the catalogs you want to
un-archive, and click Unarchive.
Viewing Catalog File Information
You can view information about a catalog file and generate a report from the Catalog Information
menu. Catalog files displayed with an A in their Status column have been archived.
1. From the Main Menu, select Utilities > Update Reference > Catalog Management.
2. Click a column header if you want to sort the catalog file list.
3. Click Report to display a printable, exportable report of the currently displayed catalog
information.
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Deleting Catalog File Information
You can delete a catalog file from the Catalog Management menu. Catalog files displayed with an
A in their Status column have been archived.
1. From the Main Menu, select Utilities > Update Reference > Catalog
Information/Management.
2. Select the check box next to any catalog you want to delete.
3. Click Delete to remove the catalog information.
Reporting Catalog File Information
You can view and report information about a catalog file and generate a report from the Catalog
Information menu.
1. From the Main Menu, select Utilities > Update Reference > Catalog Management.
2. Click a column header if you want to sort the catalog file list.
 (Optional) If you want a report in the old format, select the check box next to Old Format
report.
3. Click Report to display a printable, exportable report of the currently displayed catalog
information.
Associating Product Catalog Files and Luminex Templates
You can associate a catalog file with the Luminex template name used for a specific product. HLA
Fusion automatically associates catalog ID and template names the first time you run the analysis for
the product. After an association has been made, HLA Fusion automatically selects the catalog file
associated with the template used in the CSV file when you start analysis. You can also manually add,
remove, or change associations.
1. To add or remove an association, select Utilities > Catalog Template Association.
2. Add a New Association.
3. Select a catalog file.
4. Type in a new template name, or click Browse to select a Luminex template file (.lxt format)
to associate with the filename.
5. Remove an Association.
6. Select a catalog file.
7. Select a template name and click Remove.
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To modify an Association:
1. Select a catalog file.
2. Edit existing template name(s).
3. Click Save to save changes.
4. Click Close to return to the Main Menu
Importing Allele Frequency Files (Demographic Frequency)
You can import allele frequency files to use in analysis based on demographics.
1. From the Main Menu, select Utilities > Update Reference > Demographic/Allele
Frequency.
Allele frequency import
2. Select the Create Demographic Group option.
3. Click the Browse
button and locate Allele Frequency files.
4. Click Import.
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When an Allele Frequency file is successfully imported, the groups it contains are listed in
Demographic Group and Frequency in Database.
5. Click Save.
Note:
If the header for the column of any allele frequency file you import is empty, the entire
column is not imported into Fusion, regardless of any other data it contains. If columns
are duplicated, Fusion gives you an error message and does not import the allele
frequency file.
The data contained in the Allele Frequency file may look similar to this graphic.
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Updating Allele Frequency Files (Demographic Frequency)
You can modify allele frequency files before using them in analysis based on demographics.
1. From the Main Menu, select Utilities > Update Reference > Demographic/Allele
Frequency.
Allele frequency import
2. Select the Update Alleles and Frequency option.
3. Click the Browse
button and locate the Allele Frequency file you want to update.
4. Double-click on the file, or click Open in the browser window.
5. Do any or all of the following to modify the file:

Add/delete alleles

Delete existing demographics

Change the allele frequencies

Convert allele format
6. Click Translate Alleles
7. Click Update.
8. Click Close.
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Managing CREG List Information
You can modify existing CREG lists or create new ones for use in PRA and Single Antigen LABScreen,
FlowPRA, LAT, or LCT analysis. Take the following steps to create or modify a CREG list:
1. Select Utilities > Update Reference > CREG Information Management.
The CREG Management window displays.
CREG Management screen
2. Select an existing CREG group from the CREG Type drop-down list, or Enter a name for a
new group in the New CREG Type field.
Do one of the following:

Enter new or modify existing information in the Group Name and/or Group Detail
fields and click Save.

Highlight a row of existing group information, and click Delete Group.
3. When you have completed CREG group creation or modification, click Close.
Note:
Please verify your data before saving, and please do not mix alleles with the older
nomenclature format with alleles in the newer format within the same CREG table.
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Changing Product Configuration Settings
Changes to product analysis settings apply only to samples not previously analyzed. Previously
analyzed samples must be re-analyzed for the changes to be applied.
From the Product Configuration menu you can

Change Micro SSP product configuration

Change Ab1 filename configuration for SBT analysis

Change product settings for LABScreen Mixed analysis

Change antibody screening analysis settings

Change default negative serum values for LABScreen analysis
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Changing Molecular Product Configuration
Changes to LABType and Micro SSP analysis settings apply only to samples that have not yet been
saved or confirmed. To change analysis settings for previously saved or confirmed samples, you must
change the settings from the product analysis window and re-analyze the sample.
1. From the LABType or Micro SSP home page click Edit, or select Utilities > Molecular
Product Configuration > Molecular Analysis Configuration from the HLA Fusion
main menu.
2. Select either LABType or Micro SSP from the Product Type drop-down menu.
LABType and Micro SSP Configuration settings
3. Change configuration values as needed.

Save Force 1 Pairs stores force 1 pairs in the database during analysis. The Force 1 pairs
are also displayed in reports that contain this information.

Allow Auto-Accept All can only be selected by someone with Supervisor user privileges,
and allows you to select a button on LABType session summary to accept the batch analysis
results for all samples.

Computer-Assigned Serology can only be selected by someone with Supervisor user
privileges, and automatically populates LABType and Micro SSP analysis serology
assignment fields, as well as stores results in the database. If this is selected, a warning
message displays as a reminder that the assignments are estimates, and should not be
accepted without verification.
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Serology auto-assignment warning
4. Click the OK
button to acknowledge the cautionary message.
5. Click Save
to save your changes.
6. Click Close
to return to the Update Reference menu.
P and G Code Configuration for LABType
P and G code definition downloads are similar to NMDP. They can be imported from files or by using
Auto Update.
You can use the LABType Analysis Configuration screen to
choose which code you want to use for all your LABType sessions
to be imported.
If you’ve selected P or G code on the LABType
Analysis Configuration screen, you can re-apply the
code set, (or an updated code set) to a particular
session on the Session Summary screen by clicking the
Apply P/G Code button located at the bottom, right
of the screen.
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You can also apply P or G grouping by clicking the Set
Config button during LABType analysis and selecting either
P or G grouping from the drop-down list.
Changing Antibody Product Configuration
To globally change the antibody
configuration for any product:
1. Select Utilities > Antibody
Product Configuration > Set
Analysis Configuration.
2. Select a Product type from the
Product Type drop-down.
Note that antibody configuration settings are
different for each product.
3. Click the Save
button to store
your configuration settings.
You may also click the Reset to OLI
button to restore the antibody
configuration to the One Lambda default
settings.
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Creating a Combined LABScreen Session Catalog
To run a Class I and Class II combined LABScreen analysis session, create a combined catalog to use
for your session. You must use a Class I catalog file and a Class II catalog file that have the same
positive and negative control beads, but do not have any other beads in common.
1. Select Utilities > Antibody Product Configuration from the HLA Fusion main menu.
2. Click Create Combined Products to open the Combined Products menu.
Combine LABScreen catalog files
3. Select the first product catalog to be combined and click
4. Select the second product catalog to combine and click
.
.
The new catalog file name appears at the bottom of the selection menu.
5. Click Save

to save the new combined catalog file for use in LABScreen analysis.
Optional: Click Clear to reset the selections and start over.
6. Click the Close
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Changing LABScreen Default Negative Serum Control Value
Negative control sera can be adjusted or added for each product or lot. You can change the trimmed
mean fluorescence value for each bead individually.
1. Select Utilities > Antibody Product Configuration from the HLA Fusion main menu.
2. Click Set Default Negative Value to open the Default Negative Serum Value screen.
Setting default negative serum value
3. Select a catalog file, (Catalog ID).
4. Select an existing Negative Serum value from the
Select NS drop-down,
or
Select Add New NS Name from the pull-down
menu to create a new negative serum.
5. Type a name for the new negative serum into the
Current NS field.
6. Edit Default NS values for the desired beads in the
right column.
7. Click the Save
8. Click the Close
button to store the changes.
button.
Changing the LABScreen Mixed Product Configuration
You can change LABScreen Mixed analysis positive and negative threshold settings for each product or
lot. The new cut-off threshold values are used in every analysis session for that product or lot.
1. From the LABScreen home page click Edit, or select Utilities > Antibody Product
Configuration from the HLA Fusion main menu.
2. Click Set Mixed Product Configuration to open the LABScreen Mixed Configuration
menu.
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LABScreen Mixed Product configuration
3. Select a product catalog from the Catalog ID drop-down
list.
4. Edit threshold values. For LABScreen Mixed catalogs, the
threshold values can be set at the bead level.
5. Click Save
6. Click
to save the new values.
Close.
NS File Import
Importing NS Files
Negative Serum (NS) files can be imported to be
referenced during analysis.
1. From the Main Menu, select Utilities >
Antibody Product Configuration >
NS File Import.
2. Click the Browse
select NS files.
button to locate and
3. Click Import NS File.
When an NS file is successfully imported, it
is listed in Existing NS Files.
4. Click the Close
button to return to
the Update Reference menu.
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Choosing General Settings
You can set a number of general system settings, including printer defaults and URLs and Paths.
1. Select Utilities > General Settings from the HLA Fusion main menu.
The General Settings dialog box is displayed.
Fusion General Settings
2. Use the drop-down menus, or select check boxes to make your selections on this dialog box.
3. When you have made all of your selections, click Save.
Printer Defaults
From the Printer Setup tab on the General Settings dialog box, you can select settings such as default
printer and paper size, which will be in place when you print reports or do a print screen.
1. Select Utilities > General Settings, and click the Printer Setup tab.
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Printer Setup
2. Select from the following options for both the Print Screen and Print Report panels of the
dialog box:
Note:

If you want to see a print preview or print report dialog each time you print, make sure the
Yes option is selected. Otherwise, select No.

If you do not want to select a printer each time you print, select the default printer and
paper size from the drop-down menus.
This default printer configuration may be overwritten by the specific page properties of
certain reports.
3. Click Save.
Setting HLA Fusion Default URLs and Directory Paths
The URLs & Paths option under the General Settings menu allows you to set the default URLs for
OLI and NMDP websites to download reference and catalog files, and product updates. This option
also allows you to set the directory path where HLA Fusion, by default, stores catalogs, session/batch
files, reports, etc. Modifying URLs or paths ahead of time allows you to avoid having to browse for
files each time you need them.
1. Click [Edit] on the right side of the General Configuration panel of the HLA Fusion default
home page, or select Utilities > General Settings from the HLA Fusion main menu.
2. Select the URLs tab, or the Paths tab.
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Paths Tab
URL’s Tab
3. Enter a URL and verify that it’s correct by clicking the Browse
button.
button to locate the directory you want to use for the specified
4. For paths, use the Browse
purpose, (i.e., where you want to store reports when they are generated).
5. Click the Save
Button to store your preferences.
Activating Products
The Products Selection option on the Utilities menu allows you to activate or de-activate the various
OLI analysis products that may be used with HLA Fusion.
1. From the Main Menu, select Utilities > Products Selection.
Select/Activate products
2. Select or clear the check box next to the product(s) you wish to activate or de-activate.
3. Click the OK
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Software Validation
The HLA Fusion software has functionality to help with the validation process required by Labs,
Clinics, and hospitals seeking to comply with GCP, GLP and GMP. Validation of the HLA Fusion
software for your lab environment for regulatory or performance reasons, can be automated by using
the IQ (Installation Qualification) option from the Utilities > Validation menu. Your lab may
choose to run these as a standard regulatory validation process, to help troubleshoot issues, or to
provide information to prepare for a software upgrade.
IQ (Installation Qualification)
The IQ process assists you with installation qualification of HLA Fusion software by providing a builtin function. Once the Installation qualification completes, a results report is generated, which you can
save, print or export to Excel.
If your IQ results concern you, export them to an Excel file and e-mail the file to OLI
customer support.
Note:
1. From the Main Menu, select Utilities > Validation > IQ.
The validation test runs. When it is complete, a report is displayed, with the following categories of
data:

Systems Information (e.g., operating system)

Environment (e.g., directory path where the HLA Fusion program files are stored)

URLs (e.g., the URL for the catalog download site)

Database Information (e.g., name of the database)

Number and types of files installed (e.g., dll)

Lab Information (e.g., name and address of your lab)

Analysis Configuration for each product (e.g., low bead count for LABType)
2. Choose to save the report, preview it, print it, or export it to Excel.
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Typical IQ Report
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