HLA Fusion Research User Manual v2_0

HLA Fusion Research User Manual v2_0
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User Manual
HLA Fusion™ Research
v. R2.x.x
2010/10
For Research Use Only. Not For Use In Diagnostic Procedures.
21001 Kittridge Street, Canoga Park, CA 91303-2801
Advancing Transplant Diagnostics
Tel: (818) 702-0042 Fax: (818) 702-6904
www.onelambda.com
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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 2010 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
Chapter 1
Chapter 2
Version 2.0
Introduction
What is HLA Fusion™ Research? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
README Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Program Updates
.................................................1
Limitations of the Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Technical Support
................................................2
Scope of This Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Navigation
Logging On To Fusion Research
.....................................5
Retrieving a Forgotten User Name or Password . . . . . . . . . . . . . . . . . . . . . . . . 6
Key System Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Screen Resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
File Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Character Length . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Fusion Research Home Pages
......................................9
Accessing HLA Fusion™ Research Software Functions
. . . . . . . . . . . . . . . . . . 13
Main Menu Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Exit
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Toolbar Buttons
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Find
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Print Report
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Preview Report
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Print Screen
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Magnify
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
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Chapter 3
Chapter 4
Chapter 5
Show Navigator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Patient
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Related Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Side By Side Analysis
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Product Data Analysis
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Sample Navigation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
ConsenSys™ Analysis
Starting a ConsenSys Analysis Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Starting a ConsenSys Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Adding an Ab1 File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Using the ConsenSys Analysis window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Keyboard Shortcuts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Sample Comments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Flagging a Sample for Further Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Accept Base Calls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Edit Base Calls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Saving and Confirming ConsenSys Analysis Results . . . . . . . . . . . . . . . . . . . . . . . . 30
Save Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Confirm Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
SSO Analysis
Starting SSO Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Opening a SSO Analysis Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Displaying a SSO Analysis Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Configuring SSO Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Minimum Positive Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Minimum Bead Count . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Set Sure Reaction Bead. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
SSO Analysis window Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Using the SSO Data Analysis window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Analyze SSO Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Make Typing Assignments in SSO Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Typing Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Flagging a Sample for Further Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Manual Assignments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
SSO Batch Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Save Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Confirm Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Print Screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Micro SSP Analysis
Starting Micro SSP Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Displaying a Micro SSP Analysis Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Configuring Micro SSP Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Change Current Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
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Chapter 6
Chapter 7
Version 2.0
Assign Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Bw4/Bw6 in Serology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Demographic Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Entering Micro SSP Reactions Input Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Entering Micro SSP Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Using the Micro SSP Analysis window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Micro SSP Analysis window Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
View Well Details. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Add New Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Using the Reaction Pattern Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Number of Allowable False Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Force One False Reaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Micro SSP Combined Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Making Typing Assignments in Micro SSP Analysis . . . . . . . . . . . . . . . . . . . . . . . . 61
Allele Code Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Manual Allele Code Assignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Serology Assignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Other Assignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Unknown Allele Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Remove Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Sample Comments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Flagging a Sample for Further Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Save Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Confirm Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Session Summary and Logs
What is Session Summary?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Example Session Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Creating and Managing Session Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Creating a Session Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Managing Session Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Printing Session Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Reports
Using the Reports Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Accessing the Reports Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Select Report Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Refine Report Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Session/Sample Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
View, Print or Export Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Export Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Accessing Reports from the My Favorite Menu. . . . . . . . . . . . . . . . . . . . . . . . . . 78
Reports Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Customizing Report Appearance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
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Chapter 8
Chapter 9
Creating Custom Data Export Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Creating Custom Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Sample Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Molecular Typing Sample Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Antibody Screening Sample Summary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
View Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Patient Info . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Report Types. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Sample Management
Sample Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Importing Sample Lists. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Information Formats for Sample Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
New packing list format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Pack list: Old Standard ‘X’ samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Old packing list format, '11' for AB/DR samples . . . . . . . . . . . . . . . . . . . . . . . . . 92
Comma delimited format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Tab delimited format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
SDF format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Local/Sample/Patient ID Only . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Viewing and Editing Sample Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Test Lists. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Creating New Test Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Viewing and Editing Existing Test Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Deleting Existing Test Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Exporting Test Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Luminex Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Creating Luminex Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Create Sample Worklists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Create Plate Design. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Patient Information
Importing Patient/Donor Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Managing Patient/Donor Records. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Adding New Patient/Donor Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Lookup Patient/Donor Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Editing Patient/Donor Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Associating a Patient/Donor ID with Sample IDs . . . . . . . . . . . . . . . . . . . . . . . 104
Associating Patient and Donor Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Printing Patient/Donor Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Exporting Patient/Donor Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Archiving Patient/Donor Records. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Deleting Patient/Donor Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Creating Patient/Donor Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Patient Antibody Tracking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
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Chapter 10
Chapter 11
Chapter 12
Version 2.0
Profile Management
User Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Viewing the User List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Adding New Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Editing User Profiles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Changing Passwords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Resetting Passwords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Changing User Privileges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Inactivating Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Lab Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Editing the Lab Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Managing Lab Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Utilities
Managing Catalog Reference Files
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Updating Catalog Files from a Local or Network Drive
. . . . . . . . . . . . . . . 117
Updating Catalog Files from the One Lambda Download Site . . . . . . . . . . . 119
Updating Molecular Typing Reference Files
. . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Updating NMDP Codes from a Local or Network Drive
. . . . . . . . . . . . . . 120
Updating NMDP Files from the NMDP Web Site . . . . . . . . . . . . . . . . . . . . . . . 120
Creating a Local Code File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Updating the Local Code File
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Updating Serology Equivalent Code File from the One Lambda Web Site . . . . 122
Archiving Catalog Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Viewing Catalog File Information
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Associating Product Catalog Files and Luminex Templates
. . . . . . . . . . . . 124
Importing Allele Frequency Files (Demographic Frequency)
. . . . . . . . . . . 125
Updating Allele Frequency Files (Demographic Frequency)
. . . . . . . . . . . . 127
Changing Product Configuration Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Changing Molecular Product Configuration
. . . . . . . . . . . . . . . . . . . . . . . . . 129
Changing Ab1 Filename Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
General System Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
General Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Choosing Default Printer Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Setting HLA Fusion Research Default URLs and Directory Paths . . . . . . . . . . . 132
Activating Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Software Validation
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Special Characters to Avoid in Filenames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
LABXpress
Managing Sample Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Managing Test Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Creating New Test Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Viewing and Editing Existing Test Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Deleting Existing Test Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
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Index
Exporting Test Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Creating Luminex Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Creating Sample Worklists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
Creating a Plate Design. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Creating a Run Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Determining the Run Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Starting and Monitoring a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
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Chapter 1
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 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 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.
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Program Updates
Note:
For best results, always make sure you are using the latest version of HLA Fusion™ <Emphasis>Research
software.
You may obtain updates of HLA Fusion™ <Emphasis>Research by request. Please contact your One Lambda, Inc.
representative for a copy of the software or see the Technical Support section below for more contact information.
Product information updates (catalog files, etc.) for HLA Fusion™ <Emphasis>Research are available through your
One Lambda Inc. representative, or from the One Lambda website:
http://download.onelambda.com
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™ <Emphasis>Research is
limited by Microsoft SQL Server Desktop Engine or SQL Server 2000. (The user must manually archive data.)
HLA Fusion™ <Emphasis>Research assumes that data for each required input is in standard format that has not been
modified.
The HLA Fusion™ <Emphasis>Research analyzes a data file in the following format.
•
The data file is one of the following:
•
.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 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.
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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.
Scope of This Manual
This manual provides information on how to import raw data and then to 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™ <Emphasis>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
•
Exit button
This manual helps you start using One Lambda’s HLA Fusion™ <Emphasis>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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Chapter 2
Navigation
This chapter 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
1. Double-click the HLA Fusion Research icon on your computer desktop.
from Start > Programs > One Lambda > HLA Fusion Research.
You can also open the program
The Security Login dialog box is displayed.
Figure 2-1: HLA Fusion Research Login Screen
2. Enter your HLA Fusion Research User Name and Password.
3. Click Log In to open the program.
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Note:
The SQL 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 user name, click the Forgot User Name 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.
•
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 (see Editing User Profiles, p. 301).
The password is displayed when the questions are answered correctly.
Figure 2-2: Forgot Password Dialog Box
Key System Settings
Screen Resolution
HLA Fusion Research software requires a screen resolution of 1280 x 960. The software displays a message
if your current resolution is less than the expected settings.
Figure 2-3: Screen Resolution Message
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.
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In addition, If your computer is running the Microsoft® Windows 7® operating system, the text display
setting must be set to Smaller - 100% (default). Take these steps if you need to adjust the screen text
display size:
1. Right-click on the computer desktop.
2. Select the Display option. The Screen Resolution window displays.
Figure 2-4: Windows 7 Screen Resolution Window
Select this to change
text size
3. Select the Make text and other items larger or smaller (see Figure 2-5).
Figure 2-5: Text Size Options
Select this setting
File Permissions
All HLA Fusion Research users must have read and write permissions to the following directories and files:
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•
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
Figure 2-6: Fusion Research Default Home Page
Reference File Update
opens from any Home
page when Updates
available link is clicked;
greyed-out files means
the file is not located in
the default file location
Opens Catalog
Management
window
Opens
Reference File
Update window
Opens Analysis
Product
Selection
window
Opens User
List window
Home Page
pane—click
a button to
display the
associated
home page
Slides open
session/sample
Navigator
Opens
Printer Setup
window
Opens
Navigator
search
criteria
window
Red if audit
logging is OFF;
green if audit log
is ON.
Opens Fusion
Research Setup
window with
general (audit trail
or auto-download
enable and Patient
type default),
printer, URL and
path setup options
This user interface option allows you access to the product home pages, data import and analysis windows.
It also allows you to view or access system or product data, reference file downloads and configuration
settings.
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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. To display the home page for one
of the products listed in the bottom left area of the page, click the appropriate button, as in this example for
SSO:
•
From the main home page, click the ConsenSys home page button
•
Click the ConsenSys button
•
Select Analyze Data > LABScreen.
Note:
.
from the HLA Fusion Research toolbar.
Migrated and upgraded databases also use this same interface (Figure 2-6, Fusion Research
Default Home Page, p. 9).
Launching Navigator
1. 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, see step 2.
2. Move your cursor over the Navigator tab on the right border of the application window to slide the
Navigator into view.
Figure 2-7: Navigator Interface
3. To close the Navigator, click the close button
.
Navigator Tree
Using the Navigator tree, you can easily move between analysis sessions and samples.
1. 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.
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Figure 2-8: List of Products
Navigator tab
Examples of HLA Fusion
Research Products
2. Click a sample name to display it an the analysis window.
Figure 2-9: List of Sessions in the Navigator
Results Grouping
The sessions and samples displayed though the Navigator tool can be sorted by various criteria:
•
Product type
•
Session Date
•
Catalog (Session Name)
The default is to group by Product. See the next few sections for details about these two 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. If you are already in the analysis mode for a certain product, just the sessions that fit
the Find criteria for that product display. Click the + sign next to the product type you are interested in to
display its sessions.
Figure 2-10: Navigator Sorted by Product Type
Unreviewed sessions
Reviewed sessions
Components of the session name as displayed
in the Navigator are defined in Find, p. 17
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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.
•
Click a session name to display the samples within this session and a session summary. For LABType
and LABScreen, the system also performs a batch analysis and displays the results in the session
summary.
•
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.
Group by Session Date
When you select the Date option, sessions are displayed in order of their creation dates.
Figure 2-11: Navigator Sorted by Session Date
•
Otherwise, the use of this tool is the same as described above in Group by Product.
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Group by Catalog
When you select the Catalog option, sessions are displayed in alphanumeric order by catalog name.
Figure 2-12: Navigator Sorted by Catalog
•
Otherwise, the use of this tool is the same as described above in Group by Product.
Accessing HLA Fusion™ Research Software Functions
Main Menu Options
Figure 2-13: HLA Fusion Research Main Menu Options
Main menu options
You can access HLA Fusion Research functionality at any time from the main menu, 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 either a molecular or antibody product for which you can import CSV
files, or manually enter reactions, and analyze data. For details, see the individual product analysis chapters
in this user manual.
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Figure 2-14: Analyze Data Menu Options
Reports
When you select this menu item, the Reports page is displayed, allowing you to create reports of your
analysis data. See Chapter 10, Reports, p. 250 for information on how to use the Reports window.
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 (see Chapter 12, Sample Management, p. 275
for details) and for creating sample work lists and plate designs.
Figure 2-15: Sample Menu Options
Patient Info
Options under this menu item pertain to importing patient/donor lists, managing individual patient/donor
information, and tracking patient antibody data. See Chapter 13, Patient Information, p. 286 for details.
Figure 2-16: Patient Info Menu Options
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
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options, depending on your system navigation preference. See Chapter 14, Profile Management, p. 299 for
details.
Figure 2-17: Profile Menu Options
Utilities
The options under this menu item pertain to importing catalog, code and serology files, configuring the
molecular and antibody products you analyze, setting up your HLA Fusion Research system, and system
validation. See Chapter 15, Utilities, p. 305 for details.
Figure 2-18: Utilities Menu Options
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.
•
Notification of updates and a description of new features in the latest 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.
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 autodownload feature from the Fusion Research default home page (see Fusion Research Home
Pages, p. 9).
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Figure 2-19: Help Menu Options
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 to select No to keep the current session open.
Toolbar Buttons
HLA Fusion Research provides a toolbar, displayed just below the main menu options, with access to
commonly used functions.
Figure 2-20: HLA Fusion Research Toolbar
Main Menu
Toolbar
The following table names each toolbar button. The sections below describes the function of each button.
Button
Name
Home
Find
Print Report
Preview Report
Print Screen
Magnify
Show Navigator
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Button
Name
Patient
Related Records
Side-by-Side Analysis
Product Data Analysis
Sample Navigation Tools (only visible during
sample analysis). The <<Summary link
returns to the associated sample summary
table.
Find
Click the Find
button to display a dialog box that allows you to search for records using various criteria.
You can choose to search by Patient ID, Sample ID, Session ID, or Other. Other allows you to provide
multiple search criteria: 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.
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Figure 2-21: Find Records and Navigator Settings
Navigator session
sort options
Date Range
Navigator session
name display
options—selected
fields display in
the Navigator in
the same order
they appear in
the listing to the
left
Print Report
From any analysis window, you can click the Print Report
button to display a list of the reports that
you can print; reports listed are specific to the product you are currently analyzing. If you have set a default
printer for your system (configured through Utilities > Printer Setup), the selected report is
automatically sent to the specified printer. Otherwise, a dialog box is displayed from which you can select a
printer. For more information on reports, see Chapter 10, Reports, p. 250.
Figure 2-22: Example Print Report Options
Preview Report
From any analysis window, click the Preview Report
button to display a list of reports you can
preview—reports listed are specific to the product you are currently analyzing. Selected reports display in a
preview window. Use the print and export buttons in the preview window to output the report in selected
format. Click the close button to close the preview window.
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Figure 2-23: Example Preview Report Options
Print Screen
From any analysis windows, click the Print Screen
button to display a new window containing the
screen shot of the current analysis window. Click the Print button to send the screen shot to the printer. To
close this window, click the close button .
Figure 2-24: Example of Print Screen Results
Magnify
From any analysis window, click the Magnify
button to activate the magnifying glass and enlarge any
section of the window. 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.
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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.
Navigator tab
See Launching Navigator, p. 10 for more information about using the Navigator.
Patient
From any analysis window, click the Patient
button to display the Patient/Donor Info window where
you can enter or edit information related to a patient and associate it with the current sample (see Managing
Patient/Donor Records, p. 287).
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Figure 2-25: Patient/Donor Information Window
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.
Note:
This function can be accessed also by right-clicking a sample in the Navigator. See the productspecific chapters of this manual for more information about using this feature.
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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.
Figure 2-26: Sample List for Side By Side Analysis
•
Select a previous sample analysis from the displayed list to compare to the current one. The two analysis
windows are then displayed 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.
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Figure 2-27: Example of a Side By Side Analysis Window
Current analysis
Previous analysis
Note:
This function can be accessed also by right-clicking a sample in the Navigator.
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.
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 next to the
drop- down field. You can also click <<Summary to go to the summary for that session.
Figure 2-28: Sample Navigation Tools
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•
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/back arrow buttons to select different samples.
•
Clicking <<Summary takes you to the session summary for the current sample.
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Chapter 3
ConsenSys™ Analysis
HLA Fusion™ <Emphasis>Research ConsenSys analysis uses sequence based typing techniques to analyze sequence
data and to determine an HLA typing. To correctly input Ab1 files for analysis, they must be in the expected file name
format entered in the Ab1 Filename Configuration Menu (see Changing Ab1 Filename Configuration, p. 87).
Starting a ConsenSys Analysis Session
To begin a ConsenSys analysis session, build a session using Sample IDs or Ab1 files. This information can also be
saved as a Plate Record for later use. You can also analyze Ab1 files directly.
HLA Fusion™ <Emphasis>Research analysis uses sequence-based typing techniques to analyze sequence data and
determine an HLA typing. 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 HLA Fusion™ <Emphasis>Research results
•
Add sample comments
•
Flag a sample for more testing
•
Accept or edit base calls
Starting a ConsenSys Session
1. Click the ConsenSys home page button
page.
or toolbar button
Version 2.0
to open the ConsenSys home
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Figure 3-1: ConsenSys Home Page
2. Click Manual Entry. When the dialog box for starting a ConsenSys session manually displays, you will notice that
the system has assigned a session name. Optionally, you can rename the session.
Figure 3-2: ConsenSys Manual Entry Dialog Box
3. Accept the current date or select a different test date and click Next >.
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4. Click Create New Session/Tray. A window is displayed to allow for subsequent session/tray information.
Figure 3-3: Session/Tray Information Window
5. Enter all required information in the fields at the top of the window. (To add an Ab1 file(s), see Adding an Ab1 File,
p. 27.)
6. Click Start Analysis. 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 using the CTRL key.
3. Click the Start Analysis button to analyze the Ab1 files.
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Using the ConsenSys Analysis window
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 Consensus 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. To resize the electropherogram, hold down the Shift Key
and use the arrow keys to change the size. Right click an electropherogram for more options.
Keyboard Shortcuts
The computer keyboard sequences listed below allow you to navigate and manipulate the ConSensys analysis window.
Key
Shift
←
×
←
×
←
CTRL
×
×
Go to previous marked position
Go to previous position
→
×
→
×
→
×
Go to sequence end position
Increase trace width (when not in fixed width view)
×
→
Go to next marked position
Go to next position
↑
×
↑
×
↑
×
Zoom in on low level signal
Decrease the height of the trace window
×
↑
Reduce the trace scale
Go to previous sample
↓
×
↓
×
↓
Go to sequence start position
Reduce trace width (when not in fixed width view)
←
↓
Description
×
Zoom out to show high intensity signal
Increase the height of the trace window
×
Increase the trace scale
Go to next sample
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Key
Shift
CTRL
TAB
Confirm the current IUB code call and move to the next
unconfirmed position
A
A
Set the current IUB code to A
×
C
×
Show/hide the C trace
Set the current IUB code to G
×
T
T
Toggle the amino acid translation view
Set the current IUB code to C
G
G
Show/hide the A trace
×
A
C
Description
Show/hide the G trace
Set the current IUB code to G
×
Show/hide the T trace
B
Set the current IUB code to B
D
Set the current IUB code to D
H
Set the current IUB code to H
K
Set the current IUB code to K
M
Set the current IUB code to M
R
Set the current IUB code to R
S
Set the current IUB code to S
V
Set the current IUB code to V
W
Set the current IUB code to W
X
Set the current IUB code to X
Y
Set the current IUB code to Y
+
Add an insertion marker at the current position
-
Add a deletion marker at the current position
F
Open the sequence find dialog
I
Show/hide trace information
[
Step back through the sequence primer layers
Sample Comments
If you choose to enter comments about the sample, they are displayed for the results in the current analysis session in
all analysis, data look up and reporting functions in HLA Fusion™ <Emphasis>Research.
1. From the Analysis window, click Comments.
2. Enter comments about the sample into the Comments and Warnings window, and click Done.
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Flagging a Sample for Further Testing
Marking a sample for more testing displays the More Tests check box for the sample’s results in the current analysis
session in all analysis, data look up and reporting functions in HLA Fusion™ <Emphasis>Research.
•
From the Analysis window, select the More Tests check box.
Accept Base Calls
You can individually accept the close base calls determined by HLA Fusion™ <Emphasis>Research. When you accept
a base call, you are moved to the next marked base position.
•
From the Analysis window, click Accept Base to accept the computer-suggested base call and move to the next
base.
Edit Base Calls
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. Any base call can be edited.
•
From the Analysis window, click on a base and click one or more of the assignment buttons to change the base
assignment.
Assignment Buttons
Saving and Confirming ConsenSys Analysis Results
HLA Fusion™ <Emphasis>Research software provides computer suggested typing results. Final assignments can only
be made by the user.
From the Analysis window you can:
•
Save results
•
Confirm results
Save Assignments
Lab technicians and supervisors can save analysis results for further review and approval. Samples are marked as
Ready.
•
From the Analysis window, click Save>> to save analysis results.
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Confirm Assignments
Lab Supervisors can review and confirm analysis results. Samples are marked as Approved.
•
From the Analysis window, click Confirm>> to confirm analysis results.
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Chapter 4
SSO Analysis
The SSO Genotyping analysis feature of the program 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 to view, adjust, and assign results for each one.
Opening a SSO Analysis Session
1. Select SSO home page button
displayed.
Note:
or the SSO toolbar button
. The SSO Home page is
For information on the options available through the links on the right of the window
(Figure 4-1), see Chapter 11, Utilities.
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Figure 4-1: SSO Home Page
Click to open Catalog
Manager window
Click to open Update
Reference File window
Click to open Available
Reference Update window
Click Edit to
modify LABType
global settings
Click links to
display selected
catalog,
worksheet, or
probe/primer
documents.
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).
2. Select a session from the CSV File Name list. The SSO Session Import window displays.
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Figure 4-2: SSO Session Import Window
Date will be highlighted yellow
if regional settings do not
match between the current
CSV file and Fusion Research.
Session ID
Catalog ID
Lists already
imported CSV
files
Default path
for sessions
Luminex CSV
session files
Sets Patient ID to be the
same as the Sample ID
SSO home page
button
Note:
Double-click
sample IDs see
SSO sample list;
sample IDs can
be edited
Double-click
patient IDs to
see current
patient list
Select to
allow auto
analysis of
all session
Lists Positive Control (PC)
samples
values for each sample
upon
import
Sample/
Patient
Details table
Assign patient type
to corresponding
patient ID
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.
3. Select a file from the list of CSV files to import, or click the folder icon above the list to browse to
LABType CSV file(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.
4. The system assigns a session ID (the CSV filename) automatically. Optionally, you can change the ID.
The ID can be alphanumeric (contain letters and numbers), and will be listed alphabetically with any
other SSO session files in your database.
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Figure 4-3: Session ID Field
Note:
A session ID must be unique to the Fusion Research 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 (see Special Characters to Avoid in Filenames, p. 339).
5. 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 List button on the toolbar. The Import Patient window is displayed,
allowing you to import the patient information file. See Importing Patient/Donor Lists, p. 100 for
details.
•
To manually add patient data, type data 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.
6. Select a catalog file. Your catalog file selection method varies, depending on the CSV file and the catalog
files you have imported for LABType:
Note:
If you need to import more catalogs, click the Download link on the LABtype home page and
see Chapter 11, Utilities, p. 117 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 catalogs
during this import session. You may need to click the Home button and then click the LABType
button again to return to the import process.
•
Note:
•
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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. You can go to Step 8.
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, and
you can go to Step 8. If there is more than one match, a catalog validation dialog box is displayed
with the best bead matches. You can confirm the selected catalog file by clicking the Close button.
Or, you can double-click a catalog file name on the list of Suggested Catalogs.
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Figure 4-4: Catalog Validation Dialog Box
Click to display a list of any
bead mismatches between
selected catalog and CSV files.
Displays list of all
catalog files with
the same or
better level of
bead matches.
•
Following catalog file validation, the system may ask you if you would like to associate that template
name with the specified catalog file (see Figure 4-5). If you click Yes to associate the two, the system
automatically selects this catalog file for future imports of any CSV files that reference this template.
Figure 4-5: Catalog Template Association Dialog Box
Select check box if you do not
want to be asked this question
during future imports; to
display again, select Utilities >
Catalog Template and select
the check box next to Enable
during CSV Import.
7. 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
(see Figure 4-6).
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Figure 4-6: Highlight Sample Row for Deletion
Click here
•
Press the Delete key on your computer keyboard to delete the sample and prevent it from being
imported as part of the session.
8. When session and sample information has been verified, click the Import button. The newly imported
session is displayed in the Navigator tree, in blue at the top of the list. If you select the Auto Analysis
check box, the session is imported as well as analyzed when you click Import; it is displayed on the
Navigator as an analyzed session.
9. 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.
Displaying a SSO Analysis Window
1. Open a SSO session.
2. Click on a sample to display its analysis in the Analysis window. See Analyze SSO Data, p. 48 for more
information.
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Quadrant 2
Quadrant 1
Quadrant 3
Quadrant 4
•
Select a sample from this list to make the sample active in the Analysis window. Alternatively, you can use the
arrow buttons to move between the samples.
•
Click any column header among the sample list to sort the table by that column. Click the arrow buttons to display
the samples per 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 tool allows you to define certain parameters for the analysis. To launch this tool, right-click on the
gray panel below the toolbar.
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Right click here to
launch Configuration tool
The Configuration window is displayed, as shown below.
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 and 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.
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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.
SSO Analysis window Overview
From the Analysis window you can:
•
View sample analysis results
•
Change histogram scaling
•
Add comments and mark for more testing
•
Print analysis information
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.
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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 below.
To change the histogram scale, click inside the Max Scale field, type in new limits, and press Enter. 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.
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Reaction Patterns Tab
1. From the Analysis window Quadrant 1, click on the Rxn tab to display the Reaction Pattern Table.
Expand Table
Sort by Bead ID
Sort by Allele
Sort by Reaction Pattern
2. Use the Find Allele tool to display the reaction pattern in the first row of the table. Type an allele into the text box
and click on the Find Allele button to sort by allele.
3. To sort beads by reactivity for the allele, click on the gray area on the left of the allele name. The positive
reactions would be moved to the left of the table. Click on the Rxn Reset button to reset the table to original
configuration.
4. Double-click on the blue panel between the Find Allele and Rxn Reset buttons and the reaction table will be
expanded. To bring the table back to its original size, double-click on the same position again.
5. Click on any column header to sort the table by well position.
Positive reactions are listed above the blue line, and negative reactions below.
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.
1. Click the arrow buttons to navigate between beads and display the profile of the selected bead in Quadrant 2.
Alternatively, you can select the bead from under the Bead drop-down choices.
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2. Hover your cursor over any sample. The sample details are displayed, as shown below.
3. If you wish to exclude a bead from analysis, you can select the check box for Exclude.
4. The # False option allows to force false reactions. HLA Fusion™ Research re-analyzes the reaction allowing for
one false reaction. By default, the software analyzes a sample until an HLA typing can be determined or until the
analysis reaches the maximum number of false reactions set in the analysis configuration table. This is a useful tool
for checking results, for example, it can be used to look for perfect matches with homozygosity or rare allele
assignments. If desired, increase the number of false reaction to be forced and click on the Reanalyze button next.
To adjust Sample Cutoff Values, do the following.
1. Select the Adjust Cutoff check box to activate the adjust cut-off feature.
2. Click on histogram to set new cut off value to that position. Click the Reanalyze button to re-analyze the sample.
You can change a bead cut-off value for each sample individually.
3. Clear the Adjust Cutoff check box to lock the cut off.
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4. Click on the Reset button to reset the changed values back to default. The following options would be displayed to
choose from.
Raw Tab
The Raw Data Table displays all raw data and test details for the current sample.
1. From the Analysis window Quadrant 2, click the Raw tab to display the Raw Data Table.
Expand Table
Sort by Column
2. To change the threshold value, enter a new value in the Threshold field and press Enter. Normalized bead values
that fall within the specified threshold range of the cutoff for that bead are highlighted. The raw table will be
updated instantly highlighting the rows in yellow. The Bead IDs for the highlighted row is displayed in the Close
Bead Rxn box.
3. Click the Maximize button to expand the Raw Data Table. Click the X to close.
4. Double-click the blue horizontal panel in the raw tab to expand the raw data table within the Analysis window. To
bring the table back to its original size, double-click the same position.
5. Clicking on any column header would sort the raw data table by that column.
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Bead Info Tab
1. From the Analysis window Quadrant 2, click the Bead Info tab to display the allele specificity of the selected bead.
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.
Red = positive reaction; Blue = negative reaction; Green = selected bead in quadrant 2.
The diamonds inside the histograms indicate the current cut-off position. Arrowheads identify the direction and
position of cut off changes made to a bead.
1. 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.
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2. Hover your cursor over any sample. The sample details are displayed, as shown below.
3. 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.
4. The magenta bars on the left represent the raw data for positive controls. The up or down arrowheads below
indicates the location of the adjusted cut off.
5. You can expand the histogram by double-clicking on the blue panel between quadrants 3 and 4. To resize the
histogram to its original size, double-click on the blue panel between quadrants 1 and 3.
SSO Analysis window - Quadrant 4 - SSO Results and Assignment panel
Quadrant 4 displays possible typing assignments for the current sample. The left side shows possible allele pair
assignments suggested by the software. You must make assignments manually. The right shows possible coded
assignments.
Manual Assignment
As the color code displayed in the figure above, the alleles highlighted in yellow are positive match, red ones are
mismatches, and unhighlighted ones are negative. To make typing assignments, please see Make Typing Assignments in
SSO Analysis, p. 48.
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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 detail and reaction data for the
selected sample and probe.
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
Assign All
Assign
Remove
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 are mismatch, and the rest unhighlighted 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.
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1. Select an allele or several alleles from the Summary using the Control key in your keyboard, and click the Assign
button to assign the SSO locus group in the Final Assignment panel.
2. To assign allele pairs, select one or more pair results from the allele assignment panel and click Assign.
3. Click the Assign All button to assign all Positive SSO locus groups. The selected allele(s) are displayed under the
Final Assignment.
4. To remove any or all alleles from Final Assignment sections, select them and click the Remove (X) button.
Flagging a Sample for Further Testing
This option flags a sample for further testing in the current analysis session and reports in HLA Fusion™ Research.
More testing flag is saved with analysis.
•
In the Analysis window, select the More Test check box below the Assignments area.
Reanalyze
Click on the Reanalyze button to reanalyze the data based on user changes in the current session or sample.
Manual Assignments
Manual assignments must be entered in standard format with each allele separated by two spaces.
•
Type the allele name in the text box below Final Assignment section and click on the
entered allele is displayed in the Final Assignment field.
button. The newly
SSO Batch Analysis
The 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
Save Assignments
Lab Technicians and Supervisors can save analysis results for further review and approval. Samples are marked as
Ready.
•
From the Analysis window, click Save>> to save analysis results and move to the next sample. Prior to confirming,
a sample can be re-saved, if needed.
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Confirm Assignments
When an analysis has been saved, lab Supervisors can review and confirm analysis results. Confirmed samples are
marked as Approved. The Confirm button is gray when you view a saved but unconfirmed sample. The Confirm button
is purple when you view an already confirmed sample. Samples may be reconfirmed.
1. 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 currently displayed analysis screen.
•
50
From the Analysis window tool bar, click the Print Screen button. A screen shot of the current screen is displayed
in a new window.
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Chapter 5
Micro SSP Analysis
The Micro SSP™ HLA typing trays use the sequence-specific primer technology. These trays are available in 96-well
and 384-well format. The Micro SSP analysis feature of the program analyzes manually entered reaction patterns as a
new session, and can continue the analysis of a previous 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. The software 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 the Lab Technicians and for final approval by the Lab
Supervisors.
Starting 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.
1. Select MicroSSP home page button
Home page is displayed.
Note:
or the Micro SSP toolbar button
. The Micro SSP
If you are not using the default Fusion Research user interface, the data and links shown on the
right side of the window in Figure 5-1 are not displayed. For information on accessing this same
product data and configuration options, see the Utilities chapter.
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Figure 5-1: Micro SSP Home Page
Click to open Catalog
Manager window
Click to open Update
Reference File window
Click to open Available
Reference Update window
Click to modify
Micro SSP global
settings
Click links to
display selected
catalog,
worksheet, or
probe/primer
documents.
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).
2. Click the Manual Entry button. The Manual Entry window is displayed.
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Figure 5-2: Micro SSP Manual Entry Window
Open Open Browse Go to
Sample Patient for Gel analysis
lists
list
Image window
Start new batch
Save current Batch
information
Close this
window
3. The system assigns a Batch Name automatically. Optionally, you can change the name.
Note:
A batch name must be unique to the Fusion Research database for each product type. If it
already exists, the software prompts you to rename the batch. 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 (see Special Characters to Avoid in Filenames, p. 136).
4. 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 and
see Chapter 11, Utilities, p. 117 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 catalogs
during this import session. You may need to click the Home button and then click the Micro
SSP button again to return to the import process.
5. Accept the session name in the Session field, or modify it.
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6. Enter a name in the Sample Name field. If this is an existing sample name, other fields, such as the
Patient ID and Ethnicity, are populated with existing data.
7. Click the drop-down arrow in the Sample Date field and select a date. The analysis window for this
session is displayed.
8. If you want to associate a gel image with the sample, double-click in the Gel Image field and browse the
location of the image you want to add to the sample.
Note:
The only format supported for the Gel IMage import is JPEG format.
Figure 5-3: Select Gel Image Browser
9. 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.
10. Take one of the following actions once you are ready to stop creating the batch:
•
Click Next> to open the Micro SSP analysis window.
•
Click Save to save the current batch information to return to later.
•
Click New Batch to start creation of a new batch.
•
Click Close to exit the Manual Entry window.
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Displaying a Micro SSP Analysis Window
1. Open a Micro SSP session.
2. Click on a sample to display its analysis in the Analysis window. See Using the Micro SSP Analysis window, p. 57
for more information.
Reaction
Pattern
table
Input and
analysis
of
samples
Results
area
Pair
Click to view or add a
gel image (must be a
JPEG image to add it).
displays allele pairs
Match groups and condenses
pairs with same
reaction pattern
Click to translate to new
allele nomenclature format
(only applies if old results;
new results will already be
in new allele format)
Configuring Micro SSP Data Analysis
The defaults for the configurations can be set from the Utilities menu in the main HLA Fusion™ Research window.
Please refer to the Utilities chapter for more information on setting the default configurations. Configurations can be
set from within the analysis window for the current analysis. If you are starting an analysis session, you can change
configuration options before you begin the session.
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Change Current Configuration
Before starting analysis, you can change analysis options for the current session and all subsequent sessions by using
the Configuration menu shown below. Changes to configuration settings in analysis affect the current sample, any
samples added after the change for the current session only.
1. To change configuration settings for all new sessions, right click on the blue panel below the toolbar. A list of
configuration options will be displayed.
Assign Code
By default, the system assigns the NMDP codes to the alleles. However, the user can optionally change these codes to
either No Code, Local Code or Cross Code.
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 are involved in Bw4/Bw6 research, you may optionally change the
configuration to this option.
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Demographic Information
The Demographic Information option offers to determine allele frequency within a particular population.
Entering Micro SSP Reactions Input Panel
The Micro SSP reaction input panel is set up in the same format as the test gel. 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 position is displayed.
From the Analysis window you can:
•
Enter reaction patterns and begin analysis
•
Change default reaction pattern values
•
Change configuration settings
Entering Micro SSP Reactions
To enter a reaction, simply click on the well until it displays the correct reaction value or type in reaction value for well.
The reaction for one sample may be entered at a time. You can enter a new sample at any time during analysis of a new
or existing session by clicking Add New Sample. New samples use the same catalog information as the rest of the
session and also the most current configuration settings.
1. From the Analysis window, enter a sample name in the Sample ID box.
2. Enter test reactions by clicking on a well to change the reaction value, or by typing in a reaction value (1, 8 or 0).
3. Click the Analyze button.
Note:
If the sample has already been analyzed once, click the Reanalyze button.
4. To enter a new sample, click the Add New Sample button at any time during analysis. Be sure to Save or Confirm
any changes to an analysis before adding a new sample.
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™ Research suggests possible
typing results, but you make the final assignment. Any adjustments made in the Analysis window are sample-specific
and affect only individual samples.
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From the Analysis window you can do the following:
•
View and print sample analysis results
•
Use the Reaction Pattern Table
•
Add comments and mark for more testing
•
Change the allowable number of false reactions
•
Force one false reaction
Micro SSP Analysis window Overview
Micro SSP analysis allows you to view analysis details, make adjustments and make typing assignments using the
Analysis window.
View Well Details
You can view details about the current sample by holding your mouse pointer over a well in the Reaction Pattern
Grid.
1. From the Analysis window, hold your cursor over a well to view details.
Add New Sample
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 position is displayed.
Using the Reaction Pattern Table
The Micro SSP reaction pattern table can be sorted by allele name, reaction pattern or well position. The following
distinguish the various table entries:
•
Positive alleles are highlighted in yellow.
•
If a well is a potential false positive, its column is highlighted red.
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•
If it is a potential false negative, its column is highlighted green.
•
Cross Loci wells are indicated with a # symbol in the Cross Loci row for that well position.
•
The table can be sorted by typing an allele into the field. This moves the allele to the first row and freezes the row.
Expand Table
Sort by Well Position
Sort by Allele
Sort by Reaction Pattern
1. To Sort by Allele, double click on an allele name to bring that allele to the top of the table. Type an allele or partial
allele name in the Find Allele field, and click the Find Allele button. Matches are moved to the top of the Reaction
Pattern Table.
2. To Sort by Reaction Pattern, click on the left most column of the allele name on the gray area. The positive
reactions would be skewed to the left of the table. Click the Rxn Reset button to reset the table to original
configuration.
3. To Sort by Well Position, click on any column header to sort all alleles by reaction value.
4. Double-click the gray panel above the table. The reaction table is expanded. To bring the table back to its original
size, double-click the gray panel once again.
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Number of Allowable False Reactions
If HLA Fusion™ Research 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 reaction has been reached or a solution
is found. The number of false reactions sets the maximum allowable false reactions for an analysis.
•
In the # False Rxn field within the Analysis window, click the up or down arrow to change the number of
allowable false reactions.
Force One False Reaction
When a sample has a result with no false reactions (exact match result), the Force 1 feature forces HLA Fusion™
Research to re-analyze the reaction to allow for one possible false reaction in any well. This feature is used to search
for results that have close reactions to the actual reaction.
1.
From the Analysis window, click Force 1 to force the program to analyze the sample with one false reaction.
2. Click Rxn Reset to return to the default results.
Micro SSP Combined Analysis
HLA Fusion™ Research compares the sample IDs in the current session with sample IDs in existing sessions, and
gives you the option to analyze the sample using readings for both Serology sessions. You can also combine sample
readings from a LABType session with those from a Serology session as detailed below.
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1. From the Analysis window, click on the Analyze Combined button. The next pop-up window displays previous
session name to choose from.
2. To select the desired previous session(s), check the box next to it and click the Analyze button.
Note:
You will notice that the Analyze Combined button in the Analysis window changes to Reanalyze
Combine button. This is an indication that the selected sessions have been combined and reanalyzed.
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 trays. The reaction wells tray
you combined with the current sample is marked with a * next to the well position.
Note:
When running a combined analysis with a new sample/test, the user must first enter reactions and analyze
sample, and then Analyze Combined can be performed.
Making Typing Assignments in Micro SSP Analysis
HLA Fusion™ Research provides computer-suggested allele pairs and coded assignments. Final typing assignments
can only be made by the user.
From the Analysis window you can:
•
Assign non-coded allele pairs
•
Assign a coded allele pair
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•
Assign serological equivalents
•
Make manual assignments
•
Remove assignments
•
Save and Confirm assignments
Possible Allele Pairs
The Possible Allele Pairs panel displays all possible typing assignments for the current sample. If there is only one
coded allele pair typing assignment, you can assign it and move to the next sample with one button. Only the coded
assignment is saved.
Allele Pair Assignments
1. Select an allele pair in the Possible Allele Pairs panel.
2. Click the Assign button next to Assigned Allele Pairs to add the assignment to the final assignment area.
Alternatively, you can double click on the allele pair to assign it to the final assignment area.
3. To remove an assignment, highlight the assignment in the final assignments area and click on X.
Assign
Manual Allele Pair Assignment
Manual assignments must be entered in standard format (locus*four digits space locus*four digits).
Manually Enter Assignment
1. Type an assignment into the text box right below Assigned Alelle Pairs.
2. Click Enter and the typed allele is displayed in the Assigned Alelle Pairs text box.
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Allele Code Assignments
Select
Assign
Manually Enter Assignment
The allele codes displayed in the Possible Allele Code text box are condensed ones that the system suggests from the
list of possible allele pairs displayed.
•
To assign an allele, select its code and click the Assign button.
Manual Allele Code Assignment
1. Type an assignment into the text box right below Assigned Allele Code.
2. Click Enter and the typed allele code would be appear in the Assigned Allele Code text box
Serology Assignment
Select
Assign
Manually Enter Assignment
Highlighting a serological typing pair displays all allele equivalent possibilities for the current sample. Serological
equivalents are saved in addition to any allele or code assignments.
1. The Possible Serology panel displays serological equivalents for the current sample.
2. Highlight an assignment and click the Assign button to assign serology. It would be displayed under the Assigned
Serology panel.
3. Click the X to remove typing assignment.
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Bw4/Bw6 configuration results appear here.
Other Assignment
This tool allows non-formatted final assignment.
Type an allele pair or allele code and click Enter. The typed allele would be assigned and included in the report.
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. You can store these unknowns for later submission in a .txt file named nmdp_code_report.txt and
located in the C:\Program Files\One Lambda\HLAFusion\data folder. Code information is stored in the text file as it is
added with the newest additions at the bottom.
1. From the Analysis window, click the XX code in the Possible Allele Code box to display the XX Code bar.
2. When you select an allele code under the Possible Allele Code text box, the +Rpt/Close button appears on top of
the More Test button.
3. To add the code information to the .txt file, click +Rpt. Click Close to close the bar.
4. The allele code would be included in the text file, as shown below.
Remove Assignments
You can select more than one specificity to remove by holding down the Ctrl key and clicking multiple specificities.
•
From the Analysis window, highlight specificities in the Assignment boxes and click X to remove.
Sample Comments
Sample comments are displayed for that sample’s results in the current analysis and reports in HLA Fusion™ Research.
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•
In the Analysis window, type sample comments into the Comment field below the Assignments area. Double
clicking in this text box would invoke a new window to type comments in. Comments are saved with analysis.
Flagging a Sample for Further Testing
This option flags a sample for further testing in the current analysis session and reports in HLA Fusion™ Research.
More testing flag is saved with analysis.
1. In the Analysis window, check the More Test check box below the Assignments area.
Save Assignments
Lab Technicians and Supervisors can save analysis results for further review and approval. Samples are marked as
“Ready“.
1. From the Analysis window, click Save>> 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 analysis results. Confirmed samples are
marked as Approved. The Confirm button is gray when you view a saved but unconfirmed sample. The Confirm button
is purple when you view an already confirmed sample. Samples may be reconfirmed.
1. From the Analysis window, click Confirm>> to confirm analysis results and move to the next sample.
Note:
The application records two level analysis reviews—Save and Confirm. For re-saved and reconfirmed
analysis, only the last user to save or confirm is recorded.
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Session Summary and Logs
Chapter 6
What is 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 from the HLA Fusion™ <Emphasis>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.
Filter
Session ID
Field
Chooser
Button
Navigation
Tree
Session
Summary
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•
Double-click a sample in the Summary Table or a data point to go directly to the analysis screen for this sample.
•
Click on the Field Chooser button to the left of the table headings. The Field Chooser window is displayed. In this
window, you can select or clear the check boxes next to column headings to add or remove those columns from the
Summary Table. Checking or unchecking in this window instantly updates the table.
•
Click on any column header of the Summary Table to sort the table by that column. The up or down arrows in the
column header indicate the sorting order—up for ascending; down for descending.
•
Click on the Export button to save the Summary Table on your computer or the network. The file will be saved in
Excel (*.XLS) format.
•
Click Print to print out a report of the Summary Table.
•
Click Preview to view report of the Summary Table.
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•
In the print preview window, the slider on the left displays various sections of the comprehensive report.
•
Double click on a sample in the Summary Table to go directly to the analysis screen for that sample.
•
You can filter the samples by clicking the Filter button in the sample column header. This displays the filter-by
options, as shown below.
The session name is displayed at the top of the Summary Table.
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Creating and Managing Session Logs
HLA Fusion™ Research allows you the capability to create log files of your analysis sessions, which you can then
print or archive.
See the following sections for procedures to create, manage, and print analysis session log files.
Creating a Session Log
1. Click the Main Menu option Data.
2. Provide all necessary session input information by using the drop-down menus and search buttons on the left side
of the Data window.
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. Click the main menu option Data.
2. 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.
3. Once you have displayed the session log you want, use the Archive, Active and Delete buttons at the bottom of the
window to manage the log.
Printing Session Logs
1. Click the main menu option Data.
2. 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.
3. Once you have displayed the session log you want, use the Print Session Log button at the bottom of the window to
manage the log.
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Chapter 7
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 Microsoft
Office Document Image Writer from Microsoft.com.
In addition, you can print and export these reports from the analysis or batch summary window.
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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 must take to create a report from this window:
1. Select a report type.
2. As needed, select criteria to refine report input, such as 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:
-
From the home page, click Create Reports.
-
From the Fusion Research main menu options, select Reports.
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.
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Figure 7-1: Reports Window
Shortcuts to other
Fusion Research
menu options
Store and
access up to
18 reports
Format reports &
create data
export templates
Close
Reports
window
Report
types
Separate report
for each sample
Date
range for
displayed
sessions
Set order and
sort criteria for
report columns
Click to
filter
sessions
by
selected
criteria
Select tab to view either
by session or by sample
Save
sort
order
Preview, print
& export a
report
Export report
data in
CSV/XML/.txt
List of sessions,
filtered by report
type & input
criteria
Criteria to refine report
input (filters session
display)
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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. For a
list of reports you can generate, see Report Types, p. 216.
Report Type Menu Options
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:
-
Enter a Patient ID, Session or Sample ID fields, or browse for the information with the Browse button
-
Adjust the date range. Use the drop-down calendars in the Session Date fields to select a different start and end
date.
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-
Enter or browse for specific sample or session characteristics or status (see below).
click to filter sessions by
selected criteria
sample or session status or
characteristics criteria
•
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 sessions list, click the + sign next to any session to expand the display to show its samples.
Click tab to view samples—either all
samples or only the selected ones
Session with
some, but not all
samples selected
Session with all
samples selected
Samples
•
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.)
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.
•
(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.
•
Alternatively, you can right-click on a session and apply one of he 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 (LABType, Micro SSP, LABScreen, etc.)
-
Category Select: choose the report category—molecular or antibody.
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Note:
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.
•
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.
Toolbar Button
Function
Export Report: exports reports in one of several
available formats, including Crystal Report, Adobe
PDF, and Microsoft Word.
Print Report: prints the current report.
Toggle Group Tree: opens a tree panel on the left,
listing the samples included in the current report.
Previous and Next Page: if the report has multiple
pages, these buttons allow you to page back and forth
in the report.
Find Text: displays a dialog box that allows you to
enter text to search for in the report.
Zoom: select the magnification at which to display the
current report by clicking on the drop-down list.
•
To close the Report Viewer window, click the Close button
in upper right corner of the viewer.
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.
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2. Enter a name for the current exported report, or browse for a report file to export. Select a format from the Save as
type drop-down list (Excel, Acrobat, Word, or Rich Text format), and click OK. By default, the file is saved in
C:\OLI Fusion\data\report). You can change where these files are saved by modifying the Interface path
(see Setting HLA Fusion Research Default URLs and Directory Paths, p. 132).
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. 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
1. 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).
2. Select My Favorite > Add to My Favorite.
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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.
reports are listed below this
line on the My Favorite menu
can be selected 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.
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.
Reports Tools
Customizing Report Appearance
Note:
You must be a supervisor-level user in HLA Fusion Research 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 Research 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 Research 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).
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•
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" />
•
Please note that all the report files used in HLA Fusion Research 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 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.
2. Use the Crystal Report Designer tools to modify the appearance of your report.
3. 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 Research, the report will have the appearance you last saved in
Crystal Report Designer.
Creating Custom Data Export Templates
1. Select Tools > Setup 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.
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2. The Export Data Setup dialog box is displayed, allowing you to select the name of the export template, the fields
and options to be included, and the field order you want for the template. Select check boxes on the left to select
category, fields and options. On the right side of the dialog box, drag and drop the fields, or hold CTRL and press
the Up/Down arrow keys to change the order.
3. 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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4. 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.
5. 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. You can change where these files are saved by modifying the Interface path (see Setting
HLA Fusion Research Default URLs and Directory Paths, p. 132).
Creating Custom Reports
Certain report types allow you to customize the types of fields to include.
Note:
For Molecular Custom or Antibody Custom reports, you must make sure the Free 3 of 9 Extended font is
installed on your computer—otherwise, the barcode is not 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 (e.g., Molecular Custom,
under the Generic Typing report type menu).
2. Click the Setup button in the Report Option section of the window. The Custom Report Setup window is
displayed, allowing you to customize report content by selecting from various categories and fields.
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Molecular Custom setup
Patient Custom setup
3. Enter a name or select one from the drop-down list.
4. 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.
5. Click the Save button to save the custom report setup you have just selected.
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.
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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. 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.
4. Click the Export button to export the displayed data as an Excel file. Click the DNA button to export molecular
specificities as an Excel file.
5. Click the Close button
in the upper right corner of the window to close and return to the Reports window.
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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.
4. Click the Export button to export the displayed data as an Excel file. Click the DNA button to export molecular
specificities as an Excel file.
5. Click the Close button
in the upper-right of the window to close and return to the 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. Use the arrow buttons to navigate through samples.
4. Use the arrow buttons to navigate through samples.
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5. Click the View Analysis button
window can be resized.
6. Click the Close button
to open the analysis window for the current sample. The analysis
to close the window and return to the Reports window.
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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 card is displayed.
3. Click the Test Info tab to see that 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 button
in the upper right corner to close and return to the Reports window.
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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 Research 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 MicroSSP 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)
MicroSSP - (data from analyzed Micro SSP samples)
•
-
SSP Report - (detailed typing report for Micro SSP™ tests that may be customized)
LCT - (data from analyzed LCT samples)
•
LCT Specificity (test details of a single sample on an LCT analysis tray)
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Chapter 8
Sample Management
Sample management lets you to enter and export sample information to allow for faster analysis and data management.
Sample information can exist in the database without any analysis data associated with it.
Sample Lists
In HLA Fusion™ Research, 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.
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. The information contained in the sample lists must be in one of the formats described in the
section Information Formats for Sample Lists, p. 91.
1. From the Main Menu, select Sample > Import Sample List.
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2. Click the Search Sample List button; browse for the sample list to be imported; and click Open.
3. Type a name in the List ID field, and, if necessary, select a Lab code or Contact ID from the drop-down list.
4. Confirm sample information, and edit if needed. Click to clear the check boxes of any samples you do not want to
import.
5. Click Import List to import the selected sample lists.
6. Click Close to return to the Main Menu.
Information Formats for Sample Lists
The information inside a sample list you import in to HLA Fusion Research 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
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Pack 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"
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
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Local/Sample/Patient ID Only
This file is a Microsoft Excel file. This file lists (in this order):
Row 1: Column Title “Local” and “Sample” and “Patient”
Column A: LocalID
Column B: SampleIDName (required)
Column C: PatientIDName
example:
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Viewing and Editing Sample Information
Sample information can be edited, but associated patient IDs cannot—only new patient IDs can be added.
1. From the Main Menu, select Sample > Manage Sample Info.
Figure 8-1: Manage Sample Window
2. Use the filters to find samples, and click View Sample.
3. Edit sample information.
Note:
You can rename a sample by modifying the name in the Sample ID field. Sample IDs are listed
alphanumerically, with all IDs 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 are not allowed to delete a sample that 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.
From 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.
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2. Type in a name for the new test list, and click Continue>>.
3. Search for samples to add to the test list using the search fields, and click Apply to view search results.
4. Highlight samples, and click Add>> to add them to the test list.
5. Click Save to save the new test list.
6. Click Close to 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 Research 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 Export 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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Luminex Lists
HLA Fusion Research can create a Luminex List from a new or existing test list. You can use this list to quickly add
information, such as sample ID, before you create a Luminex CSV output file. From the Create/Edit Test List window
you can create a Luminex list
Creating Luminex Lists
Luminex List files can be edited after they are exported, but changes are not reflected in the test list from which they
were created.
1. From the Main Menu, select Samples > Manage Test List.
2. Use the pull-down menu to select a test list, and click Continue>>.
3. Click Export to export.
4. Select a location to save the test list to and enter a file name.
5. Click Save.
6. When prompted to create Luminex List input, click Yes.
7. Click OK on the confirmation message to return to the Test List window.
8. Click Close to return to the Main Menu.
Create Sample Worklists
Note:
The Sample Worklist feature is available only if you have SQL 2005 and above installed.
Sample Worklist functionality in HLA Fusion Research software gives you the flexibility to assign various tests to
selected samples. This information is used in designing plates for Luminex processing.
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sample search criteria
1. Select Sample > Create Sample Worklist from the Fusion Research main menu.
1. Use the search criteria to specify the samples that you would like to assign tests to, and click Search.
2. Select one session, or select multiple sessions (by holding and dragging the mouse). The selected samples are
highlighted.
3. Now assign one or more tests by selecting the check boxes for the tests you want to run on the samples (listed
under LABScreen Tests and/or LABType Tests).
4. Once you are done assigning tests to all the selected samples, click Save to save the worklist.
Create Plate Design
Note:
The Plate Designer feature is available only if you have SQL 2005 and above installed.
Plate Designer functionality in HLA Fusion Research software gives you the flexibility to organize and to plan your
samples in the plate format that is ready for processing through the Luminex device. You must first have created a
sample worklist (see Create Sample Worklists, p. 97).
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1. Select Sample > Create Plate Designer from the Fusion Research main menu.
2. Select the Assay type.
3. Select the New Plate button option if you want to create a new plate; otherwise, select Edit Plate to change an
existing plate.
4. Click Go.
5. For a new plate:
•
Enter an unique plate name
•
Use the following search criteria to search and select the samples you want to add to plate for testing:
•
Test name
•
Sample name
•
Sample collection date (From and To date)
6. Click Search to display a list of samples that match your criteria.
7. Select samples (one or many at a time), and use the left << button to assign these samples to a well in the plate.
Repeat this until you have completed your plate design.
8. Click Save to save your plate design.
9. Click Print if you want to print your plate design.
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Chapter 9
Patient Information
HLA Fusion™ Research 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 Research performs minimal data validation
upon import.
Importing Patient/Donor Lists
After creating a Patient/Donor List, you can import the information into HLA Fusion Research. (See Creating
Patient/Donor Lists, p. 106 for guidelines on creating a patient list.)
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1. From the Main Menu, select Patient Info > Import Patient List.
2. Select the check box in the Import column for each patient you want to import.
3. Click the Import button to import checked patients.
4. Click Close to return to the main menu.
Note:
The HLA Fusion Research system checks the patient/donor lists you attempt to import to verify
that all characters contained in the data are supported by Fusion Research. If your list contains
unsupported characters, a message is displayed to let you know, and the list is not imported.
For a list of characters to avoid using, see Special Characters to Avoid in Filenames, p. 136.
Newly imported patient records display alleles in the new nomenclature format. Existing
patient records display alleles with the existing allele format.
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
•
Print, export and archive patient records
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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. To quickly add a large number of patient records to HLA Fusion Research, see Creating
Patient/Donor Lists, p. 106.
1. From the Main Menu, select Patient Info > Manage Patient.
Displays a list of
patients/donors in the
Fusion Research
database to select from
Converts assigned
allele code and pairs
to the new
nomenclature format,
and stores the new
format with the
pt/donor info in the
Fusion Research
database
Tools to manage
patient/donor information
2. Enter an ID in the Patient/Donor field.
3. Enter patient/donor information. Fields with an asterisk (*) are required.
4. Click Save to save the data.
5. Click Close 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.
1. From the Main Menu, select Patient Info > Manage Patient.
2. Enter a patient/donor ID and click Load to display patient information. Or, click Select Patient to browse patient
records. Highlight a patient record and click OK to display.
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Editing Patient/Donor Records
All patient/donor information (except patient/donor ID) can be edited.
1. From the Main Menu, select Patient Info > Manage Patient.
2. Select a patient/donor record.
3. Edit patient/donor information. Fields marked with an asterisk (*) are required.
4. Click Save to save data.
5. Click Close to return to the Main Menu.
Associating a Patient/Donor ID with Sample IDs
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.
1. From the Main Menu, select Patient Info > Manage Patient.
2. Select a patient/donor record.
3. Click the Test Info tab.
4. Click the Associate Sample IDs button.
5. In the Patient/Donor Sample Association window, highlight a sample ID and click > to add it to the
Patient/Donor Sample List. (Click < to remove a highlighted sample ID from the list.)
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6. Click Save to save the data.
7. Click OK to return to the patient record.
8. Click Close to return to the main menu.
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.
2. Click the Test Info tab.
3. Click the Associate Donor IDs button.
4. In the Patient/Donor Sample Association window, highlight a Donor ID and click > to add it to the
Patient/Donor Sample List. (Click < to remove a highlighted Donor ID from the list.)
5. Click Save to save data.
6. Click OK to return to patient record.
7. Click Close to return to the Main Menu.
Printing Patient/Donor Records
HLA Fusion Research prints both Record Management tabs regardless of which tab is currently being viewed.
1. From the Main Menu, select Manage Patient > 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 Manage Patient > 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.
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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 Main Menu, select Manage Patient > 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.
Deleting Patient/Donor Records
Patient/donor records can be deleted through the Manage Patient menu option.
1. From the Main Menu, select Manage Patient > Manage Patient.
2. Click the General Info tab.
3. Select a patient/donor record Select a patient/donor record.
4. Click Delete to delete the patient/donor record from the Fusion Research 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 (see
Importing Patient/Donor Lists, p. 100). The first field/section must contain the names of the patient list fields, each
separated by commas:
PatientIDName,CategoryGrp,FamilyID,FirstName,MiddleName,LastName,Ssn,Dob,Gender,Ethnici
ty,Address,City,State,Region,Country,ZipCode,Email,Phone,WkPhone,Cellular,Fax,Employer,
SpouseName,SpouseBloodType,EmergencyContact,EmrgncyTel,DCN,HospitalName,Division,BloodT
ype,Disease,RhBloodType
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Subsequent lines must contain the actual patient information separated by commas. If there is no information for the
patient in a particular field, that field still requires a comma as a placeholder. The following is an example of a patient
list created in Notepad.
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
Patient Antibody Tracking
You can track molecular and antibody typing information 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.
1. Make sure you have patient and donor information entered into HLA Fusion Research. 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 (see Associating a Patient/Donor ID with Sample IDs, p. 104).
2. Select Patient Info > Ab Tracking. The Antibody Tracking window is displayed:
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Saves samples listed
here for the future for
samples within the
chosen date range
3. Click the drop down arrow next to the Patient ID field to select from a list of patients stored in your Fusion
Research database. 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. Click the Find button to display a list of samples for this patient that are within the specified date range.
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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.
6. Select the check box in the Include column for the sample(s) you want to include in the Ab tracking graphs and
data. The graphs are displayed (to display a specific type of graph, click on the associated tab.
7. Select the check box for the antigen(s) you want to include in the tracking.
8. 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.
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Examples of the graphs
that can be displayed for
Ab Tracking
options available if
you right-click on
any graph
Note:
You can double-click on a graph to expand it, and there are right-click options available from each graph
(see graphic above).
9. (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 in your Fusion Research database.
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donor ID drop-down list
select to include on
Class II tracking
select if want to track
donor specific
antigens
antigens not tested
with OLI test kits
10. (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.
11. (Optional) Select the DQA/DPA check box to include these in Class II tracking.
12. 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.
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Profile Management
Chapter 10
HLA Fusion™ Research 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 Research also stores general laboratory
information to be used on reports including multiple contract lab codes.
User Management
From the Profile main menu you can:
•
Add new users
•
Edit existing user profiles
•
Change passwords
•
Reset passwords
•
Archive users
HLA Fusion Research uses two user levels for added security and control of typing and screening results:
Supervisor can...
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
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Supervisor can...
Lab Technician can...
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
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. 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.
4. 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.
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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. 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.
2. Edit user information.
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.
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 users lose or forget their password, HLA Fusion Research 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 and double-click to the left of a user to open their profile.
2. 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 Research application.
3. 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 Research. 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.
Lab Profile
The Lab Profile menu displays the contact information for your lab, network information used by HLA Fusion
Research, 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
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.
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 Research. 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.
2. Add, edit or delete Lab codes:
•
Click Add Lab Code to add a new lab code. Enter information into the new row.
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•
Highlight a lab code to be edited. Click Edit Lab Code to edit the lab code.
3. Edit lab code information.
•
Highlight a lab code to be deleted. Click Delete Lab Code to delete the lab code.
4. 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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Chapter 11
Utilities
HLA Fusion™ Research uses a variety of reference files and configurations 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.
Managing Catalog Reference Files
Catalog reference files contain all of the reaction-specific information needed for analysis: bead and well specificities,
QC information, cut-off values, bead and primer information, etc. 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 (see Updating Catalog Files from the One Lambda
Download Site, p. 119).
1. From the Main Menu, select Utilities > Update Reference > Update Reference File.
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file directory tree
2. Make sure the Catalog option is selected.
3. Using the file directory tree on the left, locate catalog files to be imported.
Expand to see catalog
information
List of available
catalogs, per display
criteria selected below
Option
What Displays
In Fusion
Research DB
Catalogs in your
current database
Updates/
Revisions
Catalogs that need
to be updated
Not in
Fusion
Research DB
Available catalogs
not yet in current
database
All Catalogs
All available
catalogs
Note:
Downloads all associated
documents, such as worksheets,
probe/primer sheets & datasheets
To determine which catalog is the most recent available, HLA Fusion Research looks first at the
lot number and then the revision number. A updated lot number gets flagged as the most
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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.
4. Highlight the files you want to import, or click Select All to select all files listed.
5. Click Import to import the selected catalog files.
6. A confirmation dialog box displays import results, click Close.
7. Click Close to return to the Update Reference menu.
Imported catalog files can be used without restarting Fusion Research.
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 Menu, select Utilities > Update Reference > Update Reference File.
2. Click Auto Update to open the One Lambda Catalog Updates Selection 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 Import to import the selected catalog files.
5. When the confirmation dialog box displays import results, click Ok.
6. Click Close and then Yes to return to the Update Reference menu.
Imported catalog files can be used without restarting Fusion Research.
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.
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
•
Update NMDP codes
•
Create and update Local codes
•
Update Serology Equivalent files
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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
Research can access it. The most current NMDP code file is available on the NMDP download site (see Updating
NMDP Files from the NMDP Web Site, p. 120).
1. From the Main Menu, select Utilities > Update Reference > Update Reference File.
2. Select the NMDP option.
File directory tree
NMDP Code option
Displays date of last
update
3. Navigate to the NMDP file on a local or network drive, using the Import Directory tree.
4. Click Import NMDP to import the selected file.
5. Click Close to return to the Update Reference menu.
Updating NMDP Files from the NMDP Web Site
Follow this procedure to import the NMDP list from the NMDP web site.
1. From the Main Menu, select Utilities > Update Reference > Update Reference File.
2. Select the NMDP option.
3. Click Auto Update, which automatically imports the current NMDP file for use with HLA Fusion Research. 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.
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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 Research CD to a local drive.
2. Use a text editor to edit the template and add code definitions. 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
3. Save the file as local_code.txt
4. See the next section, Updating the Local Code File, to import the file.
Updating the Local Code File
After a Local Code file has been created, it must to be updated in HLA Fusion Research. To use the codes in analysis,
see Changing Molecular Product Configuration, p. 129.
1. From the Main Menu, select Utilities > Update Reference > Update Reference File.
.
file directory tree
2. Select the Local Code option.
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.
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Updating Serology Equivalent Code File from the One Lambda Web Site
The Serology Equivalent file can be auto updated from the One Lambda download site
(http://download.onelambda.com).
1. From the Main Menu, select Utilities > Update Reference > Update Reference File.
List of available serology
equivalent files, per display
criteria selected below
Option
What Displays
In Fusion
Research DB
Files in your
current database
Updates/
Revisions
Files that need to
be updated
Not in
Fusion
Research DB
Available Files not
yet in current
database
All Serology
Files
All available
Serology Files
2. Select the Serology Equivalent option.
3. Click Auto Update to open the One Lambda Catalog Updates Selection window.
4. Select the check box next to all files you want to import.
5. Click Import to import the selected files. Catalog files are ready for use without restarting HLA Fusion Research.
6. A confirmation dialog box displays import results, click Ok.
7. Click Close and then Yes to return to the Update Reference menu.
Note:
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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Archiving Catalog Files
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 > Archive Catalog.
2. Select the Archive check box for the catalog files you want to archive.
3. Click Save to save changes and return to the Update Reference menu.
4. Click Close to return to the Update Reference menu without saving.
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 are highlighted in grey when you view the catalog list. The most recently archived catalog files
are displayed at the bottom of the list.
Indicates catalog
has been archived
Select check box to
display archived
catalogs
•
From the Archive Catalog window, clear the Archive check boxes for catalog files you want to restore to active
use, and click Save.
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 a shaded line have been archived.
1. From the Main Menu, select Utilities > Update Reference > Catalog Information.
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.
4. Click Close to return to the Update Reference menu.
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 Research
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 Research 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. From the Main Menu, select Utilities > Catalog Template Association.
2. Add, remove or modify an association:
a. Add a New Association
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•
Select a catalog file.
•
Type in a new template name, or click Browse to select a Luminex template file (.lxt format) to associate
with the filename.
b. Remove an Association
•
Select a catalog file.
•
Select a template name and click Remove.
c. Modify an Association
•
Select a catalog file.
•
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 Allele Frequency.
Figure 11-1: Allele Frequency Import
2. Select the Create Demographic Group option.
3. Click the browse
button and locate Allele Frequency files.
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4. Click Import.
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 Research, regardless of any other data it contains. If
columns are duplicated, Fusion Research gives you an error message and does not import the
allele frequency file.
The data contained in the Allele Frequency file look similar to Figure 11-2.
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Figure 11-2: Example Allele Frequency File Data
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 Allele Frequency.
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Figure 11-3: Allele Frequency Import
2. Select the Update Alleles and Frequencies 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 (click Translate Alleles)
6. Click Update.
7. Click Close.
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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 file name configuration
Changing Molecular Product Configuration
Changes 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 Main Menu, select Utilities > Molecular Product Configuration > Molecular Analysis
Configuration.
2. Select Micro SSP from the Product Type drop-down menu.
3. Change configuration values as needed.
•
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.
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•
Computer Assigned Serology can only be selected by someone with Supervisor user privileges, and
automatically populates Micro SSP analysis serology assignment fields. If this is selected, the following
warning message is displayed as a reminder that the assignments are estimates, and should not be accepted
without verification:
4. Click Save to save changes.
5. Click Close to return to the Update Reference menu.
Changing Ab1 Filename Configuration
You can modify the way Ab1 filenames are configured.
1. From the Main Menu, select Utilities > Molecular Ab1 Filename Configuration.
2. Make the format changes you want, and click Save.
3. Click Close to return the the HLA Fusion Research home page.
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General System Settings
Several HLA Fusion Research system settings can be set through this menu option under Utilities.
General Settings
For enabling certain system options, use this tab on the Fusion Settings window.
1. Select Utilities > General Settings. The Fusion Setup dialog box is displayed.
2. Select check boxes and from the drop down menu as desired to modify the current Fusion Research settings.
3. Click Save and then Close to save your changes and exit to the main Fusion Research application.
Choosing Default Printer Settings
You can set printer defaults for printing HLA Fusion Research screens or reports—whether you want to select a printer
and settings each time you print, or whether you want screens or reports to be automatically sent to the specified printer
with the specified settings.
1. Select Utilities > General Settings and select the Printer Setup tab.The Printer Setup dialog box is displayed.
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2. Select from the following options for both the Print Screen and Print Report panels of the dialog box:
•
If you want to select a printer and have the option of setting other printer settings each time you print, make
sure the Yes option is selected.
•
If you do not want to select a printer each time you print, select No, and select the default printer and paper size
from the drop-down menus.
Note:
This default printer configuration may be overwritten by the specific page properties of certain reports.
Setting HLA Fusion Research Default URLs and Directory Paths
The URLs & Paths option under the Utilities menu allows you to set the default URLs for OLI and NMDP web sites
to download reference and catalog files, and product updates. This option also allows you to set the directory path
where HLA Fusion Research, 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. From the Main Menu, select Utilities > General Settings and select the URLs or the Paths tab.
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URL tab
Paths tab
2. Click the URLs or the Paths tab.
3. Enter a URL and verify it works by clicking
want to use for the specified purpose.
.For paths, use the browse button
to locate the directory you
4. Click Save.
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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 Research.
1. From the Main Menu, select Utilities > Products Selection.
2. Select or clear the check box next to the product(s) you wish to activate or de-activate.
3. Click Ok.
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Software Validation
The HLA Fusion Research 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 Research software for your lab
environment for regulatory or performance reasons, can be automated by using the IQ (Installation Qualification) and
OQ (Operational Qualification) options 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 Research software by providing a built-in
function. Once the Installation qualification completes, a results report is generated, which you can save, print or export
to Excel.
Note:
If your IQ results concern you, export them to an Excel file and e-mail the file to OLI customer support
(see Technical Support, p. 3).
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 Research 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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Example page from an IQ report
Special Characters to Avoid in Filenames
Some file formats that HLA Fusion Research imports use special characters as field separators. Therefore, it
is recommended that you not use the following special characters when you name sessions or other files
within Fusion Research.
Character
Name
,
comma
;
semi-colon
:
colon
.
period
/
slash
\
backslash
?
question mark
%
percent sign
*
asterisk
|
vertical bar
"
double-quotation mark
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'
single-quotation mark or apostrophe
<
less than
>
greater than
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Chapter 12
LABXpress
This chapter describes how to create sample worklists, plate designs and custom runs for the LABXpress system.
Note:
Only use these procedures if you have acces to and plan to use the LABXpress system (including
pipetting machine) for automated sample processing.
You should make sure you also have access to and have reviewed the LABXpress™ User Manual.
Managing Sample Information
Sample management in HLA Fusion Research software allows you to manage sample information before adding
samples to a sample worklist. Sample information can exist in the database without any analysis data associated with it.
1. Select LABXpress > Sample > Sample Manager
2. Use the filters to find samples, and click View Sample.
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Note:
It is not recommended that you search by Sample ID—this may lead to a lengthy search, especially with
larger databases.
3. Edit sample information.
4. Click Save Changes to save the sample information.
5. Click Close to return to the Fusion Research main menu.
Managing 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 the Luminex®system. It is a useful tool when you have a group of samples to be run on
multiple tests.
From 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 HLA Fusion Research menu, select Sample > Manage Test List.
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2. Type in a name for the new test list, and click Continue>>.
3. Search for samples to add to the test list using the search fields, and click Apply to view search results.
4. Highlight samples, and click Add>> to add them to the test list.
5. Click Save to save the new test list.
6. Click Close to 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 HLA Fusion Research menu, select Sample > 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.
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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 HLA Fusion Research menu, select Sample > 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 as .txt files for use outside of HLA Fusion.
1. From the main HLA Fusion Research menu, select Sample > Manage Test List.
2. Use the pull-down menu to select a test list, and click Continue>>.
3. Click Export 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.
Creating Luminex Lists
HLA Fusion can create a Luminex List from a new or existing test list. You can use this list to quickly add information,
such as sample ID, before you create a Luminex CSV output file. From the Create/Edit Test List window, you can
create a Luminex list
Luminex List files can be edited after they are exported, but changes are not reflected in the test list from which they
were created.
1. From the main HLA Fusion Research menu, select Sample > Manage Test List.
2. Use the pull-down menu to select a test list, and click Continue>>.
3. Click Export to export.
4. Select a location to save the test list to and enter a file name.
5. Click Save.
6. When prompted to create Luminex List input, click Yes.
7. Click OK on the confirmation message to return to the Test List window.
8. Click Close to return to the Main Menu.
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Creating Sample Worklists
Note:
The Sample Worklist feature is available only if you have SQL 2005 and above installed.
Sample Worklist functionality in HLA Fusion Research software gives you the flexibility to assign various tests to
selected samples. This information is used in designing plates for Luminex processing.
Sample search criteria
1. Select Sample > Sample Worklist from the HLA Fusion Research main menu.
1. Use the search criteria to specify the samples that you would like to assign tests to, and click Search.
2. Select one sample, or select multiple samples (by holding and dragging the mouse). The selected samples are
highlighted.
3. Now assign one or more tests by selecting the check boxes for the tests you want to run on the samples (listed
under LABScreen Tests and/or LABType Tests).
4. Once you are done assigning tests to all the selected samples, click Save to save the worklist.
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Creating a Plate Design
Note:
The Plate Designer feature is available only if you have SQL 2005 and above installed.
Plate Designer functionality in HLA Fusion Research software gives you the flexibility to organize and plan your
samples in a plate format that is ready for processing through the Luminex system. You must first create a sample
worklist (see Creating Sample Worklists, p. 142).
1. Select LABXpress > Plate Designer from the main HLA Fusion Research menu.
2. Select the Assay type.
3. Select the New Plate button option if you want to create a new plate; otherwise, select Edit Plate to change an
existing plate.
4. Click Go.
5. For a new plate:
-
Enter a unique plate name
-
Use the following search criteria to search and select the samples you want to add to plate for testing:
•
Test name
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•
Sample name
•
Sample collection date (From and To date)
To edit a plate, modify the data in the fields listed above.
6. Click Search to display a list of samples that match your criteria.
7. Select samples (one or many at a time), and use the left << button to assign these samples to a well in the
plate. Repeat this until you have completed your plate design.
8. Click Save to save your plate design.
9. Click Print if you want to print your plate design.
Creating a Run Design
If you have not yet created a plate design, see Creating a Plate Design, p. 143.
1. Select LABXpress > Run Designer from the main HLA Fusion Research menu.
2. Select the Run Assay Type.
3. Select the New Run button option if you want to create a new plate; otherwise, select Edit Run to change an
existing run.
4. Click Go.
5. For a new run:
-
Enter a unique run name
-
Use the following search criteria to search and select the samples you want to add to plate for testing:
•
Plate design name
•
Plate design creation date (From and To date)
To edit a run, modify the data in the fields listed above.
6. Click Search to display a list of plate designs that match your search criteria.
7. Select the check boxes in the IsUsed column for each plate design you want to include, and click the assign button
to add all the selected designs to the run.
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Note:
You can select a maximum of 8 plate designs per run design.
The bottom portion of the screen displays the resources and volumes required to make this run on LABXpress.
To remove a plate from the Run, select the check box in the IsExists column for that plate, and click the Remove
button .
8. When you complete the run design, click Save.
Determining the Run Type
The following table lists the types of LABXpress runs you can select for each assay:
Run Type
Definition
LABScreen Plate
Driven Custom
You select a run from the plate-based run designs you have created for this assay type
in HLA Fusion Research LABXpress Run Designer (see Creating a Plate Design,
p. 143).
LABScreen Plate
Driven Express
You create a run on the fly, using pre configured plates. This requires you to supply a
barcode for each plate you include.
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Run Type
Definition
LABScreen Sample
Driven Custom
You select a run from the sample-based run designs you have created for this assay
type in HLA Fusion Research LABXpress Run Designer (see Creating a Plate Design,
p. 143).
LABScreen Sample
Driven Express
You create a sample-based run on the fly, using pre configured plates. This requires
you to supply a barcode for each plate you include.
LABType Plate
Driven Custom
You select a run from the plate-based run designs you have created for this assay type
in HLA Fusion Research LABXpress Run Designer (see Creating a Plate Design,
p. 143).
LABType Plate
Driven Express
You create a run on the fly, using pre configured plates. This requires you to supply a
barcode for each plate you include.
Starting and Monitoring a Run
For step-by-step instructions on starting and monitoring a run through LABXpress to process samples automatically,
refer to the LABXpress™ User Manual.
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Index
A
G
Activation products to interface with Fusion 134
Analyze data menu 13
Grouping results by date 12, 13
Grouping results by product 11
B
H
By date grouping of Navigator results 12, 13
By product grouping of Navigator results 11
Help menu 15
HLA Fusion
features 1
Home pages 9
key system settings 6
main menu options 13
navigating the user interface 5, 13
program updates 1
software updates 1
toolbar buttons 16
Home button 22
Home pages 9
C
Catalog reference files, managing 117
archiving 123
associating with Luminex templates 124
update form local drive or network 117
update from OLI Web site 119
viewing information 124
Changing product configuration settings 129
LABType and Micro SSP 129
ConsenSys SBT 25
Customer support 2
I
Installation qualification 135
D
Data menu 14
Default printer options, setting 131
Defaults for URL and directory paths 132
Displaying the Navigator tool 10, 11, 12, 13
by date 12, 13
by product 11
E
Exit menu 16
F
Features of the software 1
Find button 17
Forgetting your Fusion password 6
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L
Launching the Navigator tool 10
Limitations of the software program 2
M
Magnify button 19
Main menu options 13
analyze data 13
data 14
exit 16
help 15
patient info 14
profile 14
reports 14
samples 14
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utilities 15
Managing catalog reference files 117
archiving 123
associating with Luminex templates 124
update form local drive or netwrok 117
update from OLI Web site 119
viewing information 124
Molecular typing files, updating 119
allele frequency 125, 127
local code files 121
NMDP codes 120
N
Navigating the user interface 5, 13
Navigator tool
displaying 10
grouping results 11
by date 12, 13
by product 11
launching 10
results grouping 11
by date 12, 13
by product 11
Navigator tree 10
NMDP
Cross codes 51
O
One Lambda
technical support 2
Operational qualification 135
P
Password, forgetting 6
Patient button 20
Patient Info menu 14
Preview Report button 18
Print Report button 18
Print Screen button 19
Printer options, setting up defaults 131
Product configuration settings, changing 129
LABType and Micro SSP 129
Product Data Import button 23
Products, activating 134
Profile menu 14
Program updates 1
Reporting software problems 2
Reports menu 14
Results grouping in the Navigator tool 11
by date 12, 13
by product 11
S
Samples menu 14
Select CSV Files window 35
Show Navigator button 20
Software features 1
Software limitations 2
Software problems, reporting 2
Software updates 1
Software validation 135
System settings 6
character length 8
file permissions 7
screen resolution 6
T
Technical support 2
Toolbar buttons 16
Find 17
Magnify 19
Patient 20
Preview Report 18
Print Report 18
Print Screen 19
Product Data Import 23
Related Records 21
Sample Drop Down 23
Show Navigator 20
Side By Side Analysis 22
U
Updating molecular typing files 119
allele frequency 125, 127
local code files 121
NMDP codes 120
URL and directory paths, setting 132
User interface, navigating 5, 13
Using the Navigator tree 10
Utilities menu 15
V
Validating software 135
R
Related Records button 21, 23
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