User Manual LABScreen HLA Antibody Detection

User Manual LABScreen HLA Antibody Detection
User Manual
LABScreen® HLA Antibody
Detection Software
LABScreen v. 3.1
2007/02
For In Vitro Diagnostic Use.
20001 Kittridge Street, Canoga Park, CA 91303-2801
Tel: (818) 702-0042 Fax: (818) 702-6904
www.onelambda.com
Advancing Transplant Diagnostics
Manual_Template_R1
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©Copyright
2007 One Lambda, Inc.
LABScreen is a registered trademark of One Lambda, Inc.
™LABScan 100 is a trademark of One Lambda, Inc.
®Luminex is a registered trademark of Luminex Corporation.
®
Windows is a registered trademark of Microsoft Corporation.
®
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. The software may
be used to aid in suggesting results, but should not be used as the sole method for determining
reportable results. The 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.
Table of Contents
Chapter 1: Introduction
Disclaimer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Product Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
LABScreen Mixed. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
LABScreen PRA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
LABScreen SA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
About this Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Installing LABScreen Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5
5
5
6
6
6
6
7
Chapter 2: Main Menu and Controls
LABScreen Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
File Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
LABScan 100 Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Analysis Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Maintenance Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Reports Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Update Parameters Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Main Window Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Chapter 3: Analysis
File Naming Conventions for LABScreen Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Importing PRA and Single Antigen Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Importing Mixed Antigen Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Importing Quantiplex (MESF) Beads Data (For Investigational Use Only). . . . . . . . . . . . . . . .
Reprocessing a LABScan 100 File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Analyzing Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Viewing Results by Antigen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Adjusting Cutoffs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Color Coding in Revise Cutoff/Raw Data Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Changing Parameters Locally (Temporarily) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Excluding Antigens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Processing Multiple Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
15
15
19
21
24
24
31
34
35
36
36
37
Chapter 4: File and Data Maintenance
Archiving Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Retrieving Archived Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
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Packing the Database. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Rebuilding the Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Chapter 5: Parameters and Algorithms
Updating Global Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Reaction Definitions, Specificity Selection Methods and Report Header Information . . . .
Changing the Date Format. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Advanced Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
PRA Parameter Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
SA Advanced Parameter Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Mixed Advanced Parameter Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
MFI to MESF Conversion Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Calculation of the Normalized BackGround Ratio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Determination of Positive/Negative Cutoff. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Reaction Positive Classification Guidelines and Formulas. . . . . . . . . . . . . . . . . . . . . . . . . .
Statistical and Scoring Formulas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Antigen Specificity Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
41
41
42
42
42
43
44
45
47
47
48
49
50
51
Appendix A: LABScreen Reports
LABScreen Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Reports Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Patient Antibody Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Patient Antibody Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Patient Cell Typing Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
LABScreen Mixed Data Full Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Mixed Data Individual Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Mixed Data Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
PRA Data Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
SA Raw Data Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
SA Analysis Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Antigen Distribution Listing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Sample Raw Data Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Class and Class II Panel Listings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Class and Class II Analysis (Antibody Screening) Reports . . . . . . . . . . . . . . . . . . . . . . . . . 67
Class I and Class II Analysis (Antibody Screening) Reports (Reversed) . . . . . . . . . . . . . . . 68
Class I and Class II Analysis (Antibody Screening) Reports (2 x 2 Listing) . . . . . . . . . . . . 69
Changing Report Paper Size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Index
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Chapter 1: Introduction
Welcome to LABScreen® Software. LABScreen Software is an HLA screening application that aids users of
One Lambda products with identifying the presence or absence of specific antibodies in an individual’s serum
sample.
This software imports data from the LABScan™ 100 analyzer for the purpose of suggesting HLA antibody
specificities. LABScreen Software can generate a large variety of reports and is designed to store large
amounts of patient demographic data and analysis result from previous testing to aid in the understanding of a
patient’s histocompatibility status.
Disclaimer
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. The software may be used to aid in suggesting results, but should not be
used as the sole method for determining reportable results. The 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.
Product Description
One Lambda LABScreen antibody screening tests use color-coded microbeads coated with purified Class I or
Class II HLA antigens to detect Class I or Class II HLA antibodies in human sera. Up to 100 beads may be
combined in one suspension for a single test. The sera to be tested are incubated with LABScreen beads. HLA
antibodies present in the test sera bind to the antigens and are then labeled with R-Phycoerythrin (PE)-conjugated goat anti-human immunoglobulin G (IgG). (IgG is the major circulating antibody in mammals and participates in many immune responses.) The LABScan 100 flow analyzer detects the fluorescent emission of the
phycoerythrin from each bead as it is extracted from the tray well. The reaction pattern of the test serum is
compared to the lot-specific worksheet defining the antigen array. From this comparison, percent PRA and
HLA specificity can be made. If done by hand, this comparison is a tedious and error-prone undertaking.
When done using LABScreen Software, the assignments can be made in seconds.
In a typical LABScan data collection session, the analyzer will continue to draw beads from the tray well until
the minimum bead count threshold has been reached by all the beads. This minimum bead count threshold is
generally set at 100 beads.
LABScreen products are available in three principal versions which are listed below in the order of increasing
(i.e. finer) resolution:
LABScreen Mixed
The Mixed Antigen test contains a mix of both Class I and Class II antigens and is used to detect Class I and
Class II antibodies in a single test. The bead set in a Mixed Antigen panel consists of 10 to 17 beads: 5 to 9 test
beads with Class I antigens, 3 to 5 test bead with Class II antigens, plus negative and positive control beads.
Each of the test beads is coated with cloned antigens of up to eight different cell line. The Mixed assay is
typically used a preliminary screening test. For reasons of economy the bead set is restricted in number. If a
Mixed analysis detects antibodies of interest, the researcher will then subject the serum to PRA testing.
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LABScreen PRA
Panel Reactive Antibody tests detect antibodies and their specificities against the HLA antigens in panels of
Class I or Class II antigens separately or Class I and Class II antigens simultaneously. Class I and Class II
PRA panels contain approximately 55 and 35 beads, respectively, not counting a positive and negative control
bead in each lot. In the PRA and Mixed assays, the antigens on a single bead may react with multiple
antibodies, thus providing an ambiguous screening result by itself. By comparing the reactions of multiple
beads, it is possible to determine which antibodies are present in the tested serum.
LABScreen SA
While the beads used in the other LABScreen tests may exhibit multiple specificities, each bead in a
LABScreen Single Antigen assay is specific for a single antibody. Single Antigen assays are used to confirm
the presence of specific antibodies suggested by an earlier PRA test.
About this Manual
This manual contains information helpful in using the LABScreen software and consists of the following
chapters:
Chapter 1, Introduction, the current document, contains descriptions of the products in the LABScreen family,
an overview of the manual, system requirements, and installation instructions.
Chapter 2, Main Menu and Controls, provides a survey of where to find various LABScreen analysis and
maintenance functions.
Chapter 3, Analysis, provides step-by-step instructions for performing both Class I and Class II analyses. It
includes details on changing computer-assigned specificities, adjusting cut-off values, and displaying reaction
patterns.
Chapter 4, File and Data Maintenance, explains how to perform such routine housekeeping tasks as archiving
and retrieving data, and packing and rebuilding the database.
Chapter 5, Parameters and Algorithms, provides instructions for setting up global program parameters and
includes the statistical formulas used in the LABScreen analysis.
Appendix A, LABScreen Reports, provides examples of LABScreen analysis results reports, data reports and
panel listings.
System Requirements
The following is required to successfully install and run LABScreen software.
•
IBM compatible PC with Pentium III processor
•
5 Gigabyte hard drive
•
256 megabytes RAM
•
VGA display
•
Windows 2000 or Windows XP operating system
•
Luminex interface software version 1.7 or IS2.2
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Installing LABScreen Software
If you do not yet have the LABScreen software installed on your computer, follow these instructions to install
it.
1
Close all other Windows applications before starting the installation process.
2
Insert the One Lambda CD in your CD ROM drive.
3
From the Windows Task Bar, select Start > Run.
4
From the Run window, in the Open box, type in the location of your CD ROM drive followed by a back
slash and Labscrn31.exe (e.g., D:\Labscrn31.exe).
•
5
Or, click the Browse button to select your drive, and then double-click the Labscrn31.exe file.
Click OK to begin the installation process. The install wizard usually places the LABScreen software in
your C:\labscreen directory.
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Chapter 2: Main Menu and Controls
This section provides a brief overview of menu functions and links to detailed discussions in subsequent sections of the manual. All program functions can be accessed from the main menu or from interfaces accessible
from the main menu. A small number of tasks can be executed directly from the tool bar below the main menu.
LABScreen Menus
File Menu
File options include database record archival and deletion, data exportation and database table rebuilding.
Archive and Delete Data – tools to save four categories of data to archive files with options to physically delete
records marked for deletion. Archived data are saved to.arf files to a user-specified location. Data archival is
intended to help the user reduce the number of samples present at any given time in the LABScreen database,
thus facilitating sorting and analysis of the existing records.
Retrieve Data
– tools to retrieve the archived data as described above.
Export Data – a utility that exports reaction data and Class
I and Class II results for the specified sample IDs in
dBase, Excel or ASCI text format. Mixed Assay data can be exported only in Excel format.
Print Setup
– this is a standard system function that requires no comment.
Index Rebuild – this function reindexes database tables that may have become damaged as the result of a system malfunction.
Pack Database – this function packs the database to reduce storage requirements. Records that have been
marked for deletion are physically deleted.
Edit Menu
The edit options access system text-editing functions that require no comment. They can be invoked with the
keyboard combinations that are common to all Windows applications.
LABScan 100 Menu
Use these options to import data files generated by the LABScan 100 analyzer or to reprocess the data in files
that have already been imported. Typically, the main purpose of reprocessing is to analyze imported data using
a different product lot. From the user’s perspective, the main distinction between data importation and data
reprocessing is as follows:
•
when importing data, the user locates and selects a Luminex .csv file by means of a standard Windows
find file dialog;
•
when reprocessing data, it is only necessary to select the session name of the file from a drop-down
menu that contains session names of all the .csv files currently loaded into the database. Conveniently,
the default session names of the imported files are the same as their original filenames.
In both cases, you must supply the appropriate catalog ID(s) and lot number(s) for the assay. In all other
respects, import and reprocessing steps are identical.
These options are available:
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Import/Reprocess LABScreen PRA/SA Data – import/reprocess .csv files for full PRA/SA assays. These may be
either Class I, Class II, or combined Class I and Class II assays.
– import/reprocess .csv files for 10-17 Bead
Mixed assays. Mixed assays always contain a mix of Class I and Class II antigens.
Import/Reprocess LABScreen Mixed (10-17 bead format) Data
Import MESF Beads Data –
import MESF (Molecules of Equivalent Soluble Fluorophores) beads data. This
data is used to generate MFI to MESF conversion formulas.
– the 4-bead assay type is an obsolete product line.
However, if you do have 4-beads data that you wish to revisit, the application can be configured to import/
reprocess 4-bead .csv files as follows:
Import/Reprocess LABScreen Mixed (4-bead format) Data
1
Exit the LABScreen application.
2
Assuming that LABScreen has been installed to the default C:\ location, navigate to the
C:\labscrn\myflags folder. This folder contains a number of flag files that instruct the application to ignore
data for obsolete products.
3
Locate the file NO_LSM_4BEADS.FLG and rename it to LSM_4BEADS.FLG. When you next launch
LABScreen, the four-bead Import/Reprocess options will be enabled.
Analysis Menu
The Analysis options provide access to the LABScreen analysis functions. The options are briefly described
below. See Chapter 3, Analysis, for usage details.
Serum Information –
provides access to Class I and Class II Analysis Details (specificities tables) as well as
Class I and Class II Antibody Histories (draw, test, reaction data and product tested against) for the samples in
the database ordered by Serum ID. These tables contain data for all samples that have been imported into the
LABScreen database.
A similar set of Serum Information tables can be accessed by selecting Maintenance > Serum Information from
the main menu. These latter tables contain data only for those samples whose analyses have been reviewed and
Saved (i.e. accepted) from within a Class I or Class II Analysis Results window (Figure 3-13).
HLA Typing Information –
provides access to Class I and Class II serological typing results from LABScreen
analyses and Class I and Class II DNA typing results from LABType analyses. Each record is identified by
Cell ID.
The Serological and DNA panels are editable forms in which you can modify the current typing results by
making different Class I and Class II antibody and allele assignments.
A similar set of Cell Information tables can be accessed by selecting Maintenance > HLA Typing Information
from the main menu. These latter tables contain data only for those samples whose analyses have been
reviewed and Saved (i.e. accepted) from within a Class I or Class II Analysis Results window (Figure 3-13).
Analyze by Batch –
allows you to perform analyses on an entire previously imported PRA or Mixed Antigen
batch or on selected sera contained in the database. Serum selection criteria include By Class within the specified batch or By Range of contiguous serum records in the database. Other search filters include by technician
ID (the ID entered when imported a LABScan data file), test date, catalog ID/lot number, or sera that have not
yet been reviewed, i.e. whose analysis results have not been accepted (Saved).
Note:
When specifying multiple sera, your selection must observe the Range Rule: the end-of-range selection must follow the start-of-range selection in the Serum listing. To specify a single Patient, enter the
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same Patient ID in both the start and start-of-range fields. The Range Rule applies throughout the
selection functions of LABScreen.
Analyze Class I / Class II / Class I & II –
use this to perform the respective analyses on a single serum.
Analyze Single Antigen – allows you to perform a batch analysis on a previously imported Single Antigen data
file, or on selected sera within the database. Serum selection criteria are identical to those described above for
PRA or Mixed Antigen Analyze by Batch option.
Analyze Epitopes
– not yet implemented
Maintenance Menu
This menu provide tools for reviewing and editing a variety of records in the LABScreen database. Options
include:
Readings – NIH scores, catalog lot data, and raw data for each tested serum in the database. The serum ID, cat-
alog lot data, test date and reader ID can also be edited here.
Antigen – names, loci, pertinent leukocyte cell types for the
antigen or allele (T or B) and allelic subtype infor-
mation for each antigen and allele in the database.
Public Antigen –
member antigens in CREGs (T or B) and edit fields for modifying or adding member anti-
gens.
Serum Information – analysis results and demographic information for samples that have been Saved/Accepted
upon analysis in the Class I or Class II Analysis Results window (Figure 3-13). Results for samples that have
not yet been Saved/Accepted can be accessed by selecting Analysis > Serum Information.
HLA Typing Information –
accesses tables that display cell demographic information, serological antibody typing from LABScreen analyses and DNA allele assignments from LABType analyses for samples that have
been Saved/Accepted. Similar tables for samples that have not been Saved/Accepted can be accessed by
selecting Analysis > HLA Typing Information.
– the principal interfaces where analyses of Class I and Class II results are
carried out. See Analyzing Data, p. 24.
Class I / Class II Analysis Results
LABScan 100 Raw Data – accesses panels that display raw data for each tested serum including PC and NC values, session ID and NIH scores.
Archive LABScreen Info – performs an archiving function
described under the File > Archive and Delete Data topic.
for LABScreen catalog information similar to that
Update LABScreen Info – performs a retrieval function for LABScreen catalog information similar to that
described under the File > Retrieve Data topic.
– a tool for loading product catalog information into the database and
assigning a new lot number to the product.
Add New Lot for LABScreen Mixed
Reports Menu
Options allow to generate several of the most commonly produced LABScreen reports. A number of other
reports types are available and are discussed in Appendix A, LABScreen Reports.
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Update Parameters Menu
LABScreen program parameters can be set globally by selecting the appropriate Update Parameter functions
accessed from the main menu. These settings are discussed in Chapter 5, Parameters and Algorithms.
Many of these parameters can be temporarily set to local values on the sample level in forms accessible from
the Analysis windows (see Class I Analysis Results Window, p. 26).
Main Window Controls
The control panel icons and buttons allow you to move through records within a database table, to perform
basic file management operations, and to access some of the most commonly used functions in the program.
The Navigation, New record, Cancel and Save icons are enabled when you select the Analysis, Maintenance
or Report menu options.
Many of these controls are conventional and require little comment.
Table 2-1: Main Menu Controls
Control
Function
Comments
Displays the first/last record of the currently
active database table.
There are no keyboard equivalents for this button.
Displays the previous/next record of the currently active database table.
The up/down arrows have the
same effect.
Creates a new record in an editable table.
If the table is read-only, this icon
will be disabled.
Discards all changes made since the last
Save.
In many places in the program
this button closes the current
window and returns to the previous window; when analyzing
multiple samples, it ends the
current analysis and proceeds to
the next.
Saves any changes to the database.
Generally using the Save icon to
commit a change avoids the
Save confirmation dialog box.
The Alt + S keystroke combination is equivalent to using an OK
or Save button.
Exits the program when in the home page.
Elsewhere in the program this
button serves only to close the
currently active window.
Cell Info Update
Duplicates the function of
Maintenance > HLA Typing
Information.
Sera Info Update
Duplicates the function of
Maintenance > Serum
Information.
Analysis
Duplicates the function of
Analysis > Analyze Class I and
Class II.
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Table 2-1: Main Menu Controls
Control
Function
Comments
Import PRA
Duplicates the import function of
LABScan > Import/Reprocess
LABScreen PRA Data.
Import Mixed
Duplicates the import function of
LABScan > Import/Reprocess
LABScreen Mixed (10 - 17
bead format) Data.
Import SA
Duplicates the import function of
LABScan > Import/Reprocess
LABScreen SA Data.
Update Parameters
Duplicates the function of
Update Parameters > Update
Parameters.
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Chapter 3: Analysis
File Naming Conventions for LABScreen Products
The first step in carrying out a LABScreen analysis is to import a batch file of serum information that has been
generated by the LABScan™ 100 analyzer. In some cases, the LABScreen Catalog IDs and Lot numbers are
not immediately obvious to the user.
The length of product names in LABScreen Software is limited to twelve characters. To accommodate product
files name for LABScreen Single Antigen products which may consist of as many as three products with different Catalog IDs and Lot numbers, these file naming conventions are followed:
The Catalog IDs and Lot number combinations of two groups may include one of four alphanumeric characters. The absence of an alphanumeric character indicates that the lot number is the same for both groups.
•
A = The lot as written for group one and the lot number as written plus one for group 2
•
B = The lot as written for group one and the lot number as written plus two for group 2
•
Z = The lot as written for group one and the lot number as written minus one for group 2
•
Y = The lot as written for group one and the lot number as written minus two for group 2
Please refer to the following examples:
•
LS1A1&2 007 - designates LS1A01 Lot #007 + LS1A02 Lot #007
•
LS1A1&2 06A - designates LS1A01 Lot #006 + LS1A02 Lot #007
•
LS1A2&3 05B - designates LS1A02 Lot #005 + LS1A03 Lot #007
•
LS1A1&2 04Z - designates LS1A01 Lot #004 + LS1A02 Lot #003
•
LS1A1&2 07Y - designates LS1A01 Lot #007 + LS1A02 Lot #005
The Catalog IDs and Lot number combinations of three groups consist of the character “C” plus three numbers
which designate the lot numbers for each group.
•
LS1A123 C557 - designates LS1A01 Lot #005 + LS1A02 Lot #005 + LS1A03 Lot #007
•
LS1A123 C657 - designates LS1A01 Lot #006 + LS1A02 Lot #005 + LS1A03 Lot #007
•
LS1A123 C775 - designates LS1A01 Lot #007 + LS1A02 Lot #007 + LS1A03 Lot #005
Importing PRA and Single Antigen Data
The importation of PRA and Single Antigen files is almost identical. Batch importation is a multi-step process
(Figure 3-1).
1
Click the ? to the right of the Luminex Data File field to open a standard Windows Find File dialog and
locate the LABScan .csv file.
2
Enter a two-character Technician ID to identify you on the analysis reports. You will need this identification later when you want to search for and continue the analysis on samples that you personally have
loaded into LABScreen.
3
Use the drop-down lists to specify the appropriate catalog ID(s) for the analysis. If carrying out both
Class I and Class II analyses on the sera, specify a Class I catalog in one field and a Class II in the other. It
does not matter which field you use for which Class. In any case, LABScreen will perform Class I analyses on each sample first.
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4
•
If you are analyzing samples using a Single Antigen product that combines two or three different catalog IDs and Lot numbers, see File Naming Conventions for LABScreen Products, p. 15, for guidelines
on choosing the correct catalog ID.
•
If you specify a catalog that does not match the assay, LABScreen will generate a bead conflict error
message.
•
If you specify a catalog that is not used, (say an unnecessary Class II catalog/lot when only Class I
sample data are available), and then re-import the same batch later and specify the appropriate catalog(s), LABScreen will generate a data cleanup message indicating that the unusable or old catalog
data is being purged from the database. You can ignore the message.
Select one or more report options:
•
Print Antigen Distribution Table with Report
– see Figure A-10, Typical Antigen Distribution List-
ing for an example.
•
Preview Report First – displays a preview of the data report with results (pos/neg/grey area) for each
bead for each Class. The report of each sample is on a separate page. See Figure A-4, Mixed Data Full
Report. (This is the default.)
•
Analyze After Import – imports all serum data, then performs the same function as when you select
Analysis > Analysis by Batch > By Session ID which displays the Antibody Analysis Results Table for
each sample in turn (Figure 3-13, Class I Analysis Results Window). You can move to the next serum
by clicking the Save button, the Return button or by pressing <Return>.
•
5
– imports all serum test data, performs analyses and sends
reports for each serum directly to the printer without user intervention, thus printing reports for all
imported samples automatically. Note that although the serum analyses have been performed by the
program, the results have not yet been Saved (accepted) by a researcher. Use this option when you
want LABScreen to carry out preliminary analysis of a batch of samples that you will review at a later
time.
Analyze non-prompt mode to printer
You can interrupt and terminate the analysis cycle by pressing <S> between samples.
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Table 3-1: Test Figure Table
Figure 3-1: Import PRA/SA Data
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6
Accept the default background values option. (These are the OLI defaults for the product).
Occasionally you may wish to specify an alternative set of background values from a specific tray well in
the batch. This means that all analyses for the entire batch would use those data values as background values.
To specify an alternative set of background values using data values from one well of the batch:
•
Clear the Use Default Background Values check box.
•
Open the batch’s LABScan .csv file in Excel and locate the column containing the Sample IDs.
LABScreen will use the data values in the row corresponding to the data type which LABScreen has
been set up to use. This is typically the median.
Figure 3-2: Batch Data File in Excel
•
Copy the Sample ID from the .csv file into the Negative Background from ID field. If you have entered
an invalid Sample ID, LABScreen will generate a warning message.
•
Close the .csv file, making sure not to save it as an Excel file.
When you run an analysis of the sample whose values you have specified to use as background values,
note that all the results are zero. This is expected inasmuch as all readings for that well are cancelled out
by the background values you are now using for the entire batch.
7
If you do not want to include MFI to MESF conversions in the reports, skip to Step 8.
In some cases you will want to use MESF calibration data for the Luminex machine that was used to collect the data for the samples you are analyzing in order to compare samples collected on different dates.
To activate MFI to MESF conversion:
•
Check the unlabeled box at the upper right of the Import/Report dialog to display the MFI to MESF
conversion table which shows the current values used in the regression routine that generates the conversion formula.
•
The slope and intercept of the fitted curve (a straight line) are shown above the table. The RR value
indicates the goodness of fit. By default the calibration curve is based on readings for the five beads
listed in the first column of the table. (Figure 3-3)
•
You can modify the values used to generate the conversion formula by selecting the Update Parameters > MFI to MESF Conversion Settings option from the main menu.
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Figure 3-3: Current MFI to MESF Conversion Curve
8
Choose the execution mode:
•
Report Only
– generates the LABScreen SA or PRA Raw Data Report without creating any records to
the database.
9
– imports the data, creating records in the database without generating a report.
•
Import Only
•
Import and Report
– imports the data, creating records in the database and generates reports.
When you first import the Luminex data, you have the option to Analyze After Import which starts the
analysis automatically upon import. See Analyzing Data, p. 24 for details.
Importing Mixed Antigen Data
The steps followed when importing Mixed Antigen data are largely identical to those when importing PRA
and Single Antigen data (Figure 3-4). There are, however, different reporting and background value specification options.
1
Just as when importing PRA or SA data:
•
Locate the Luminex Data File
•
Supply your two-character Technician ID
•
Specify the LABScreen product by Catalog ID and Lot #.
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Figure 3-4: Import Mixed Data
2
Choose the report output options:
– and/or one or more of the following:
•
Preview Report
•
Full Report – Class I and Class II results (Overall and for each Bead) for all samples in the batch, four
samples per page; includes raw data, NBG Ratio, and bead count; report indicates if background values are default, specified by Sample ID or manually entered. See Figure A-4, Mixed Data Full Report.
•
Individual Report – same information as in the Full Report for all samples in the batch, but with each
sample on a separate page. See Figure A-5, Mixed Data Individual Report.
•
Summary Report – summary results for each sample on a single line; report includes overall result for
Class I and Class II (Pos/Neg/Grey Area), Raw Data and counts for each sample’s NC and PC beads,
and the sample’s PC/NC ratio. See Figure A-6, Mixed Data Summary Report.
3
Choose to include MFI to MESF conversions as discussed above in Step 7.
4
Accept the default background values or specify Negative Background values by entering a Specific
Sample ID as discussed above in Step 4.
5
Alternatively, clear both check boxes and manually enter background values for the Control Beads and
Test Beads. Note that the numeric legends for the Test Beads to the left of the input fields change according to the definition of the product (Figure 3-5), but are updated only after you have pressed one of con-
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trols at the bottom of the form (Report Only, Import Data, etc.). Check these legends to make sure you are
dealing with the right product. The input fields are initially pre-populated with the default values for the
product.
Figure 3-5: Manually Entering Negative Background Values
6
You can now proceed to the analysis. See Analyzing Data, p. 24.
Note:
If you enter any Negative Background value for a test bead that is less than the minimum value threshold set globally in the LABScreen Mixed Advanced Settings, LABScreen will automatically bump the
value up to the threshold value. By default this value is 50.
Manually entered Negative Background values are not persistent. Thus, if you reprocess the same
batch at a later time, you must reenter the manual values.
Importing Quantiplex (MESF) Beads Data (For Investigational Use Only)
Note:
The new Quantiplex features are a Beta version only, and may be subject to change when the actual
OLI Bead product is released.
If you choose to include MFI to MESF data conversion, you will need initially to create manually a separate
lot for each Luminex LABScan analyzer from which you import LABScreen batch data. Moreover, you will
need to update the values for that lot on the days when it is in use so you can associate a time-stamped conversion formula with the data collected on that day by that analyzer.
In order to create a MFI to MESF conversion lot, carry out the following steps.
1
Locate a Quantiplex Bead Data sheet (Figure 3-6). This is an Excel file that will be provided to you by the
laboratory staff who run the LABScan 100 analyzers.
2
Select Update Parameters > LABScreen MFI to MESF Conversion Settings > Update Initial Pairs to enable all
the fields in the form.
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Figure 3-6: Quantiplex Beads Data File
Figure 3-7: Creating a New MESF Conversion Lot
3
Transfer the data from the Median and SFI columns in the Quantiplex Beads Data Sheet (Figure 3-6) to the
Current MFI and MESF columns in the MFI to MESF Conversion Settings form (Figure 3-7). Note that the
Beads ID numbers are not necessarily in ascending order, but the EFI values are. Make sure that the order
in the Conversion Settings fields is the same as in the Beads Data Sheet.
4
Enter a name in the Save As Lot # field and press Save As. (You don’t need to clear the Update Default Values check box as this option applies only to the simple Save button directly above it.)
5
You can confirm the existence of the new conversion lot in the LABScreen database table by accessing the
MESF Lot Selection look-up (Figure 3-8). Do this by clicking the search button (?) to the right of the Lot
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# field at the top of the MFI to MESF Conversion Settings form. After you have confirmed that the new
record is there, close this form and return to the main menu.
Figure 3-8: Lot Selection Look-Up Table
6
Select LABScan 100 > Import MESF Bead Data to access the like-named form. It should now display the
newly created lot in the MESF Beads Lot # field (Figure 3-9). Click the browse button (?) to locate a
Luminex .csv file containing LABScan calibration data. The filenname probably contains the characters
QPLX, Quantiplex, or the like.
Figure 3-9: Importing MESF Beads Data
7
Click Import Data. If you have chosen a compatible conversion file, LABScreen will display a “Bead
Number Matched” message, then briefly display the linear conversion formula associated with that lot.
8
When you next import any kind of session data (PRA, Single Antigen or Mixed Antigen), note that the
current MFI to MESF Conversion Lot appears in the Lot # field in the upper right corner of the Import/
Report form (Figure 3-10).
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Figure 3-10: Import/Report Dialog Detail
9
You can use the Lot # browse button (?) to select a different calibration lot for a different Luminex
machine, or you can use the Updated browse button to select an updated calibration lot with a different
time stamp for the same machine (Figure 3-11).
Figure 3-11: Different Time-Stamped Versions of Conversion Record
Reprocessing a LABScan 100 File
If you wish to reanalyze the same LABScan data using a different product lot (usually a newer one), you can
reprocess a LABScan 100 file that has been previously imported. Follow these instructions:
1
Instead of providing a Luminex data file name as in a regular import, select the Luminex session name
from the pull-down.
2
Specify the different product(s).
3
All other processing options are the same as when importing.
Analyzing Data
If you check the Analyze After Import option when importing the LABScan data, LABScreen immediately
proceeds to analysis. If you choose to only import the data by leaving the Analyze After Import option
unchecked, you will need to start up the analysis after the import.
1
On the Main menu, click Analysis and then select one of the following:
•
Analyze by Batch – use this option to process multiple samples, one after another; See Processing
Multiple Samples, p. 37.
•
Analyze Class I – use this and the following options to analyze one sample at a time.
•
Analyze Class II
•
Analyze Class I and Class II
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The three single-sample options invoke the LABScreen Antibody Screening window (Figure 3-12). When
first accessed, it will not be populated with values. Later, if you decide to analyze another sample, this
window will show the results of the just-completed analysis.
Figure 3-12: LABScreen Antibody Screening before Sample Selection
2
Select a Sample ID by clicking on the question mark (? ) next to the Sample ID field (Figure 3-12), and
selecting an ID from the pick list.
If you check the Update Demographics option, the program will open the Sample Information demographic information form before performing the analysis. The demographics form can also be accessed
from other points in the program.
3
The analysis starts as soon as you select a Sample ID or finish updating the demographic information. The
analysis results appear in the full Analysis Results window (Figure 3-13) which contains five panels. Each
panel will be discussed separately.
•
Specificities Table (Figure 3-14)
•
Percent Positives Panel (Figure 3-15)
•
Control Panel (Figure 3-16)
•
Chi-Squares Table (Figure 3-17 and Figure 3-18)
•
CREG Display (Figure 3-19)
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Figure 3-13: Class I Analysis Results Window
Figure 3-14: Analysis Result Specificities Table
Specificities Table – this table (Figure 3-14) displays statistical results for the antigens that qualify as
specificities for the sample (R-Value > 0.25 and Score > 2). LABScreen displays its assignments in the
Overall column.
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The area outlined in red contains editable fields. You can delete a computer assignment or add your own
antigens to check the effect of the change on the statistics. If you attempt to include an antigen that does
not belong to the panel, LABScreen will display an error message.
When you make any edit to the table, the small C (Computer) in the upper left changes to M (Manual). The
product(s) used in the analysis are displayed in the Cat IDs Analyzed field beneath the table.
Percent Positives Panel
– this panel displays cumulative percentages for each category of NIH scores
(Figure 3-15).
Note that the definitions of score assignment (2, 4, 6, 8) reflect the global settings made in the Update
accessed from the main menu, and do not reflect any local or temporary settings made for the particular sample via the Adjust Cutoffs functions (Figure 3-16). Similarly, the reaction
definitions reproduced in report footers reflect global and not local settings.
Parameters > Settings dialogs
Figure 3-15: Percent Positives Panel
•
Control Panel – the buttons in this panel (Figure 3-16) control the analysis functions of the Analysis
Results window and are discussed in some detail in Table 3-2, Analysis Window Controls. A further
set of controls used when adjusting cutoffs and setting background values is discussed in Table 3-3,
Adjust Cutoffs and Change Background Controls.
Figure 3-16: Analysis Window Control Panel
•
– antigens that meet the R-Value and Score criteria for being classified as specificities are displayed in the Specificities Table (Figure 3-14). By default, the R-Value threshold is 0.25,
and the Score must be greater than 2. (The Score, S, is defined as TP - FN.) The statistics of remainder
antigens, i.e. those antigens that display false positives and which do not meet the R-Value and Score
Chi-Squares Table
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criteria, are displayed in the Chi-Squares Table (Figure 3-17) when you press the Chi-Square button in
the control panel. Many samples display no remainder antigens.
Figure 3-17: Chi-Square Table for Remainder Antigens
If you access the Chi-Square table when the CREG display option has been invoked, the Chi-Square
table displays the CREGs of the remainder antigens (Figure 3-18).
Figure 3-18: Chi-Square Table for Remainder Antigen CREGs
•
– some antigens shown in the Specificities Table may be member antigens in CrossReactive groups. Possible CREGs, the complete listing of their known member antigens, and abbreviated statistics are displayed at the lower right of the Analysis Results window. More complete statistics for possible CREGs can be displayed in the Specificities Table by toggling the CREG /Agn buttons
in the control panel.
CREG Display
Figure 3-19: CREG Display
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Table 3-2: Analysis: Window Controls
Control
Function
See
Generates a Class I or Class II Antibody
Screening Report when you Save the analysis
of the current sample
Figure 3-16, Analysis Window
Control Panel
Saves any manual edits to the analysis and
Accepts the sample analysis; Saved/Accepted
samples appear in the Maintenance > Class I/
II Results tables; before being Saved/
Accepted the samples appear only in the
Analysis > Serum Information tables
Figure 3-12, LABScreen Antibody Screening before Sample
Selection
Exits the Analysis Results window without
saving/accepting the sample analysis results;
when doing batch analyses, moves to the next
analysis or sample
Performs and displays Chi-Sq. analyses for
remainder antigens (antigens not included in
the Specificities Table); if the CRGE options is
selected, the Chi-Sq. tables shows the CREGs
of which the remainder antigens are members
Figure 3-17, Chi-Square Table
for Remainder Antigens
Toggle for the Chi-Sq. button (above), hiding
the Chi-Sq. display
Prints analysis report; right-click previews the
report
Figure A-13, Class I and Class II
Antibody Screening Reports
Prints raw data report; right-click previews the
report
Figure A-11, Sample Raw Data
Report
Inverts NIH scores: 8s become 1s, 6s become
2s, 2s become 6s and 1s become 8s. LABScreen recalculates the statistical analysis
using the inverted scores, thus testing for the
absence of antigens rather than their presence.
Figure 3-14, Analysis Result
Specificities Table
Toggles with the -/+ button (above), restoring
the original NIH scores
Accesses the Sample demographic
Information form; this form can be accessed
from several places within the program.
Clears all entries from Specificities Table
including computer assignments
Figure 3-14, Analysis Result
Specificities Table
The “Eraser” resets the entries in the Specificities Table to the original computer assignments
Recalculates sample statistics after user edits
to the Specificities Table.
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Table 3-2: Analysis Window Controls (cont.)
Control
Function
See
Displays Revise Cutoff/Raw Data grid only
Figure 3-28, Color Coding in
Revise Cutoff/Raw Data Grid
Displays Revise Cutoff/Raw Data grid and
Reaction Histogram. Note that local modifications to cutoffs are not indicated in Report
footers and in the Percent Positives panel legend.
Figure 3-27 and Figure 3-28
Displays Reaction Histogram only
Allows user to temporarily change the Reaction Definition, R-Value and Score parameters, and report options for the Antibody
Screening Report for the current sample
(Figure A-13). Global parameter changes
must be made using the Update Parameters
form from the main menu.
Changing Parameters Locally
(Temporarily), p. 36
Displays the Reaction Listing by antigens
table; by default only FPs and FNs are shown;
TPs and TNs can optionally be displayed as
well; when the CREG option is invoked, the
Reaction Listing shows the CREGs of the
member antigens present on each bead
Figure 3-21, Reaction Listing
with CREGs
Displays any CREG with member antigens
among the detected specificities in the Specificities Table
Figure 3-21, Reaction Listing
with CREGs
Causes the Specificities Table to display
detected antigen specificities (default display)
Accesses a pick list containing all antigens
and alleles currently in the LABScreen database; upon selection of an antigen, displays a
Reaction Table listing all beads in the product
that exhibit the antigen
Viewing Results by Antigen,
p. 31
Excludes the specified antigens from analysis
(permanently or temporarily), thus reducing
the masking effect of those antigens on other
antigens
Excluding Antigens, p. 36
Excludes the patient’s own antigens from the
analysis if they have been entered in the
patient information.
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Figure 3-20: Reaction Listing with CREGs
Figure 3-21: Reaction Listing with CREGs
Viewing Results by Antigen
This option allows you to inspect the behavior of antigens that do not meet the R-Value and Score criteria.
Consider the analysis results of the sample shown in Figure 3-22.
•
In this example, the six antigens that meet the R-Value and Score criteria are shown in the Specificities
Table (see Antigen Specificity Calculation, p. 51):
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Figure 3-22: Class I Analysis Result for A10 233 34 W9121
•
If we consult the Chi-Square display for the remainder antigens in this sample, we can see a listing of all
the other antigens that have at least 2 FPs and an R-Value over 0.20 (Figure 3-23).
Figure 3-23: Chi-Sq Values for A10 233 34 W912 Remainder Antigens
•
We can use the Reaction by Antigen function to see how the remainder antigens reacted in the test by clicking the By Agn button and choosing a remainder antigen from the Antigen Lookup pick list.
Figure 3-24: Antigen Lookup
•
The Reaction Listing for the A11 antigen is shown in Figure 3-25. Since the point of this feature is to let us
view all beads carrying the antigen, all reaction types are displayed by default. The complete specificities
of all beads that also have the A11 specificity are listed.
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Figure 3-25: Reaction Listing for A11 in A10 233 34 W912
Table 3-3: Adjust Cutoffs and Change
Background Controls
:
Control
Function
For Details, See
Spin Box - increments/decrements all NBG
Background Values by the same amount
Applies value specified in the Spin Box
Resets BG values to Default values (before
any user edits)
Applies any changes and recalculates the NIH
scores; applies yellow alert color to any NBG
ratio that is +/- 0.25 of the cutoff between NIH
scores of 1 and 2.
Restore NBG Values to previous values
Display Cutoff Adjustment entry fields for
Weak Positive, Positive, Strong Positive &
Very Strong Positive (PRA) or Negative, Grey
Area & Positive (Mixed)
Saves changes, returns to Analysis Results
window
Cancels; returns to Analysis Results window
Saves background values for current sample
to a .BGV file.
Loads background values from a saved .BGV
file for analysis of current sample.
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Table 3-3: Adjust Cutoffs and Change Background Controls
Control
Function
For Details, See
Replaces the NBG values with the Raw Data
Values for the sample. Used when processing
a sample as a negative control serum. The
user would copy the sample results into the
local background values, then use the Save to
function to save the NBG values to a .BGV
file.
Sorts entries in Data Grid/Reaction Histogram
by descending NBG Ratio score
Sorts entries in Data Grid/Reaction Histogram
by descending NIH score; sub-sorts by
descending bead number
Sorts entries in Data Grid/Reaction Histogram
by ascending bead number
Sorts entries in Data Grid/Reaction Histogram
by descending raw data value
Adjusting Cutoffs
You can adjust cutoff thresholds numerically or graphically.
To adjust cutoffs numerically:
•
Click the Cutoff button at the bottom of the Revise Cutoff/Raw Data window to display the cutoff adjustment entry fields (Figure 3-26).
•
Enter the desired values for each threshold. The smallest increment the fields accept is 0.1.
•
Click Apply to save your adjustments. The new threshold values will be reflected in the Reaction Histogram (Figure 3-27).
•
Finally, click Save in the tool bar at the bottom left to make the changes persistent. The adjusted cutoff values apply only to the current sample.
Figure 3-26: Cutoff Adjustment Entry Fields (PRA)
To adjust cutoffs graphically:
•
Grab a cutoff line and drag it to the desired location. The coordinates in the tool tip are [Bead Position,
NBG Ratio] (Figure 3-27). The revised values also appear in the Cutoff Adjustment Entry Fields
(Figure 3-26).
•
Click the Save File icon at the bottom left to preserve the changes
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Color Coding in Revise Cutoff/Raw Data Grid
When you adjust cutoff values, beads in the data grid that have undergone a change in NIH score are marked
with a red X, and their new NIH scores are also shown in red. (See bead #17 in Figure 3-28).
LABScreen applies the yellow alert color to any NBG ratio that is +/- 0.25 of the cutoff between NIH scores of
1 and 2.
Figure 3-27: Reaction Histogram with Cutoff Lines
Figure 3-28: Color Coding in Revise Cutoff/Raw Data Grid
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Changing Parameters Locally (Temporarily)
You can change parameters for the current sample from the Analysis window. Temporary parameter setting are
not persistent. Thus, if you return to the sample at a later time, you must reset the parameters to the desired values. See Updating Global Parameters, p. 41 for details on the parameter settings.
Excluding Antigens
1
To exclude antigens from the Analysis, click Agn Exclude to access the Antigen Selection for Analysis
form. The usual selection conventions apply:
•
Shift-click to select adjacent antigens
•
Ctrl-click to select non-contiguous antigens
•
A button with single arrow moves selected antigens
•
A button with double arrow moves all antigens in the field
Figure 3-29: Antigen Selection For Analysis Window
2
A temporary exclusion applies only to the sample currently under analysis. If you return to the same
sample at a later time, you must reapply the temporary exclusion.
3
A permanent exclusion applies to the current sample and to other samples in other batches at all times.
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Processing Multiple Samples
Figure 3-30: Antibody Screening By Batch
You can process multiple samples after importing as follows:
1
Select Analysis > Analyze By Batch from the Main menu to access the LABScreen Antibody Screening
By Batch dialog (Figure 3-30).
2
Choose from among these subtractive filters to specify how you want to process the batch.
•
By Session ID –
•
By Range –
•
By Tech ID – processes samples loaded into LABScreen by the user with the specified ID; this ID is the
one supplied when you Import a LABScan file; it can be viewed and edited in the Maintenance >
Reading > Data Entry form
•
By Cat# /Lot# – as stated; Cat IDs and Lot# can be viewed and edited in the Maintenance > Reading >
Data Entry form
•
By Test Date – as stated; this ID can be viewed and edited in the Maintenance > Reading > Data Entry
processes a batch based on the session ID.
processes a specified range of samples with adjacent Sample IDs
form
•
Not Yet Analyzed – only those samples that have not yet been Saved?Accepted by the user during anal-
ysis are presented. You can revisit a Saved sample by selecting the appropriate single-sample Analyze
option and entering its Sample ID.
3
Specify whether you are analyzing Class I, Class II, or both, by checking the appropriate boxes.
•
If you want to select specific Sample IDs within each batch, check the Select Specific Samples
check box to access the pick-list shown in Figure 3-31:
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Figure 3-31: Sera ID Selection Window
•
4
Select samples by selecting or clearing the “X” next to each sample ID. Click Select All to include all
samples in the range. Click Select None to clear all check boxes.
Click Analyze to proceed.
Note:
If your criteria for selecting multiple samples produces more than 96 matches, the pick list in
Figure 3-31 will appear even if you have not checked the Select Specific Samples option. You can
deselect samples to reduce the size of the group and thus reduce the processing time.
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Chapter 4: File and Data Maintenance
This chapter provides instructions for completing these tasks:
•
Archive and retrieve serum, reaction, and results information
•
Export reaction and results information
•
Pack the database
•
Rebuild the database
Archiving Data
The Archive Data option is available from the File menu. You can archive:
•
Serum information
•
Reaction information
•
Class I or Class II analysis results
1
From the Main menu, select File > Archive and Delete Data.
2
Select one of the data options listed above.
3
Although the windows for archiving each type of data differ in some respects, the procedure for archiving
and deleting records from these tables is basically the same for each type of data. The examples in this
chapter use the Serum Information screens.
Figure 4-1: Archive LABScreen Serum Information Dialog Box
4
Specify the beginning and ending serum IDs of the range you want to archive or delete. To archive a single
record, specify the same value for both the beginning and ending serum ID in the range. Click the ? button
to select specific serum IDs.
5
Specify whether to include records marked for deletion.
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6
Specify whether to premanently delete records marked for deletion after they have been archived.
7
Supply a name for the archived file. LABScreen automatically adds the .arf extension. Click OK to create
the file. A message confirms the count of the records archived.
Retrieving Archived Data
The Retrieve Data option is also accessed from the File Menu. It is effectively the same as the Archive Data
function but only in reverse. As such, it requires no separate discussion.
Packing the Database
Figure 4-2: Pack Database Options
Use the Pack Database function to compress the tables shown in Figure 4-2.
Note:
Using the Pack Database option permanently deletes all records that are marked for deletion. Make
sure that you want to remove these records before you use this option.
Rebuilding the Index
If you experience circumstances that affect the integrity of your database tables, you may be able to use the
Index Rebuild function to restore your database tables. This function is completely analogous to the Index
Retrieval function and requires no separate comment.
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Chapter 5: Parameters and Algorithms
Updating Global Parameters
The Parameters Settings form (Figure 5-1) is used to set global analysis parameters and report defaults. It is
accessed by selecting Update Parameters > Update Parameter from the Main menu.
Reaction Definitions, Specificity Selection Methods and Report Header Information
Table 5-1: Update Parameters > Parameter Settings
Control
Function
See
Reaction Definition
Specifies NIH score threshold for determining
positive reactions in Class I and Class II
analyses.
Legend
Displays currently defined symbols for different strengths of reactions in PRA and SA
which are set in the Advanced Settings forms.
Specificity Selection
Determines whether R-Value or Score is to be
used to make the first specificity assignment
and then subsequent assignments.
The software calculates R-Values for all possible antigens, then selects the antibody specificity with the highest R-Value. Once the first
specificity has been select by the R-Value
method, the Score calculation is used to
assign the rest of the specificities.
Be advised that it may be admissible to use
the R-Value calculation for both Primary and
Secondary assignments, but it is not recommended to use the Score method for the Primary assignment.
If you choose to change the threshold values,
you should perform validation testing based
on the frequencies in your population.
R-Value, p. 50, Score, p. 50
CREG Selection
Determines whether the analysis will use
UNOS or FULLER CREGs. If no entry is
made, the analysis uses both. If one or the
other is entered, the analysis uses only that
one. By default both types are used.
Figure 3-13, Class I Analysis
Results Window
Report
Specifies which report elements are included
by default in the Antibody Screening Report;
the preset default is TP, FN and FP only.
The 2 X 2 option generates a separate report
that lists the statistics for all antigens in the
assay in the order of the highest R-Value to
the lowest.
Figure A-13, Class I and Class II
Antibody Screening Reports;
Figure A-15, Class I and Class II
Antibody Screening Reports
(2 x 2 Listing)
Headings
Institution-specific information that is included
in report headers.
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Figure 5-1: Global Parameter Settings Form
Changing the Date Format
The Select Data Format function accessed from the Update Parameters menu is self-explanatory and requires
no comment.
Advanced Settings
PRA Parameter Settings
The PRA Advanced Settings form (Figure 5-2) is used to set cutoff levels and NIH score symbols for LABScreen PRA analyses. It is accessed by selecting Update Parameters > LABScreen PRA Adv Settings from the
Main menu.
Table 5-2: Update Parameters > PRA Advanced Settings
Control
Function
Legend
States the formulas used to determine reaction strengths in assigning NIH scores.
Cutoffs
Cutoff constants used in the Reaction
Classification formulas.
See
Reaction Positive Classification
Guidelines and Formulas, p. 49
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Table 5-2: Update Parameters > PRA Advanced Settings
Control
Function
Symbols
NIH score symbols used the reports and database tables. By default these are 1, 2, 4, 6
and 8. A bead is designated as “Problematic”
is it does not have a reading.
These fields accept any characters in the
extended ASCI character set.
Legend (at bottom)
States the LABScreen default values for reference.
See
Figure 5-2: LABScreen PRA Advanced Setting Dialog Box
SA Advanced Parameter Settings
The SA Advanced Settings form (Figure 5-3) is used to set cutoff levels and NIH score symbols for Single
Antigen analyses. It is accessed by selecting Update Parameters > LABScreen SA Adv Settings from the Main
menu.
Table 5-3: Update Parameters > SA Advanced Settings
Control
Function
Legend
States the formulas used to determine reaction strengths in assigning NIH scores based
on the Working Range of the reaction.
Cutoffs
Cutoff constants used in the Reaction
Classification formulas.
See
Reaction Positive Classification
Guidelines and Formulas, p. 49
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Table 5-3: Update Parameters > SA Advanced Settings
Control
Function
Symbols
NIH score symbols used the reports and database tables. By default these are 1, 2, 4, and
8. A bead is designated as “Problematic” if it
does not have a reading. In contrast to PRA
scoring, Single Antigen NIH scoring does not
include a “6” reaction classification.
These fields accept any characters in the
extended ASCI character set.
Legend
The legend at the bottom of the form states
the LABScreen default values for reference.
See
Figure 5-3: LABScreen SA Advanced Settings Form
Mixed Advanced Parameter Settings
The Mixed Advanced Settings form (Figure 5-4) is used to set Grey Area and Positive Reaction criteria for
Mixed analyses. It is accessed by selecting Update Parameters > LABScreen Mixed Adv Settings from the Main
menu.
Table 5-4: Mixed Advanced Settings
Control
Function
Legend
State how Background values are defined.
Minimum
Sets minimum default background value for
test beads.
See
Reaction Positive Classification
Guidelines and Formulas, p. 49
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Table 5-4: Mixed Advanced Settings
Control
Function
Legend
States the initial default values LABScreen for
reference for Class I, Class II and Other (e.g.
MICA). Note that these are the initial and not
the previous settings.
Class I, Class II,
Other
Current cutoff values for Class I, Class II and
Other (e.g. MICA).
See
Figure 5-4: LABScreen Mixed Advanced Setting Dialog Box
MFI to MESF Conversion Settings
Table 5-5: MFI to MESF Conversion Settings
Control/Field
Function
Lot #
Use to locate database record containing conversion curve slope and intercept.
Update legend
Timestamp for selected record
( YYYYMMDDhhmm format)
MFI to MESF conversion activate
Activates conversion globally; when selected,
MFI to MESF conversion panel (Figure 3-3) is
automatically opened during PRA/SA and
Mixed Data Import/Reprocess.
See
Figure 3-1, Figure 3-4
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Table 5-5: MFI to MESF Conversion Settings
Control/Field
Function
Bead ID
Data pairs table accommodates up to 7 beads.
Note that the Bead ID is not necessarily
always in ascending order although the MFI
values are. Initially these fields are read only.
Current MFI
MFI values used together with MESF values
for generate the Slope and Intercept of the
conversion formula.
MESF
See above
Minimum RSQ
Minimum threshold for goodness of fit. The
conversion formula is generated from the MFI/
MESF data paris using a least squares fit. If a
linear formula cannot be generated within this
threshold, the RSQ value in the Calc panel is
flagged with asterisks.
Maximum MFI
Data pairs of beads with MFI values above
this limit are discarded before the equation fit
is made.
Calc
Reruns the least squares fit using the valid
values in the cells; then displays the updated
MFI to MESF conversion formula.
Update Initial Pairs
Enables Bead ID and MESF entry fields
Save As
Saves new conversion formula to database
table after user enters name for database
record (up to 9 characters)
Restore from Default
Reloads values from currently selected database record
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Figure 5-5: MFI to MESF Conversion Settings
Algorithms
Calculation of the Normalized BackGround Ratio
The reactivity of a test sample is calculated based on the median fluorescence values which are one of the data
type in the LABScan .csv file. The strength of the reactivity is defined as the ratio (R) of the normalized sample median to the normalized background median.
The abbreviations used in this section are defined below:
•
NBG
Normalized BackGround
SN
Median fluorescence value for Sample bead N
S NC bead
Sample-specific median fluorescence value for Negative Control bead
BG N
BackGround fluorescence value for bead N is by default a predetermined background value (from OLI reference data)
BG NC bead
BackGround fluorescence value for Negative Control bead; the negative control
bead is not coated with HLA antigen and is used to determine the non-specific
binding for each bead
For LABScreen PRA or LABScreen Single Antigen, the Normalized BackGround, NBG, for each bead is
calculated as follows:
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BG N
NBG = S NC --------------BG NC
Eq. 5-1
The Normalized BackGround Ratio, NBG Ratio, for each bead is the ratio of the median raw data value
for each bead, SN, to its Normalized BackGround, NBG.
SN
S N ⁄ S NC
NBGRatio = ----------- = -----------------------------BG N ⁄ BG NC
NBG
•
Eq. 5-2
For LABScreen Mixed, a subtractive normalization is used in which the normalized median is defined as
the median value of the Class I or Class II coated bead minus the median value of the NC bead. The NBG
ratio is thus:
S N – S NC
NBGRatio = -------------------------------BG N – BG NC
Eq. 5-3
Determination of Positive/Negative Cutoff
1
For LABScreen PRA and Mixed:
1.1 Select the NBG ratio that gives a significant shift over background fluorescent value when the background value is obtained using the negative serum in 3 - 5 replicate tests. If you prefer, test 5 - 10
serum samples from non-transfused, non-transplanted male donors to obtain an average background
value.
1.2 Validate the cut-off using 5 - 10 reference alloserum samples with defined HLA antibody specificity.
The NGB ratio values for the expected positive antigen reactions should be above the cut-off.
1.3 Additional positive/negative reactions may be noted. If necessary, adjust the LABScreen assay cut-off
to match the sensitivity of a previously accepted antibody detection assay.
2
For LABScreen Single Antigen:
2.1 Test negative control serum or several negative serum samples by following Step 1.1 above.
2.2 Define Working Range, WR:
WR = NBG max – NBG min
Eq. 5-4
2.3 Define cut-off points within the Working Range:
Relative Cutoff = X% WR ( NBG max – NBG min ) + NBG min
Eq. 5-5
where X% = user-defined percent cut-off point within the Working Range for negative(1), gray
area(2), weak positive(4) or strong positive(8).
The cut-off points are relative to the maximum and minimum NBG ratios. Therefore, the definition of
Negative, Weak Positive and Strong Positive will change for every sample.
2.4 Set criteria to define positive vs. negative reactions, for example, where R is the reading value:
•
If the ratio of Rmax/Rmin > 8, then apply the calculation in Step 2.3. If the serum test value is greater
than a given % cut-off, assign the corresponding NIH score for that particular bead reaction.
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•
If the ratio of Rmax/Rmin < 8 AND
If Rmax > 5, then Rmin should be adjusted to one half of the Rmax and the relative NBG ratio cutoff
should be re-computed based on the adjusted Rmin. The reaction is then scored as above.
If Rmax < 5, then the reaction of the test serum with that bead is negative. Assign a score of “1”.
Reaction Positive Classification Guidelines and Formulas
General parameters for LABScreen assays
•
Bead counts should not be lower than 50 events per bead
•
Patient samples with high background may be due to
•
•
Hydrophobicity of the plastic or the antigen binding process can effect non-specific binding
•
Patient therapies such as immunoglobulin (IVIG), Rituxan, or thymoglobulin (ATG)
Negative Control bead (#001) median fluorescence should be lower than 1500; NC beads are blank (not
coated with HLA antigen)
NC bead fluorescence indicates the level of non-specific binding
Abnormally low NC values can be due to high albumin/IgG ratios observed in dialysis and plasma
pheresis patients
•
Positive Control bead (#002) median fluorescence should be higher than 500 and at least twice the NC
value; PC beads are coated with purified human IgG
PC bead fluorescence indicates saturation of binding sites
Low PC values may be due to washing techniques
•
Free IgG left in the assay can prevent the secondary antibody from binding to target
•
IgG-PE signal can be diluted
Low PC values may be due to dilution of IgG-PE
PRA Reaction Formulas
•
NBG Ratio < 1.5 = NIH score of “1” (negative)
•
NBG Ratio between 1.5 and 5 = NIH score of “2” (weak positive)
•
NBG Ratio between 5 and 10 = NIH score of “4” (positive)
•
NBG Ratio between 10 and 20 = NIH score of “6” (positive)
•
NBG Ratio above 20 = NIH score of “s” (strong positive)
Single Antigen Formulas
•
% of Working Range < 15 = NIH score of “1” (negative)
•
% of Working Range between 15 and 30 = NIH score of “2” (grey area)
•
% of Working Range between 30 and 70 = NIH score of “4” (weak positive)
•
% of Working Range above 70 = NIH score of “8” (positive)
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Mixed Antigen Formulas
•
NBG Ratio < 1.2 = Negative
•
NBG Ratio between 1.2 and 1.5 = Grey area
•
NBG Ratio above 1.5 Positive
Statistical and Scoring Formulas
TPs, FPs, TNs and FNs
True Positive (TP), False Positive (FP), True Negative (TN)
and False Negative (FN) are defined as shown in
Table 5-6. For example, if an antigen is present, but there no serum reaction detected, the reading would be
considered a False Negative. To make the formulas more concise, the cell designations (A, B, C, D) are used in
place of TP, FN, FP and TN.
Table 5-6: TP, FP, TN and FN Reaction Designations
Reaction
Pos
Neg
Antigen Present
TP (A)
FN (B)
Antigen Absent
FP (C)
TN (D)
R-Value
R-Value –
the Correlation Coefficient, R, is a measurement of the interdependence of two random variables.
R ranges in value from -1 to +1, indicating perfect negative correlation at -1, absence of correlation at zero,
and perfect positive correlation at +1.
The R-Value is calculated using the formula:
AD – DC
R = -------------------------------------------------------------------------------( A + B)(A + C )( B + D)( C + D )
Eq. 5-6
Values range from -1 to +1.
Chi-Square
Chi-Square
– the Chi Square estimate of confidence, Χ2, is calculated using the formula:
2
2
N ( AD – DC )
χ = ---------------------------------------------------------------------------(A + B)(A + C)(B + D)(C + D)
Eq. 5-7
Values range from 0 to infinity.
Score
Score
– the Score, S, is the difference: TP - FN. The higher this number, the stronger the correlation.
Strength
Strength
- the percent Strength is calculated by the formula:
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N8
Str = 100 ---------N TP
Eq. 5-8
N TP
Incl = -------------------------N TP + N FN
Eq. 5-9
Inclusion Index
Inclusion Index–
the Inclusion Index is the ratio:
Values range from 0 to 1.
Average
Average – this is the weighted Average of all reactions that are classified as true positives. If both 8s and 6s are
considered positive, the Average is calculated as:
8N 8 + 6N 6
Avg = ------------------------N8 + N6
Eq. 5-10
where N is the number of reactions in the true positive group. If 4s are also considered positive, both the
numerator and the denominator contain corresponding terms for the 4s:
8N 8 + 6N 6 + 4N 4
Avg = ----------------------------------------N8 + N6 + N4
Eq. 5-11
Fisher’s Two-Tail
Fisher's Two-Tail – Tail analysis refers to the analysis of the low-frequency parts of a distribution, for example,
the tails or ends of a distribution curve. Tail analysis is an appropriate statistic tool to use when analyzing antigen frequencies because of the large number of antigens and the small number of times any given antigen is
detected during the assay.
The Fisher probability test is used to examine the significance of the association between two variables in a
2 x 2 contingency table. The need for the Fisher test arises when we have data that are divided into two categories in two separate ways (reaction positive or negative; antigen present or absent), and the sample sizes are
small, or the data are very unequally distributed among the cells of the table (e.g. Table 5-6).
The question posed regards the probability of the distribution of the observed reactions presented in a 2 x 2
table such as shown in Table 5-6. The probability is calculated using the formula:
( A + B )! ( A + C )! ( B + D )! ( C + D )!
F = ------------------------------------------------------------------------------------NA!B!C!D!
Eq. 5-12
Note that 0! = 1.
Values range from 0 to +1, with 0 indicating no probability of occurrence and 1.00 complete probability.
Antigen Specificity Calculation
The antigen specificity table is generated as shown in Figure 5-6:
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1
Retrieve all data needed for the selected sample and product combination: reactions, associated raw and
normalized data and the antigens associated with each bead; compile a list of candidate antigens from
which the specificities will be determined.
2
Set up a 2 x 2 table of TPs, TNs, FPs and FNs for each candidate antigen as shown above in Table 5-6, TP,
FP, TN and FN Reaction Designations. Compute appropriate statistics including Chi-Square, Fisher's
Two-Tail, Score, Strength, and Inclusion Index for each antigen.
3
Check the statistics against the specified threshold. Currently the user may choose either the R-Value or
the score as the primary threshold criterion and the other as the secondary criterion. If no antigen meets the
minimum, exit the loop.
4
Check the candidate antigens to see which has the highest value in the selected statistics. In the case of a
tie, the first-occurring antigen is ranked higher (or highest).
5
Add the antigen with the highest valuation to the list of selected specificities; include associated statistics
in the tabulation.
6
Eliminate the selected antigen from the candidate list and remove all beads with that specificity from the
data pool.
7
Go back to Step 2 for the next iteration.
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Figure 5-6: Antigen Specificity Calculations
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Appendix A: LABScreen Reports
LABScreen generates raw data, analysis results, and panel listing reports. Many of the reports can be accessed from more
than one point in the application. Depending on layout requirements, reports are generated either in portrait or landscape
orientation.
When generating a report, you can preview the report by right-clicking on the appropriate print icon.
•
Grey area results are indicated by three asterisks (***)
•
Low PC/NC ratios are indicated by double left angle brackets (<<)
•
Low bead counts are indicated by double pound signs (##)
LABScreen Reports
Reports Menu
Use these menu options to generate several of the most commonly produced LABScreen reports. A number of other reports
types are available and are discussed later in this appendix.
Patient Antibody Summary – generates a summary Patient Sera Report (see Figure A-1, Patient Antibody Summary Report)
for each patient specified by Patient ID. A summary report lists just the % positive Rxns and the specificities from all LABScreen analyses associated with that patient. The user can specify a single patient ID or a range of contiguous patient IDs.
Patient Antibody Report – generates a detailed specificity report with overall statistics for the analysis (# Rxns, # of positive
Rxns, # of strong Rxns, etc.) and detailed data for each specificity (TP, FN, FP and TN) and statistics (Inclusion, Strength,
R-Value and Chi-Sq). The user can specify a single patient ID or a range of contiguous patient IDs.
Patient HLA Report – generates a summary report of HLA typings for all the cells associated with the specified patient(s).
The user can specify a single patient ID or a range of contiguous patient IDs.
Panel Listing
– generates a panel listing for the specified product Cat ID and Lot #.
CREG Listing –
generates a listing of the currently defined member antigens in Class I CREGs (Cross-Reacting Groups).
The modification of CREG definitions is done in the Public Antigen Maintenance Data Entry form accessible via the main
menu Maintenance options.
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Patient Antibody Summary Report
Collected typing results for all samples linked with the specified Patient ID showing only percent positive reactions and specificities.
•
Generated by selecting Report > Patient Antibody Summary Report from the main menu.
Figure A-1: Patient Antibody Summary Report
Patient Antibody Report
Collected detailed reaction data and specificities for all samples linked with the specified Patient ID.
•
Generated by selecting Report > Patient Antibody Report from the main menu.
Figure A-2: Patient Antibody Report
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Patient Cell Typing Report
Collected detailed HLA Typing for all samples linked with the specified Patient ID.
•
Generated by selecting Report > Patient HLA Report from the main menu.
Figure A-3: Patient Cell Typing Report
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LABScreen Mixed Data Full Report
Lists the results of all samples within a selected batch. Due to space restrictions, MESF values are not shown on the Mixed Data Full Report.
•
Generated by selecting LABScan 100 > Import/Reprocess Mixed batch, then selecting the Full Report option in the Data Import/Report dialog.
Figure A-4: Mixed Data Full Report
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Mixed Data Individual Report
MESF conversion values are shown only on Mixed Individual Reports.
•
Generated by selecting LABScan 100 > Import/Reprocess Mixed > Individual in the Data Import/Report dialog.
Figure A-5: Mixed Data Individual Report
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Mixed Data Summary Report
Summarizes the results of all samples within a selected batch on one line per sample.
•
Generated by selecting LABScan 100 > Import/Reprocess Mixed batch, then selecting the Summary option in the Data Import/Report dialog.
Figure A-6: Mixed Data Summary Report
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PRA Data Report
This report can be printed from the Analysis or Import windows. When MEFS conversion is activated, it contains MESF
values.
Figure A-7: PRA Raw Data Report
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SA Raw Data Report
This report can be printed from the Analysis or import windows. When MEFS conversion is activated, it contains MESF
values.
Figure A-8: Single Antigen Raw Data Report
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SA Analysis Report
This report can be printed from the Analysis window. When MEFS conversion is activated, the report also contains MESF
values.
Figure A-9: Single Antigen Analysis Report
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Antigen Distribution Listing
The Antigen Distribution Listing shows how many beads in the product would react with a given antigen. To learn the
specificities of a given bead, consult the Panel Listing for that product (Figure A-12). Class I and Class II Antigen Distribution listings are similar in format. A Distribution Listing can be generated when importing or reprocessing PRA data by
selecting the Include Panel with Report option.
Figure A-10: Typical Antigen Distribution Listing
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Sample Raw Data Report
Contains raw data values, statistics and specificities for the sample currently under analysis.
•
To generate, select Raw Data button from within the Class I/Class II Analysis Results window or from within the
Maintenance > Readings > Raw Data panel.
Figure A-11: Sample Raw Data Report
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Class and Class II Panel Listings
Panel listings can be generated by selecting Report > Panel Listing from the main menu, then specifying the LABScreen
product from a pick list. You can preview the listing by right-clicking on the print button, or export the listing to an Excel
file.
Figure A-12: Typical Antigen Panel Listing
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Class and Class II Analysis (Antibody Screening) Reports
Contains complete analysis data for the sample currently under analysis. NIH scores, NBG ratios and specificities for FPs,
FNs and TNs are also included in the report, although only the TPs are shown in Figure A-13.
•
Generated from within the Class I/Class II Analysis Result window by selecting the Print option.
Figure A-13: Class I and Class II Antibody Screening Reports
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Class I and Class II Analysis (Antibody Screening) Reports (Reversed)
Analysis report generated after reversing the NIH scores for the sample: 8s become 1s, 6s become 2s, etc. The score reversal (or inversion) in effect tests for the absence of antigens rather than their presence.
•
Generated from within the Class I/Class II Analysis Result window by clicking the +/- button, then selecting the Print
option. A detail of the report is shown below.
Figure A-14: Class I and Class II Antibody Screening Reports (Reversed)
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Class I and Class II Analysis (Antibody Screening) Reports (2 x 2 Listing)
This report contains statistics for all the antigens in the assay, including those not selected as specificities for the sample.
You can select Patient Antibody Report to generate analysis results reports for one or more patients with contiguous
Patient IDs.
•
Generated after selecting 2 x 2 Report output option for the specific sample in the Temporary Parameters Setting form
accessible from the Analysis Window or in the Update Parameters form (Figure 5-1, Global Parameter Settings Form).
In the detail of the report shown below only the beginning and ending antigens are included.
Figure A-15: Class I and Class II Antibody Screening Reports (2 x 2 Listing)
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Changing Report Paper Size
You can change the report paper size from the default U.S. letter size to A-4 as follows:
1
Exit the LABScreen application.
2
Assuming that LABScreen has been installed in the default C:\ location, navigate to C:\labscrn.
3
Sort the files by type and locate the two MS-DOS batch files, A4_size_report and Letter_size_report.
4
Launch the A4_size_report batch file. This replaces the contents of the folder C:\labscrn\Reports with the contents of the
folder C:\labscrn\REPORTS_A4. The next time you generate a LABScreen report, it will be in the A-4 format.
5
To restore the report size back to the default letter size, launch the Letter_size_report batch file.
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Index
Symbols
## – low bead count, 55
*** – grey area results, 55
<< – low PC/NC ratio, 55
A
Antigen exclusion
temporary vs permanent, 36
Antigen Specificity Calculation
algorithm flowchart, 51
ATG – anti-thymocyte globulin, 49
Average
defined, 51
B
Bead count minimum, 49
C
Catalog ID – name length
limitations, 15
Chi-Sq, 55
formula, 50
Table, 27
CREG Display, 28
CREG Selection
UNOS and/or Fuller, 41
D
Database
packing, 40
Date Format
changing, 42
Disclaimer, 5
G
Global Parameters – modifying, 41
I-J
IgG-PE, 49
Inclusion Index, 55
defined, 51
Index
rebuilding, 40
Installation Instructions, 7
L
LABScan 100
reprocessing, 24
LABScreen Menus
synopis of functions, 9
LABScreen Mixed
adding new lots, 11
enabling 4-bead analysis, 10
LABType allele assignments, 11
M
Main Menu
file, 9
reports, 55
MESF – Molecules of Equivalent
Soluble Fluorophores, 10
MFI – Median Fluorescent
Intensity, 18
N
NC values
causes of low, 49
Negative Background from ID, 18
E
Epitope analysis, 11
F
File extensions
.arf, 40
Fisher’s Two-Tail
formula for, 51
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LABScreen PRA, 5
LABScreen SA, 5
Public Antigens, 11
Q
Quantiplex Beads Data, 22
R
Range Rule, 10
Reaction Definition, 30
Rebuilding the Index, 40
Remainder Antigens
Chi-Sq table, 27
CREGs, 28
Report paper size
changing between letter and A-4, 70
Reports
Panel Listing, 70
Patient Antibody Report, 69
Reprocessing Data, 24
Rituxan, 49
R-Value, 55
defined, 50
S
Saved/Accepted sample results
where to find, 11
Score
defined, 27, 50
Single Antigen Working Range
defined, 48
Strength, 55
defined, 50
System Requirements, 6
T
P
Packing the database, 40
Patient HLA Report
generating, 70
PC values
causes of low, 49
Product Description
LABScreen Mixed, 5
In d ex
Tail analysis, 51
Thymoglobulin – anti-thymocyte
globulin, 49
TPs, FPs, TNs, FNs
2 x 2 Table, 50
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