About the Conversion Utility
The sample file format generated with Applied Biosystems Data Collection software v2.0 on the
ABI PRISM® 3100/3100-Avant Genetic Analyzers and Data Collection v3.0 on the Applied
Biosystems 3130/3130xl Genetic Analyzers is not compatible with older analysis applications
like GeneScan® and Genotyper® software, which only run with Data Collection software v1.1.
The plate records of the newer versions of data collection software no longer have a “Color”
field where the user can place a diamond in the cell corresponding to the dye color of the size
standard. This diamond is required by GeneScan software to size the DNA fragments. In
addition, the newer plate records do not have a color info column where users would copy and
paste the sample names into this field, which would then populate the sample info field in
GeneScan and Genotyper software. Genotyper software requires the word "ladder” to appear in
the sample info field of the allelic ladder samples to run the Kazam macro. The diamond and
sample info could be entered manually, but this would be very time consuming. In response to
this issue, Applied Biosystems has developed a utility that places the diamond and sample info
automatically into the sample files (*.fsa), which allows data generated on the newer Data
Collection software to work with these older applications as well as with GeneMapper® ID
software v3.1 and v3.2.
How to Use the Conversion Utility
1. Double-click on the HIDDyeBUtility.exe file within the Bin folder.
2. Within the screen that pops up, click Choose Starting Directory.
3. A dialog box will open asking you to please select the starting directory.
4. Migrate to the directory where the folder of sample files (*.fsa) is located. Select the
folder by clicking it once. Once the folder is highlighted, click Open.
5. By clicking open, the conversion will automatically occur. When the conversion is
completed successfully, the following message appears in the utility window.
Performance Verification
According to the Scientific Working Group on DNA Analysis and Methods (SWGDAM)
guidelines, data conversions of this nature require a performance check rather than a complete
performance qualification. The performance check tested data generated on one ABI PRISM
3100 Genetic Analyzer equipped with Data Collection software v2.0, one Applied Biosystems
3130xl Genetic Analyzer equipped with Data Collection software v3.0, and one ABI PRISM®
3100 Genetic Analyzer equipped with Data Collection v1.1. The Data Collection software v2.0
and v3.0 data was converted using the Conversion Utility and analyzed with GeneScan,
Genotyper and GeneMapper ID v3.2 software. The genotypes were compared against the
genotypes obtained from Data Collection v1.1 sample files running identical analysis software.
The Conversion Utility was deemed to work properly if all sample files were converted
successfully, and all machines produced identical genotypic profiles on all three analytical
applications.
Table 1. Specifications Tested
Feature
Functionality
Concordance
Metric
Percent of files successfully
converted. Successful conversion
means that a diamond was placed in
the appropriate color column for the
size standard, and the sample name
was copied into all dye lanes of the
sample info.
Percent of concordant genotypes
(converted data vs. unconverted data)
Passing Criterion
(Specification)
Actual
Result
Pass/Fail
100% Functionality
100%
Pass
100% Concordance
100%
Pass
Table 2. Functionality Results
Version of
Data
Collection
Number of
Sample Files
% Files with
Diamond in
“O” Column
% Files with
Sample Info Field
Populated
% Files
Successfully Sized
in GeneScan
% Files
Successfully
Called in
Genotyper
2.0
3.0
96
90
100%
100%
100%
100%
100%
100%
100%
100%
Table 3. Concordance Results
Data
Collection
Version
1.1
Unconverted
2.0
Converted
3.0
Converted
2.0
3.0
2.0
3.0
Unconverted
Unconverted
Converted
Converted
File Type
Analysis Software
Used
GeneScan 3.7.1
Genotyper 3.7
GeneScan 3.7.1
Genotyper 3.7
GeneScan 3.7.1
Genotyper 3.7
GeneMapper ID 3.2
GeneMapper ID 3.2
GeneMapper ID 3.2
GeneMapper ID 3.2
# of 9947A
samples
analyzed
72
# of 9947A
samples with
expected profile
72
100%
66
66
100%
70
70
100%
66
70
66
70
66
70
66
70
100%
100%
100%
100%
%
Concordance
CONCLUSION: According to the results of this performance check, the Conversion Utility can
successfully convert files generated with Data Collection software v2.0 and v3.0 without
affecting genotyping results.
GeneMapper ID software –
For Research, Forensic or Paternity Use Only. Not for use in diagnostic procedures.
Genotyper and GeneScan software –
For Research Use Only. Not for use in diagnostic procedures.
Notice to Purchaser: License Disclaimer
Purchase of this software product alone does not imply any license under any process, instrument or other apparatus, system,
composition, reagent or kit rights under patent claims owned or otherwise controlled by Applera Corporation, either expressly, or by
estoppel.
Applied Biosystems, ABI PRISM, GeneMapper, Genotyper, and GeneScan are registered trademarks and AB (design) is a
trademark of Applera Corporation or its subsidiaries in the US and/or certain other countries.
All other trademarks are the sole property of their respective owners.
Copyright© 2005. Applera Corporation. All rights reserved.