Issue addressed:

• GDAS 3.0 Pedigree Checking
• GDAS 3.0 Export in GeneHunter-compatible format
• GDAS 3.0 Genetic Map position accuracy
• GDAS 3.0 CustomSeq® .CHP file incompatibility
  

Pedigree Checking

GDAS 3.0 includes Pedigree checking functionality. Pedigree checking in GDAS 3.0 was based on MERLIN's pedigree checking algorithm which does not automatically take into account the differences in X chromosome male inheritance. The sex chromosome for males differs from other chromosomes. For the autosomal chromosomes, one copy is inherited from the father and the other copy from the mother. Therefore, males only have a single copy of the X chromosome, which is inherited from the mother. Currently, the GDAS 3.0 pedigree checking algorithm assumes autosomal inheritance for all chromosomes, including X for males. Applying the autosomal inheritance to X male chromosome flags certain genotype calls as errors, which are actually correct. The GDAS 3.0.2 patch corrects the pedigree checking algorithm to account for the differences in X chromosome male inheritance.

Export in GeneHunter-compatible format

GDAS 3.0 includes the ability to export data into GeneHunter-compatible linkage format (the GeneHunter open source software (Kruglyak, Daly, Reeve… 1996)). GeneHunter-compatible export includes allele frequency data based on NetAffx™ annotations. NetAffx allele frequency annotations were updated recently and, as a result, GeneHunter-compatible export was no longer able to export the allele frequency information. The GDAS 3.0.2 patch will update the export into GeneHunter-compatible format and ensure accurate allele frequencies are exported.

Genetic Map position accuracy

The genetic map (GM) position is incorrectly displayed in GDAS 3.0. GM positions require six decimal precision to ensure no two SNPs have exactly the same GM position. SNPs with duplicate GM positions cause problems with some downstream linkage analysis programs. In GDAS 3.0, the last three digits of GM precision are not correct. The GDAS 3.0.2 patch will ensure that all six decimal places are accurate.

CustomSeq® .CHP file incompatibility

GDAS .CHP file access for GeneChip® CustomSeq® Array customers - Affymetrix has identified an incompatibility between GeneChip® DNA Analysis Software (GDAS) 3.0 and CustomSeq® Array library files. When CustomSeq Array users analyze or attempt to open a .CHP file, the error "The server threw an exception" appears on the screen. When the user clicks OK, the application terminates.

• CustomSeq Array customers who have upgraded to GDAS 3.0 will experience this problem.
• CustomSeq Array customers using GDAS 2.0 are not affected.

The GDAS 3.0.2 patch will allow CustomSeq Array customers to analyze and open .CHP files within the GDAS 3.0 environment. If running GDAS 3.0 in a server environment, the GDAS 3.0.2 patch must be applied to both client and server. CustomSeq Array .CHP files created using GDAS 3.0 should be re-analyzed and re-created after the GDAS 3.0.2 patch has been installed.

Instructions for installing the GDAS 3.0.2 patch on client and server:

If running GDAS 3.0 in a server environment, the GDAS 3.0.2 patch must be applied to both client and server.

1. GDAS 3.0 must be installed prior to installing GDAS 3.0.2 patch.
2. Point the web browser to the download link, select and start the download.
3. The download file will be a .zip file.
4. Open the .zip file.
5. Extract the files (.exe file and a word document of what the patch addresses).
6. Double click on the .exe file to launch the install program; follow installer instructions.