Hi all using Illumnia GenomeStudio 2.0.2 software, specifically the Genotyping 2.0.2 module, I have independently processed data from three different SNP arrays:

• HumanOmniExpress-24v1.1
• HumanOmniExpress-24v1.2
• GSA arrays

Using the PLINK Input Report Plug-in v2.1.4 for GenomeStudio Genotyping module I have generated output files from my SNP array data -> .bat, .map, .ped, .phenotype, and .script files

The .map file is of concern here, it contains:

Column 1 -> Chromosome Column 2 -> SNP name Column 3 -> Genetic distance (in cM) Column 4 -> Physical position of SNP (according to hg19, as this is the manifest file that I have used when loading my GenomeStudio project).

The problem that I have encountered:

Regardless of the SNP array being used, there is a section of markers for each chromosome where cM positions suddenly start decreasing in value incorrectly. As far as I can tell, the CM values should only increase or stay the same (ie if two SNPs are in close proximity) when sorted by the physical position of the SNP.

-> This has occurred in output files from independent projects of different array types.

-> I have tried outputting the data again on another occasion with the same issue occurring.

-> I have output files exactly like these from a HumanOmniExpress-24v1.1 chip that were outputted using a plink plugin with the previous version of GenomeStudio and this issue not be evident. Is there a problem with Illumina's Plink plugin?

Has anyone using the Illumina GSA arrays in particular encountered this? or found any clever ways around it? Thanks in advance.

J.