How To Retrieve "True" Alleles Of Genotypes From Geo Obtained With Illumina Human610-Quad V1.0?

Question

[tflutre]

I am interested in a genotype dataset on GEO (GSE26105) that was obtained using the Illumina Human610-Quad v1.0 BeadChip (GPL8887).

Thanks to the answer to my previous question, I was able to understand the platform data. But now I am struggling with the genotypes data because they are encoded as AA, AB or BB (no other information):

library(GEOquery)
gse.geno <- getGEO('GSE26105', destdir='.', GSEMatrix=TRUE)
mat.geno <- exprs(gse.geno)

I am aware of Illumina's technical note describing the TOP/BOT strand and the A/B alleles (and I think I understand it). But here, in the GEO dataset, there are only A's or B's, no TOP's nor BOT's. How/where can I find this information?

Answer 1

[Wen.Huang]

I had done this before, through a relatively painful way (see below). An easier way might be to get an annotation file from Illumina's technical service, they are really nice in this respect.

1) All of the 610 SNPs are also on the 1M chip, you can get a list of these IDs from GEO (or your FinalReport output). The reason to get these IDs is that this chip is not available on UcSC

2) Get the UCSC table for the 1M chip. Subset the 610 chips given your IDs from 1). The table contains all the allele and strand information. You need to be really careful with the strand though. I remember I was able to decide whether the UCSC allele code is top or bottom from the strand information in this table.

I hope it helps.

[tflutre]

Thanks for your answer. I downloaded the file ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snpArrayIllumina1M.txt.gz. Then, with a lot of "data mangling" in R, I kept only the non-ambiguous SNPs from the Illumina 610 chip for which I had strand information on the Illumina 1M chip.