Eqtl Analysis & Snps In Microarray Probes

Question

[Darren J. Fitzpatrick]

Hi,

I have a set of probes from a custom microarray. I have the probe coordinates as mapped to the most recent genome build.

I wish to quantify the amount of probes with SNPs in them. I am only interested in quantifying probes with SNPs in Caucasians with a frequency > 0.05.

I attempted mapping the probes to the dbSNP chromosome reports. However, these do not contain SNP frequency nor population information.

Does anyone have any suggestions?

Thanks!

Answer 1

[Larry_Parnell]

Many dbSNP entries do have minor allele frequency data for certain populations. If your SNPs of interest do not, perhaps you can use a tool like SNAP (Broad Institute) to find those SNPs that are in absolute (r=1.0) or high LD (linkage disequilibrium (r > 0.8). An alternative is to use HapMap to capture the minor allele frequency data you want.

[Darren J. Fitzpatrick]

Hi Larry - As per your suggestion, I opted to use the HapMap data from the latest release. By mapping my expression probes to dbSNP irrespective of population, ~2/3 of my probes contained SNPs. By restricting to the CEU HapMap population ~4000 of the 36,000 had SNPs. Thanks.