Question: Eqtl Analysis & Snps In Microarray Probes
gravatar for Darren J. Fitzpatrick
8.0 years ago by
Ireland/ United Kingdom
Darren J. Fitzpatrick1.1k wrote:


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?


eqtl snp microarray • 1.7k views
ADD COMMENTlink written 8.0 years ago by Darren J. Fitzpatrick1.1k
gravatar for Larry_Parnell
8.0 years ago by
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Larry_Parnell16k

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.

ADD REPLYlink modified 8.0 years ago • written 8.0 years ago by Darren J. Fitzpatrick1.1k
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