Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.

ABSTRACT:

Background

Quantitative trait locus (QTL) theory predicts that genetic influence on complex traits involves multiple genes of small effect size. To detect QTL associations of small effect size, large samples and systematic screens of thousands of DNA markers are required. An efficient solution is to genotype case and control DNA pools using SNP microarrays. We demonstrate that this is practical using DNA pools of 100 individuals.

Results

Using standard microarray protocols for the Affymetrix GeneChip Mapping 10 K Array Xba 131, we show that relative allele signal (RAS) values provide a quantitative index of allele frequencies in pooled DNA that correlate 0.986 with allele frequencies for 104 SNPs that were genotyped individually for 100 individuals. The sensitivity of the as

SUBMITTER: Meaburn E 

PROVIDER: S-EPMC1079828 | biostudies-literature | 2005 Apr

REPOSITORIES: biostudies-literature