Database mining for selection of SNP markers useful in admixture mapping

Abstract Background New technologies make it possible for the first time to genotype hundreds of thousands of SNPs simultaneously. A wealth of genomic information in the form of publicly available databases is underutilized as a potential resource for uncovering functionally relevant markers underlying complex human traits. Given the huge amount of SNP data available from the annotation of human genetic variation, data mining is a reasonable approach to investigating the number of SNPs that are informative for ancestry information. Methods The distribution and density of SNPs across the genome of African and European populations were extensively investigated by using the HapMap, Affymetrix, and Illumina SNP databases. We exploited these resources by mining the data available from each of these databases to prioritize potential candidate SNPs useful for admixture mapping in complex human diseases and traits. Over 4 million SNPs were compared between Africans and Europeans on the basis of a pre-specified recommended allele frequency difference (delta) value of ≥ 0.3. Results The method identified 15% of HapMap, 11% of Affymetrix, and 14% of Illumina SNP sets as candidate SNPs, termed ancestry informative markers (AIMs). These AIM panels with assigned rs numbers, allele frequencies in each ethnic group, delta value, and map positions are all posted on our website http://www.ssg.uab.edu/downloads/admixture_mapping/SNPAIMs.txt. All marker information in this data set is freely and publicly available without restriction. Conclusion The selected SNP sets represent valuable resources for admixture mapping studies. The overlap between selected AIMs by this single measure of marker informativeness in the different platforms is discussed.