Research

Database mining for selection of SNP markers useful in admixture mapping

Tesfaye M Baye^1,2 , Hemant K Tiwari² , David B Allison^2,3,4 and Rodney C Go⁵

¹  Current address: Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA

²  Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA

³  Clinical Nutrition Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA

⁴  Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA

⁵  Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA

author email corresponding author email

BioData Mining 2009, 2:1doi:10.1186/1756-0381-2-1

Published:	14 February 2009

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 webcite. 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.