Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arrays
Article first published online: 22 DEC 2010
© 2010 Wiley-Liss, Inc.
Volume 35, Issue 1, pages 80–83, January 2011
How to Cite
Tandon, A., Patterson, N. and Reich, D. (2011), Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arrays. Genet. Epidemiol., 35: 80–83. doi: 10.1002/gepi.20550
- Issue published online: 22 DEC 2010
- Article first published online: 22 DEC 2010
- Manuscript Revised: 20 AUG 2010
- Manuscript Received: 1 APR 2010
- NIH. Grant Number: U01-HG004168
- Burroughs Wellcome Career Development Award
- ancestry informative markers;
- admixture mapping;
- African American disease studies
Admixture mapping is a widely used method for localizing disease genes in African Americans. Most current methods for inferring ancestry at each locus in the genome use a few thousand single nucleotide polymorphisms (SNPs) that are very different in frequency between West Africans and European Americans, and that are required to not be in linkage disequilibrium in the ancestral populations. Modern SNP arrays provide data on hundreds of thousands of SNPs per sample, and to use these to infer ancestry, using many of the standard methods, it is necessary to choose subsets of the SNPs for analysis. Here we present panels of about 4,300 ancestry informative markers (AIMs) that are subsets respectively of SNPs on the Illumina 1 M, Illumina 650, Illumina 610, Affymetrix 6.0 and Affymetrix 5.0 arrays. To validate the usefulness of these panels, we applied them to samples that are different from the ones used to select the SNPs. The panels provide about 80% of the maximum information about African or European ancestry, even with up to 10% missing data. Genet. Epidemiol. 35:80–83, 2011. © 2010 Wiley-Liss, Inc.