Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arrays
Year: 2010
Type: article
Abstract: 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.
Source: Genetic Epidemiology
DOI: 10.1002/gepi.20550
Authors: Arti Tandon, Nick Patterson, David Reich
Institutions: Broad Institute, Harvard University
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
Awards: A Whole Genome Admixture Scan for Multiple Sclerosis, Genome-wide sequencing of prostate cancer in men of African ancestry, Leveraging functional data to predict disease risk in multi-ethnic populations, Population structure in whole-genome disease scans, Building a Latino admixture map & pilot study to find Type 2 Diabetes risk, Advanced Tools for Reconstructing Population History
OpenAlex ID: W2091734039