Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array

Xu Zhang; Wenbo Mu; Cong Liu; Wei Zhang

doi:10.7287/peerj.preprints.545v1

Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array

Xu Zhang^1,2, Wenbo Mu³, Cong Liu³, Wei Zhang ^2,3

1 Department of Medicine, The University of Illinois, Chicago, IL, USA

2 The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China

3 Department of Pediatrics, The University of Illinois, Chicago, IL, USA

DOI: 10.7287/peerj.preprints.545v1

Published: 2014-10-18
Accepted: 2014-10-18

Subject Areas: Bioinformatics, Genetics
Keywords: admixture mapping, single nucleotide polymorphism, Pan-African array, ancestry-informative marker, African American

Copyright: © 2014 Zhang et al.
Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.

Cite this article: Zhang X, Mu W, Liu C, Zhang W. 2014. Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array. PeerJ PrePrints 2:e545v1 https://doi.org/10.7287/peerj.preprints.545v1

Abstract

Genetic admixture has been utilized as a tool for identifying loci associated with complex traits and diseases in recently admixed populations such as African Americans. In particular, admixture mapping is an efficient approach to identifying genetic basis for those complex diseases with substantial racial or ethnic disparities. Though current advances in admixture mapping algorithms may utilize the entire panel of SNPs, providing ancestry-informative markers (AIMs) that can differentiate parental populations and estimate ancestry proportions in an admixed population may particularly benefit admixture mapping in studies of limited samples, help identify unsuitable individuals (e.g., through genotyping the most informative ancestry markers) before starting large genome-wide association studies (GWAS), or guide larger scale targeted deep re-sequencing for determining specific disease-causing variants. Defining panels of AIMs based on commercial, high-throughput genotyping platforms will facilitate the utilization of these platforms for simultaneous admixture mapping of complex traits and diseases, in addition to conventional GWAS. Here, we describe AIMs detected based on the Shannon Information Content (SIC) or F_st for African Americans with genome-wide coverage that were selected from ~2.3 million single nucleotide polymorphisms (SNPs) covered by the Affymetrix Axiom Pan-African array, a newly developed genotyping platform optimized for individuals of African ancestry.