Cargando…
Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array
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...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2014
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226639/ https://www.ncbi.nlm.nih.gov/pubmed/25392759 http://dx.doi.org/10.7717/peerj.660 |
_version_ | 1782343651823714304 |
---|---|
author | Zhang, Xu Mu, Wenbo Liu, Cong Zhang, Wei |
author_facet | Zhang, Xu Mu, Wenbo Liu, Cong Zhang, Wei |
author_sort | Zhang, Xu |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4226639 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-42266392014-11-12 Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array Zhang, Xu Mu, Wenbo Liu, Cong Zhang, Wei PeerJ Bioinformatics 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. PeerJ Inc. 2014-11-04 /pmc/articles/PMC4226639/ /pubmed/25392759 http://dx.doi.org/10.7717/peerj.660 Text en © 2014 Zhang et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , 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) and either DOI or URL of the article must be cited. |
spellingShingle | Bioinformatics Zhang, Xu Mu, Wenbo Liu, Cong Zhang, Wei Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array |
title | Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array |
title_full | Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array |
title_fullStr | Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array |
title_full_unstemmed | Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array |
title_short | Ancestry-informative markers for African Americans based on the Affymetrix Pan-African genotyping array |
title_sort | ancestry-informative markers for african americans based on the affymetrix pan-african genotyping array |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226639/ https://www.ncbi.nlm.nih.gov/pubmed/25392759 http://dx.doi.org/10.7717/peerj.660 |
work_keys_str_mv | AT zhangxu ancestryinformativemarkersforafricanamericansbasedontheaffymetrixpanafricangenotypingarray AT muwenbo ancestryinformativemarkersforafricanamericansbasedontheaffymetrixpanafricangenotypingarray AT liucong ancestryinformativemarkersforafricanamericansbasedontheaffymetrixpanafricangenotypingarray AT zhangwei ancestryinformativemarkersforafricanamericansbasedontheaffymetrixpanafricangenotypingarray |