Document Detail


A small number of candidate gene SNPs reveal continental ancestry in African Americans.
MedLine Citation:
PMID:  23278390     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Using genetic data from an obesity candidate gene study of self-reported African Americans and European Americans, we investigated the number of Ancestry Informative Markers (AIMs) and candidate gene SNPs necessary to infer continental ancestry. Proportions of African and European ancestry were assessed with STRUCTURE (K = 2), using 276 AIMs. These reference values were compared to estimates derived using 120, 60, 30, and 15 SNP subsets randomly chosen from the 276 AIMs and from 1144 SNPs in 44 candidate genes. All subsets generated estimates of ancestry consistent with the reference estimates, with mean correlations greater than 0.99 for all subsets of AIMs, and mean correlations of 0.99 ± 0.003; 0.98 ± 0.01; 0.93 ± 0.03; and 0.81 ± 0.11 for subsets of 120, 60, 30, and 15 candidate gene SNPs, respectively. Among African Americans, the median absolute difference from reference African ancestry values ranged from 0.01 to 0.03 for the four AIMs subsets and from 0.03 to 0.09 for the four candidate gene SNP subsets. Furthermore, YRI/CEU Fst values provided a metric to predict the performance of candidate gene SNPs. Our results demonstrate that a small number of SNPs randomly selected from candidate genes can be used to estimate admixture proportions in African Americans reliably.
Authors:
Nuri Kodaman; Melinda C Aldrich; Jeffrey R Smith; Lisa B Signorello; Kevin Bradley; Joan Breyer; Sarah S Cohen; Jirong Long; Qiuyin Cai; Justin Giles; William S Bush; William J Blot; Charles E Matthews; Scott M Williams
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Annals of human genetics     Volume:  77     ISSN:  1469-1809     ISO Abbreviation:  Ann. Hum. Genet.     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-01-02     Completed Date:  2013-04-19     Revised Date:  2014-01-09    
Medline Journal Info:
Nlm Unique ID:  0416661     Medline TA:  Ann Hum Genet     Country:  England    
Other Details:
Languages:  eng     Pagination:  56-66     Citation Subset:  IM    
Copyright Information:
© 2012 Blackwell Publishing Ltd/University College London.
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MeSH Terms
Descriptor/Qualifier:
African Americans / genetics*
European Continental Ancestry Group / genetics*
Female
Genetic Markers
Genotype
Humans
Male
Obesity / ethnology,  genetics
Polymorphism, Single Nucleotide*
Grant Support
ID/Acronym/Agency:
P30 CA068485/CA/NCI NIH HHS; P30 CA68485/CA/NCI NIH HHS; R01 CA092447/CA/NCI NIH HHS; R01CA092447/CA/NCI NIH HHS; T32 GM080178/GM/NIGMS NIH HHS; T32GM080178-03S1/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Genetic Markers
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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