Genome-wide SNP typing reveals signatures of population history

Austin L. Hughes, Robert Welch, Vinita Puri, Casey Matthews, Kashif Haque, Stephen J. Chanock, Meredith Yeager

Research output: Contribution to journalArticle

Abstract

Single-nucleotide polymorphism (SNP) arrays have become a popular technology for disease-association studies, but they also have potential for studying the genetic differentiation of human populations. Application of the Affymetrix GeneChip Human Mapping 500K Array Set to a population of 102 individuals representing the major ethnic groups in the United States (African, Asian, European, and Hispanic) revealed patterns of gene diversity and genetic distance that reflected population history. We analyzed allelic frequencies at 388,654 autosomal SNP sites that showed some variation in our study population and 10% or fewer missing values. Despite the small size (23-31 individuals) of each subpopulation, there were no fixed differences at any site between any two subpopulations. As expected from the African origin of modern humans, greater gene diversity was seen in Africans than in either Asians or Europeans, and the genetic distance between the Asian and the European populations was significantly lower than that between either of these two populations and Africans. Principal components analysis applied to a correlation matrix among individuals was able to separate completely the major continental groups of humans (Africans, Asians, and Europeans), while Hispanics overlapped all three of these groups. Genes containing two or more markers with extraordinarily high genetic distance between subpopulations were identified as candidate genes for health differences between subpopulations. The results show that, even with modest sample sizes, genome-wide SNP genotyping technologies have great promise for capturing signatures of gene frequency difference between human subpopulations, with applications in areas as diverse as forensics and the study of ethnic health disparities.

Original languageEnglish (US)
Pages (from-to)1-8
Number of pages8
JournalGenomics
Volume92
Issue number1
DOIs
StatePublished - Jul 2008
Externally publishedYes

Fingerprint

Single Nucleotide Polymorphism
Genome
Population
Hispanic Americans
Genes
Technology
Health
Medical Genetics
Principal Component Analysis
Ethnic Groups
Gene Frequency
Sample Size

Keywords

  • Complex disease
  • Human populations
  • Single-nucleotide polymorphism

ASJC Scopus subject areas

  • Genetics

Cite this

Hughes, A. L., Welch, R., Puri, V., Matthews, C., Haque, K., Chanock, S. J., & Yeager, M. (2008). Genome-wide SNP typing reveals signatures of population history. Genomics, 92(1), 1-8. https://doi.org/10.1016/j.ygeno.2008.03.005

Genome-wide SNP typing reveals signatures of population history. / Hughes, Austin L.; Welch, Robert; Puri, Vinita; Matthews, Casey; Haque, Kashif; Chanock, Stephen J.; Yeager, Meredith.

In: Genomics, Vol. 92, No. 1, 07.2008, p. 1-8.

Research output: Contribution to journalArticle

Hughes, AL, Welch, R, Puri, V, Matthews, C, Haque, K, Chanock, SJ & Yeager, M 2008, 'Genome-wide SNP typing reveals signatures of population history', Genomics, vol. 92, no. 1, pp. 1-8. https://doi.org/10.1016/j.ygeno.2008.03.005
Hughes AL, Welch R, Puri V, Matthews C, Haque K, Chanock SJ et al. Genome-wide SNP typing reveals signatures of population history. Genomics. 2008 Jul;92(1):1-8. https://doi.org/10.1016/j.ygeno.2008.03.005
Hughes, Austin L. ; Welch, Robert ; Puri, Vinita ; Matthews, Casey ; Haque, Kashif ; Chanock, Stephen J. ; Yeager, Meredith. / Genome-wide SNP typing reveals signatures of population history. In: Genomics. 2008 ; Vol. 92, No. 1. pp. 1-8.
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