Demographic history and rare allele sharing among human populations

High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targete...

Full description

Saved in:

Bibliographic Details
Published in:	Proceedings of the National Academy of Sciences - PNAS Vol. 108; no. 29; pp. 11983 - 11988
Main Authors:	Gravel, Simon, Henn, Brenna M, Gutenkunst, Ryan N, Indap, Amit R, Marth, Gabor T, Clark, Andrew G, Yu, Fuli, Gibbs, Richard A, Bustamante, Carlos D
Format:	Journal Article
Language:	English
Published:	United States National Academy of Sciences 19-07-2011 National Acad Sciences
Subjects:	alleles Asians Biological Sciences Chromosomes Demographics Demography Evolution, Molecular Exons Gene Frequency Genes - genetics Genetic diversity Genetic Drift Genetic Variation Genetics Genetics, Population Genomes genomics Genomics - methods high-throughput nucleotide sequencing Human genetics Humans Models, Genetic Parametric models Population Population estimates Population genetics Population growth Population size Racial Groups - genetics Replication Sequence Analysis, DNA Sequencing Statistics surveys
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2-4x coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after
Bibliography:	http://dx.doi.org/10.1073/pnas.1019276108 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Article-2 ObjectType-Feature-1 Edited by Michael Lynch, Indiana University, Bloomington, IN, and approved June 3, 2011 (received for review December 24, 2010) Author contributions: S.G., B.M.H., G.T.M., A.G.C., F.Y., R.A.G., 1000G, and C.D.B. designed research; S.G., A.R.I., G.T.M., F.Y., R.A.G., and 1000G performed research; S.G., R.N.G., and A.R.I. contributed new reagents/analytic tools; S.G. analyzed data; and S.G., B.M.H., and C.D.B. wrote the paper.
ISSN:	0027-8424 1091-6490
DOI:	10.1073/pnas.1019276108