Genotype, haplotype and copy-number variation in worldwide human populations

Nature. 2008 Feb 21;451(7181):998-1003. doi: 10.1038/nature06742.

Abstract

Genome-wide patterns of variation across individuals provide a powerful source of data for uncovering the history of migration, range expansion, and adaptation of the human species. However, high-resolution surveys of variation in genotype, haplotype and copy number have generally focused on a small number of population groups. Here we report the analysis of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations. Analysis of SNP genotypes yields strongly supported fine-scale inferences about population structure. Increasing linkage disequilibrium is observed with increasing geographic distance from Africa, as expected under a serial founder effect for the out-of-Africa spread of human populations. New approaches for haplotype analysis produce inferences about population structure that complement results based on unphased SNPs. Despite a difference from SNPs in the frequency spectrum of the copy-number variants (CNVs) detected--including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas--the global distribution of CNVs largely accords with population structure analyses for SNP data sets of similar size. Our results produce new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human-genetic studies in diverse worldwide populations.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Africa
  • Alleles
  • Chromosomes, Human, Pair 2 / genetics
  • Gene Dosage / genetics*
  • Genetic Variation / genetics*
  • Genetics, Population
  • Genome, Human / genetics*
  • Geography*
  • Haplotypes / genetics*
  • Humans
  • Linkage Disequilibrium
  • Polymorphism, Single Nucleotide / genetics

Associated data

  • GEO/GSE10331