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

Mattias Jakobsson, Sonja W. Scholz, Paul Scheet, J. Raphael Gibbs, Jenna M. VanLiere, Hon Chung Fung, Zachary A. Szpiech, James H. Degnan, Kai Wang, Rita Guerreiro, Jose M. Bras, Jennifer C. Schymick, Dena G. Hernandez, Bryan J. Traynor, Javier Simon-Sanchez, Mar Matarin, Angela Britton, Joyce Van De Leemput, Ian Rafferty, Maja BucanHoward M. Cann, John A. Hardy, Noah A. Rosenberg, Andrew B. Singleton

Research output: Contribution to journalArticlepeer-review

625 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)998-1003
Number of pages6
Issue number7181
StatePublished - Feb 21 2008
Externally publishedYes

ASJC Scopus subject areas

  • General


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