Genotype, haplotype and copy-number variation in worldwide human populations.
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.
Jakobsson
Mattias
M
Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Scholz
Sonja W
SW
Scheet
Paul
P
Gibbs
J Raphael
JR
VanLiere
Jenna M
JM
Fung
Hon-Chung
HC
Szpiech
Zachary A
ZA
Degnan
James H
JH
Wang
Kai
K
Guerreiro
Rita
R
Bras
Jose M
JM
Schymick
Jennifer C
JC
Hernandez
Dena G
DG
Traynor
Bryan J
BJ
Simon-Sanchez
Javier
J
Matarin
Mar
M
Britton
Angela
A
van de Leemput
Joyce
J
Rafferty
Ian
I
Bucan
Maja
M
Cann
Howard M
HM
Hardy
John A
JA
Rosenberg
Noah A
NA
Singleton
Andrew B
AB
D000349:Africa; D000483:Alleles; D002889:Chromosomes, Human, Pair 2 / Q000235:genetics; D018628:Gene Dosage / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population; D015894:Genome, Human / Q000235:genetics*; D005843:Geography; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide / Q000235:genetics