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

被引:623
作者
Jakobsson, Mattias [1 ,2 ]
Scholz, Sonja W. [4 ,5 ,6 ]
Scheet, Paul [1 ,3 ]
Gibbs, J. Raphael [4 ,5 ,6 ]
VanLiere, Jenna M. [1 ]
Fung, Hon-Chung [4 ,7 ,8 ]
Szpiech, Zachary A. [1 ]
Degnan, James H. [1 ,2 ]
Wang, Kai [9 ]
Guerreiro, Rita [4 ,10 ]
Bras, Jose M. [4 ,10 ]
Schymick, Jennifer C. [4 ,11 ]
Hernandez, Dena G. [4 ]
Traynor, Bryan J. [4 ,12 ]
Simon-Sanchez, Javier [4 ,13 ]
Matarin, Mar [4 ]
Britton, Angela [4 ]
van de Leemput, Joyce [4 ,5 ,6 ]
Rafferty, Ian [4 ]
Bucan, Maja [9 ]
Cann, Howard M. [14 ]
Hardy, John A. [5 ,6 ]
Rosenberg, Noah A. [1 ,2 ,3 ]
Singleton, Andrew B. [4 ,15 ]
机构
[1] Univ Michigan, Ctr Computat Med & Biol, Ann Arbor, MI 48109 USA
[2] Univ Michigan, Dept Human Genet, Ann Arbor, MI 48109 USA
[3] Univ Michigan, Dept Biostat, Ann Arbor, MI 48109 USA
[4] NIA, Neurogenet Lab, NIH, Bethesda, MD 20892 USA
[5] UCL, Dept Mol Neurosci, London WC1N 3BG, England
[6] UCL, Reta Lila Weston Inst Neurol Studies, Inst Neurol, London WC1N 3BG, England
[7] Chang Gung Mem Hosp, Dept Neurol, Taipei 10591, Taiwan
[8] Chang Gung Univ, Coll Med, Taipei 10591, Taiwan
[9] Univ Penn, Dept Genet, Philadelphia, PA 19104 USA
[10] Univ Coimbra, Fac Med, Ctr Neurosci & Cell Biol, P-3004504 Coimbra, Portugal
[11] Univ Oxford, John Radcliffe Hosp, Dept Clin Neurol, Oxford OX3 9DU, England
[12] Natl Inst Neurol Disorders & Stroke, Neurogenet Branch, NIH, Bethesda, MD 20892 USA
[13] CSIC, Unidad Genet Mol, Dept Genom & Proteom, Inst Biomed Valencia, Valencia 46010, Spain
[14] Ctr Etud Polymorphisme Humain, Fdn Jean Dausset, F-75010 Paris, France
[15] Univ Virginia, Ctr Publ Hlth Genom, Charlottesville, VA 22908 USA
基金
英国医学研究理事会;
关键词
D O I
10.1038/nature06742
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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(1-3). 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.
引用
收藏
页码:998 / 1003
页数:6
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