Genome-wide detection and characterization of positive selection in human populations

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' meth...

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Bibliographic Details
Published in:Nature 2007-10, Vol.449 (7164), p.913-918
Main Authors: Lander, Eric S, Fry, Ben, Cotsapas, Chris, McCarroll, Steven A, Byrne, Elizabeth H, Varilly, Patrick, Lohmueller, Jason, Xie, Xiaohui, Gaudet, Rachelle, Hostetter, Elizabeth, Sabeti, Pardis C, Schaffner, Stephen F
Format: Article
Language:English
Subjects:
Antiporters - genetics
Biological and medical sciences
Edar Receptor - chemistry
Edar Receptor - genetics
Evolutionary biology
Fundamental and applied biological sciences. Psychology
Gene Frequency
Genes
Genetic research
Genetics of eukaryotes. Biological and molecular evolution
Genetics, Population
Genome, Human - genetics
Genomics
Geography
Haplotypes - genetics
Human
Human genome
Humans
Lassa virus
Methods
Models, Molecular
Polymorphism
Polymorphism, Single Nucleotide - genetics
Population genetics
Population genetics, reproduction patterns
Protein Structure, Tertiary
Selection, Genetic
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Summary:With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.
ISSN:0028-0836
1476-4687
1476-4679
DOI:10.1038/nature06250