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Integrating common and rare genetic variation in diverse human populations

David Altshuler, +68 more
- 02 Sep 2010 - 
- Vol. 467, Iss: 7311, pp 52-58
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TLDR
An expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.
Abstract
Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of <or=5%, and demonstrated the feasibility of imputing newly discovered CNPs and SNPs. This expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.

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Citations
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Journal ArticleDOI

EigenGWAS: finding loci under selection through genome-wide association studies of eigenvectors in structured populations

TL;DR: This work develops a novel approach to identify regions of the genome underlying population genetic differentiation in any genetic data where the underlying population structure is unknown, or where the interest is assessing divergence along a gradient, and shows through theory and simulation that this approach can identify regions under selection along gradients of ancestry.
Journal ArticleDOI

Genome-wide genetic homogeneity between sexes and populations for human height and body mass index

TL;DR: Two distinct genome-wide methods are used to estimate the autosomal genetic correlation between men and women for human height and body mass index, and it is shown that the between-sex genetic correlation is not significantly different from unity for both traits.
Journal ArticleDOI

Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets.

TL;DR: This study represented an important step in identification and analysis of RBP–lncRNA interactions and showed that these interactions may play crucial roles in cancer and genetic diseases.
Journal ArticleDOI

Neanderthal Introgression at Chromosome 3p21.31 was Under Positive Natural Selection in East Asians

TL;DR: Evidence of Neanderthal introgression within the chromosome 3p21.31 region is presented, and suggestive evidence supports latitude-dependent selection and suggests that this allele was lost during the exodus of ancestors of modern Eurasians from Africa and reintroduced to Eurasian from Neanderthals.
Journal ArticleDOI

Genotype imputation via matrix completion

TL;DR: Compared with leading imputation programs, the matrix completion algorithm embodied in the program MENDEL-IMPUTE achieves comparable imputation accuracy while reducing run times significantly.
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A haplotype map of the human genome

John W. Belmont, +232 more
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Journal ArticleDOI

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Kelly A. Frazer, +237 more
- 18 Oct 2007 - 
TL;DR: The Phase II HapMap is described, which characterizes over 3.1 million human single nucleotide polymorphisms genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed, and increased differentiation at non-synonymous, compared to synonymous, SNPs is demonstrated.
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