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ARTICLE doi:10.1038/nature09534 A map of human genome variation from

Summary: ARTICLE doi:10.1038/nature09534
A map of human genome variation from
population-scale sequencing
The 1000 Genomes Project Consortium*
The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation
for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the
project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput
platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four
populations; high-coverage sequencing of two mother­father­child trios; and exon-targeted sequencing of 697
individuals from seven populations. We describe the location, allele frequency and local haplotype structure of
approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000
structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast
majority of common variation, over 95% of the currently accessible variants found in any individual are present in this
data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated
genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used
to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base
substitution mutations to be approximately 1028
per base pair per generation. We explore the data with regard to
signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes,
due to selection at linked sites. These methods and public data will support the next phase of human genetic research.


Source: Abecasis, Goncalo - Department of Biostatistics, University of Michigan
Batzer, Mark A. - Department of Biological Sciences, Louisiana State University


Collections: Biology and Medicine; Biotechnology; Mathematics