A map of human genome variation from population-scale sequencing

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 g...

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Main Author:	Tumian, Afidalina
Format:	Article
Language:	English
Published:	Nature 2010
Subjects:	QH426 Genetics
Online Access:	http://irep.iium.edu.my/35279/ http://irep.iium.edu.my/35279/ http://irep.iium.edu.my/35279/ http://irep.iium.edu.my/35279/1/1000G.pdf

id	iium-35279
recordtype	eprints
spelling	iium-352792014-03-12T08:48:35Z http://irep.iium.edu.my/35279/ A map of human genome variation from population-scale sequencing Tumian, Afidalina QH426 Genetics 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 mother–father–child 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 10−8 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. Nature 2010-10-28 Article PeerReviewed application/pdf en http://irep.iium.edu.my/35279/1/1000G.pdf Tumian, Afidalina (2010) A map of human genome variation from population-scale sequencing. Nature, 467 (7319). pp. 1061-1073. ISSN 0028-0836 http://www.nature.com/nature/journal/v467/n7319/full/nature09534.html 10.1038/nature09534
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English
topic	QH426 Genetics
spellingShingle	QH426 Genetics Tumian, Afidalina A map of human genome variation from population-scale sequencing
description	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 mother–father–child 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 10−8 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.
format	Article
author	Tumian, Afidalina
author_facet	Tumian, Afidalina
author_sort	Tumian, Afidalina
title	A map of human genome variation from population-scale sequencing
title_short	A map of human genome variation from population-scale sequencing
title_full	A map of human genome variation from population-scale sequencing
title_fullStr	A map of human genome variation from population-scale sequencing
title_full_unstemmed	A map of human genome variation from population-scale sequencing
title_sort	map of human genome variation from population-scale sequencing
publisher	Nature
publishDate	2010
url	http://irep.iium.edu.my/35279/ http://irep.iium.edu.my/35279/ http://irep.iium.edu.my/35279/ http://irep.iium.edu.my/35279/1/1000G.pdf
first_indexed	2023-09-18T20:50:36Z
last_indexed	2023-09-18T20:50:36Z
_version_	1777409968763305984

A map of human genome variation from population-scale sequencing

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