Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia

The 1000 Genomes Project (1KG) aims to provide a comprehensive resource on human genetic variations. With an effort of sequencing 2,500 individuals, 1KG is expected to cover the majority of the human genetic diversities worldwide. In this study, using analysis of population structure based on genome...

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Main Authors:	Lu, Dongsheng, Xu, Shuhua
Format:	Online
Language:	English
Published:	Frontiers Media S.A. 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3701331/

id	pubmed-3701331
recordtype	oai_dc
spelling	pubmed-37013312013-07-11 Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia Lu, Dongsheng Xu, Shuhua Genetics The 1000 Genomes Project (1KG) aims to provide a comprehensive resource on human genetic variations. With an effort of sequencing 2,500 individuals, 1KG is expected to cover the majority of the human genetic diversities worldwide. In this study, using analysis of population structure based on genome-wide single nucleotide polymorphisms (SNPs) data, we examined and evaluated the coverage of genetic diversity of 1KG samples with the available genome-wide SNP data of 3,831 individuals representing 140 population samples worldwide. We developed a method to quantitatively measure and evaluate the genetic diversity revealed by population structure analysis. Our results showed that the 1KG does not have sufficient coverage of the human genetic diversity in Asia, especially in Southeast Asia. We suggested a good coverage of Southeast Asian populations be considered in 1KG or a regional effort be initialized to provide a more comprehensive characterization of the human genetic diversity in Asia, which is important for both evolutionary and medical studies in the future. Frontiers Media S.A. 2013-07-04 /pmc/articles/PMC3701331/ /pubmed/23847652 http://dx.doi.org/10.3389/fgene.2013.00127 Text en Copyright © Lu and Xu. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Lu, Dongsheng Xu, Shuhua
spellingShingle	Lu, Dongsheng Xu, Shuhua Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia
author_facet	Lu, Dongsheng Xu, Shuhua
author_sort	Lu, Dongsheng
title	Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia
title_short	Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia
title_full	Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia
title_fullStr	Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia
title_full_unstemmed	Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia
title_sort	principal component analysis reveals the 1000 genomes project does not sufficiently cover the human genetic diversity in asia
description	The 1000 Genomes Project (1KG) aims to provide a comprehensive resource on human genetic variations. With an effort of sequencing 2,500 individuals, 1KG is expected to cover the majority of the human genetic diversities worldwide. In this study, using analysis of population structure based on genome-wide single nucleotide polymorphisms (SNPs) data, we examined and evaluated the coverage of genetic diversity of 1KG samples with the available genome-wide SNP data of 3,831 individuals representing 140 population samples worldwide. We developed a method to quantitatively measure and evaluate the genetic diversity revealed by population structure analysis. Our results showed that the 1KG does not have sufficient coverage of the human genetic diversity in Asia, especially in Southeast Asia. We suggested a good coverage of Southeast Asian populations be considered in 1KG or a regional effort be initialized to provide a more comprehensive characterization of the human genetic diversity in Asia, which is important for both evolutionary and medical studies in the future.
publisher	Frontiers Media S.A.
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3701331/
_version_	1611991758728593408

Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia

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