Using ancestry-informative markers to identify fine structure across 15 populations of European origin

The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may hel...

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Main Authors:	Huckins, Laura M, Boraska, Vesna, Franklin, Christopher S, Floyd, James A B, Southam, Lorraine, Sullivan, Patrick F, Bulik, Cynthia M, Collier, David A, Tyler-Smith, Chris, Zeggini, Eleftheria, Tachmazidou, Ioanna
Format:	Online
Language:	English
Published:	Nature Publishing Group 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169539/

id	pubmed-4169539
recordtype	oai_dc
spelling	pubmed-41695392014-10-01 Using ancestry-informative markers to identify fine structure across 15 populations of European origin Huckins, Laura M Boraska, Vesna Franklin, Christopher S Floyd, James A B Southam, Lorraine Sullivan, Patrick F Bulik, Cynthia M Collier, David A Tyler-Smith, Chris Zeggini, Eleftheria Tachmazidou, Ioanna Article The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5% we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia. Nature Publishing Group 2014-10 2014-02-19 /pmc/articles/PMC4169539/ /pubmed/24549058 http://dx.doi.org/10.1038/ejhg.2014.1 Text en Copyright © 2014 Macmillan Publishers Limited http://creativecommons.org/licenses/by/3.0/ This work is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/
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	Huckins, Laura M Boraska, Vesna Franklin, Christopher S Floyd, James A B Southam, Lorraine Sullivan, Patrick F Bulik, Cynthia M Collier, David A Tyler-Smith, Chris Zeggini, Eleftheria Tachmazidou, Ioanna
spellingShingle	Huckins, Laura M Boraska, Vesna Franklin, Christopher S Floyd, James A B Southam, Lorraine Sullivan, Patrick F Bulik, Cynthia M Collier, David A Tyler-Smith, Chris Zeggini, Eleftheria Tachmazidou, Ioanna Using ancestry-informative markers to identify fine structure across 15 populations of European origin
author_facet	Huckins, Laura M Boraska, Vesna Franklin, Christopher S Floyd, James A B Southam, Lorraine Sullivan, Patrick F Bulik, Cynthia M Collier, David A Tyler-Smith, Chris Zeggini, Eleftheria Tachmazidou, Ioanna
author_sort	Huckins, Laura M
title	Using ancestry-informative markers to identify fine structure across 15 populations of European origin
title_short	Using ancestry-informative markers to identify fine structure across 15 populations of European origin
title_full	Using ancestry-informative markers to identify fine structure across 15 populations of European origin
title_fullStr	Using ancestry-informative markers to identify fine structure across 15 populations of European origin
title_full_unstemmed	Using ancestry-informative markers to identify fine structure across 15 populations of European origin
title_sort	using ancestry-informative markers to identify fine structure across 15 populations of european origin
description	The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5% we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia.
publisher	Nature Publishing Group
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169539/
_version_	1613135640950472704

Using ancestry-informative markers to identify fine structure across 15 populations of European origin

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