Work

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

Year: 2014

Type: article

Abstract: 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.

Source: European Journal of Human Genetics

DOI: 10.1038/ejhg.2014.1

Authors: GCAN, Laura M Huckins, WTCCC3, Vesna Boraska, Christopher S Franklin, James A B Floyd, Lorraine Southam, Patrick F Sullivan, Cynthia M Bulik, David A Collier, Chris Tyler-Smith, Eleftheria Zeggini, Ioanna Tachmazidou

Institutions: Wellcome Sanger Institute, University of Split, University of North Carolina at Chapel Hill, King's College London

Language: English

Topic: Forensic and Genetic Research

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: hybrid

Estimated APC paid: $2,790

Funders: Unity through Knowledge Fund, Wellcome Trust, Foundation of Hope for Research and Treatment of Mental Illness, National Institute for Health and Care Research, British Heart Foundation, Medical Research Council, National Institute on Aging, National Institute of Mental Health

Awards: G2207605493, NIHR Senior Investigator Award, Megakarocyte and Platelet Biology and Genomics, G4839860845, G5144943808, Developmental Psychopathology of Restrictive and Binge Eating in Childhood, Understanding the genetic basis of common human diseases: core funding for the Wellcome Trust Centre for Human Genetics., DTG Competition 2011/8, NIHR Senior Investigator Award, Premature cardiovascular disease and platelet quantitative traits: identification and functional characterisation of novel high-penetrance mutations and rare alleles, Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers, Longevity Consortium

OpenAlex ID: W2119502270

FWCI: 3.065

Cites: 22

Cited by: 36

Related to: 10