Title
Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair
Date Issued
01 February 2018
Access level
open access
Resource Type
journal article
Author(s)
Liu F.
Chen Y.
Zhu G.
Hysi P.G.
Wu S.
Adhikari K.
Breslin K.
Pośpiech E.
Hamer M.A.
Peng F.
Muralidharan C.
Acuna-Alonzo V.
Canizales-Quinteros S.
Bedoya G.
Rothhammer F.
Bortolini M.C.
Gonzalez-Jose R.
Zeng C.
Xu S.
Jin L.
Uitterlinden A.G.
Arfan Ikram M.
van Duijn C.M.
Nijsten T.
Walsh S.
Branicki W.
Wang S.
Ruiz-Linares A.
Spector T.D.
Martin N.G.
Medland S.E.
Kayser M.
Publisher(s)
Oxford University Press
Abstract
Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P<5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62-0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans.
Start page
559
End page
575
Volume
27
Issue
3
Language
English
OCDE Knowledge area
Genética humana
Scopus EID
2-s2.0-85042605116
PubMed ID
Source
Human Molecular Genetics
ISSN of the container
09646906
Sponsor(s)
TZL and UYG studies: National Natural Science Foundation of China (NSFC) (grant numbers 91631307 to SW, 30890034 and 31271338 to LJ, 91731303 and 31771388 to SX), the Science and Technology Commission of Shanghai Municipality (grant number 16JC1400504 to LJ and SW), the Chinese Academy of Sciences (grant number XDB13041000 to SW and SX), the National Basic Research Program (2015FY111700 to LJ and SW), the National Program for Top-notch Young Innovative Talents of The ‘Wanren Jihua’ Project to SX, the National Thousand Young Talents Award to SW, Max Planck-CAS Paul Gerson Unna Independent Research Group Leadership Award to SW. Rotterdam Study: Erasmus MC University Medical Center, Rotterdam, Unilever and funds from the Netherlands Genomics Initiative/Netherlands Organization of Scientific Research (NWO) within the framework of the Netherlands Consortium of Healthy Ageing (NCHA). The generation and management of GWAS genotype data for the Rotterdam Study (RS I, RS II, RS III) was executed by the Human Genotyping Facility of the Genetic Laboratory of the Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands. The GWAS datasets are supported by the Netherlands Organisation of Scientific Research NWO Investments (nr. 175.010.2005.011, 911–03-012), the Genetic Laboratory of the Department of Internal Medicine, Erasmus MC, the Research Institute for Diseases in the Elderly (014–93-015; RIDE2), the Netherlands Genomics Initiative (NGI)/Netherlands Organisation for Scientific Research (NWO) Netherlands Consortium for Healthy Aging (NCHA), project nr. 050–060-810. Author FL is supported by the Erasmus University Rotterdam (EUR) fellowship and a Chinese recruiting program ‘The National Thousand Young Talents Award’. The Rotterdam Study is funded by Erasmus Medical Center and Erasmus University, Rotterdam, Netherlands Organization for the Health Research and Development (ZonMw), the Research Institute for Diseases in the Elderly (RIDE), the Ministry of Education, Culture and Science, the Ministry for Health, Welfare and Sports, the European Commission (DG XII), and the Municipality of Rotterdam. European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 285487 (EUROFORGEN-NoE). Rotterdam Study: Erasmus MC University Medical Center, Rotterdam, Unilever and funds from the Netherlands Genomics Initiative/Netherlands Organization of Scientific Research (NWO) within the framework of the Netherlands Consortium of Healthy Ageing (NCHA). The generation and management of GWAS genotype data for the RotterdamStudy (RS I, RS II, RS III) was executed by the Human Genotyping Facility of the Genetic Laboratory of the Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands. The GWAS datasets are supported by the Netherlands Organisation of Scientific Research NWO Investments (nr. 175.010.2005.011, 911-03-012), the Genetic Laboratory of the Department of Internal Medicine, Erasmus MC, the Research Institute for Diseases in the Elderly (014-93-015; RIDE2), the Netherlands Genomics Initiative (NGI)/Netherlands Organisation for Scientific Research (NWO) Netherlands Consortium for Healthy Aging (NCHA), project nr. 050-060-810. Author FL is supported by the Erasmus University Rotterdam (EUR) fellowship and a Chinese recruiting program 'The National Thousand Young Talents Award'. The Rotterdam Study is funded by Erasmus Medical Center and Erasmus University, Rotterdam, Netherlands Organization for the Health Research and Development (ZonMw), the Research Institute for Diseases in the Elderly (RIDE), the Ministry of Education, Culture and Science, the Ministry for Health, Welfare and Sports, the European Commission (DG XII), and the Municipality of Rotterdam. QIMR study: Australian National Health and Medical Research Council (NHMRC) grants 241944, 339462, 389927, 389875, 389891, 389892, 389938, 442915, 442981, 496739, 552485, 552498 and Australian Research Council grants A7960034, A79906588, A79801419, DP0770096, DP0212016, DP0343921 for building and maintaining the adolescent twin family resource through which samples were collected. SEM is supported by an NHMRC fellowship APP1103623. TwinsUK study: Wellcome Trust, Medical Research Council, European Union (FP7/2007-2013), the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust in partnership with King's College London. ERF Study: Joint grant from the Netherlands Organization for Scientific Research (NWO, 91203014), the Center of Medical Systems Biology (CMSB), Hersenstichting Nederland, Internationale Stichting Alzheimer Onderzoek (ISAO), Alzheimer Association project number 04516, Hersenstichting Nederland project number 12F04(2).76, and the Interuniversity Attraction Poles (IUAP) program. As a part of EUROSPAN (European Special Populations Research Network) ERF was supported by European Commission FP6 STRP grant number 018947 (LSHG-CT-2006-01947) and also received funding from the European Community's Seventh Framework Programme (FP7/2007-2013)/grant agreement HEALTHF4- 2007-201413 by the European Commission under the programme 'Quality of Life and Management of the Living Resources' of 5th Framework Programme (no. QLG2-CT-2002-01254). Highthroughput analysis of the ERF data was supported by joint grant from Netherlands Organization for Scientific Research and the Russian Foundation for Basic Research (NWO-RFBR 047.017.043). CANDELA study: Leverhulme Trust (F/07 134/DF to ARL), BBSRC (BB/I021213/1 to ARL); Universidad de Antioquia, Colombia (CPT-1602, Estrategia para sostenibilidad 2016-2018 grupo GENMOL to GB). TZL and UYG studies: National Natural Science Foundation of China (NSFC) (grant numbers 91631307 to SW, 30890034 and 31271338 to LJ, 91731303 and 31771388 to SX), the Science and Technology Commission of Shanghai Municipality (grant number 16JC1400504 to LJ and SW), the Chinese Academy of Sciences (grant number XDB13041000 to SW and SX), the National Basic Research Program (2015FY111700 to LJ and SW), the National Program for Top-notch Young Innovative Talents of The 'Wanren Jihua' Project to SX, the National Thousand Young Talents Award to SW, Max Planck-CAS Paul Gerson Unna Independent Research Group Leadership Award to SW. POL study: National Science Centre in Poland SONATA 8 no 2014/15/D/NZ8/00282. Foundation for Polish Science within the programme START 2017 to EP. US study: US National Institute of Justice (NIJ) Grant 2014-DN-BX-K031 and the US Department of Defense (DOD) DURIP-66843LSRIP-2015. Funding to pay the Open Access publication charges for this article was provided by the National Thousand Young Talents Award to FL. QIMR study: Australian National Health and Medical Research Council (NHMRC) grants 241944, 339462, 389927, 389875, 389891, 389892, 389938, 442915, 442981, 496739, 552485, 552498 and Australian Research Council grants A7960034, A79906588, A79801419, DP0770096, DP0212016, DP0343921 for building and maintaining the adolescent twin family resource through which samples were collected. SEM is supported by an NHMRC fellowship APP1103623. ERF Study: Joint grant from the Netherlands Organization for Scientific Research (NWO, 91203014), the Center of Medical Systems Biology (CMSB), Hersenstichting Nederland, Internationale Stichting Alzheimer Onderzoek (ISAO), Alzheimer Association project number 04516, Hersenstichting Nederland project number 12F04(2).76, and the Interuniversity Attraction Poles (IUAP) program. As a part of EUROSPAN (European Special Populations Research Network) ERF was supported by European Commission FP6 STRP grant number 018947 (LSHG-CT-2006–01947) and also received funding from the European Community’s Seventh Framework Programme (FP7/2007–2013)/grant agreement HEALTH-F4–2007-201413 by the European Commission under the programme ‘Quality of Life and Management of the Living Resources’ of 5th Framework Programme (no. QLG2-CT-2002–01254). High-throughput analysis of the ERF data was supported by joint grant from Netherlands Organization for Scientific Research and the Russian Foundation for Basic Research (NWO-RFBR 047.017.043). CANDELA study: Leverhulme Trust (F/07 134/DF to ARL), BBSRC (BB/I021213/1 to ARL); Universidad de Antioquia, Colombia (CPT-1602, Estrategia para sostenibilidad 2016–2018 grupo GENMOL to GB).
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