Cited by 1,712Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and AnimalsGenetic and phenotypic traits in livestock

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Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits

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Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Yang, Jian, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Ferreira, Teresa, Morris, Andrew P, Medland, Sarah E, Madden, Pamela A F, Heath, Andrew C, Martin, Nicholas G, Montgomery, Grant W, Weedon, Michael N, Loos, Ruth J, Frayling, Timothy M, McCarthy, Mark I, Hirschhorn, Joel N, Goddard, Michael E, Visscher, Peter M·2012·Nature Genetics

DOI 10.1038/ng.2213PMC PMC3593158

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Abstract

We present an approximate conditional and joint association analysis that can use summary-level statistics from a meta-analysis of genome-wide association studies (GWAS) and estimated linkage disequilibrium (LD) from a reference sample with individual-level genotype data. Using this method, we analyzed meta-analysis summary data from the GIANT Consortium for height and body mass index (BMI), with the LD structure estimated from genotype data in two independent cohorts. We identified 36 loci with multiple associated variants for height (38 leading and 49 additional SNPs, 87 in total) via a genome-wide SNP selection procedure. The 49 new SNPs explain approximately 1.3% of variance, nearly doubling the heritability explained at the 36 loci. We did not find any locus showing multiple associated SNPs for BMI. The method we present is computationally fast and is also applicable to case-control data, which we demonstrate in an example from meta-analysis of type 2 diabetes by the DIAGRAM Consortium.

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Authors: Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Yang, J., DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Ferreira, T., Morris, A. P., Medland, S. E., Madden, P. A. F., Heath, A. C., Martin, N. G., Montgomery, G. W., Weedon, M. N., Loos, R. J., Frayling, T. M., McCarthy, M. I., Hirschhorn, J. N., Goddard, M. E., & Visscher, P. M.
Affiliations: QIMR Berghofer Medical Research Institute (AU)
Centre for Human Genetics (GB)
Washington University in St. Louis (US)
University of Exeter (GB)
Addenbrooke's Hospital (GB)
Broad Institute (US)
The University of Melbourne (AU)
The University of Queensland (AU)
Corresponding author: Visscher, Peter M
ORCID: Yang, Jian
Ferreira, Teresa
Morris, Andrew P
Medland, Sarah E
Madden, Pamela A F
Heath, Andrew C
Martin, Nicholas G
Montgomery, Grant W
Weedon, Michael N
Loos, Ruth J
Frayling, Timothy M
McCarthy, Mark I
Hirschhorn, Joel N
Goddard, Michael E
Visscher, Peter M
Venue: Nature Genetics
Publisher: Springer Science and Business Media LLC
Published: 2012-03-18
Volume: 44
Issue: 4
Pages: 369-375
ISSN: 1061-4036 (ISSN-L)
1546-1718
DOI: 10.1038/ng.2213
PMC: PMC3593158
OpenAlex: W2152885121
Cited by: 1,712
References: 37
Citations by year: 2026: 144 · 2025: 168 · 2024: 230 · 2023: 186 · 2022: 172 · 2021: 159 · 2020: 124 · 2019: 127 · 2018: 104 · 2017: 92 · 2016: 61 · 2015: 43 · 2014: 42 · 2013: 44 · 2012: 16
FWCI: 27.95
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature Genetics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Site cant be reached (submittedVersion)
University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
Funders: Wellcome Trust (WT083270, 090532)
U.S. Public Health Service (HHSN 268200625226C)
National Institute on Alcohol Abuse and Alcoholism (AA-10248, K05AA017688, R01AA013321, AA13320, AA13321, AA-014041, R01AA013326, AA13326, R01AA013320, R01AA014041, R01AA007535)
National Heart, Lung, and Blood Institute (HHSN268201 100012C, HHSN268201100007I, HHSN268201100007C, HHSN2682 01100008C, HH-SN-268201100006C, HHSN268201100011C, HHSN2682011-00005I, HHSN2682011-00009I, R01 HL-59367, HHSN268201100005C, HHSN268201100005G, HHSN268201100010C, HHSN268201100011I, R01HL087641, R01HL059367, HHSN26820 1100009C, HHSN2682011-00008I, R01HL086694)
National Institute on Drug Abuse (R56DA012854, DA12854, R01DA012854)
National Human Genome Research Institute (U01HG004402)
National Center for Research Resources (UL1RR025005)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Keywords: GWAS summary statistics, linkage disequilibrium, height, body mass index, type 2 diabetes, heritability, complex traits, case-control data
MeSH terms: Algorithms, Body Height, Data Interpretation, Statistical, Diabetes Mellitus, Type 2, Genotype, Humans, Phenotype, Genetic Variation, Meta-Analysis as Topic, Linkage Disequilibrium, Genome, Human, Body Mass Index, Case-Control Studies, Polymorphism, Single Nucleotide, Cyclin-Dependent Kinase Inhibitor p15, Genome-Wide Association Study, Genetic Loci

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Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits

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