Evidence map›Paper›PMID 24762786›Full record

ArticleNature protocols2014

Quality control and conduct of genome-wide association meta-analyses.

Thomas W Winkler, Felix R Day, Damien C Croteau-Chonka, Andrew R Wood, Adam E Locke, Reedik Mägi, Teresa Ferreira, Tove Fall, Mariaelisa Graff, Anne E Justice and 12 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature protocols, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 340 papers, 55 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
340citing papers in PubMed, 55 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

340 citing papers in PubMed, 55 syntheses or guidelines pooled it.

  1. Genome-wide meta-analysis with 1,590,596 individuals identifies 12 novel risk loci for systemic lupus erythematosus.Mammalian genome : official journal of the International Mammalian Genome Society · 2026
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  17. A genome-wide association meta-analysis of all-cause and vascular dementia.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024
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280 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors.

Thomas W WinklerDepartment of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany.
Felix R DayMedical Research Council (MRC) Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.ORCID 0000000337897651
Damien C Croteau-Chonka1] Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
Andrew R WoodGenetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
Adam E LockeDepartment of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Reedik MägiEstonian Genome Center, University of Tartu, Tartu, Estonia.
Teresa FerreiraWellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Tove Fall1] Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden. [2] Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
Mariaelisa GraffDepartment of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA.
Anne E JusticeDepartment of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA.
Jian'an LuanMedical Research Council (MRC) Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.
Stefan GustafssonDepartment of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Joshua C RandallWellcome Trust Sanger Institute, Cambridge, UK.
Sailaja Vedantam1] Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [3] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
Tsegaselassie WorkalemahuDepartment of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA.
Tuomas O KilpeläinenThe Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
André Scherag1] Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany. [2] Clinical Epidemiology, Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.
Tonu Esko1] Estonian Genome Center, University of Tartu, Tartu, Estonia. [2] Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [4] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
Zoltán Kutalik1] Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland. [2] Institute of Social and Preventive Medicine (IUMSP), Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland. [3] Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Iris M Heid1] Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany. [2].
Ruth J F Loos1] The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [3] The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [4].
Genetic Investigation of Anthropometric Traits (GIANT) Consortium

Funding

The Genetic Epidemiology of Asthma in Costa RicaR37HL066289 · NHLBI · BRIGHAM AND WOMEN'S HOSPITAL · PI WEISS, SCOTT T · 2007 to 2015
$14.6M
SYSTEMS APPROACHES TO THE EPIDEMIOLOGY, GENETICS AND GENOMICS OF LUNG DISEASEST32HL007427 · NHLBI · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI DAWN L DEMEO, Edwin K Silverman · 1985 to 2026
$13.6M
Cell Interactions in the Inflamed Intestinal MucosaR01DK075787 · NIDDK · BOSTON CHILDREN'S HOSPITAL · PI JOEL N HIRSCHHORN · 2007 to 2026
$13.1M
Cardiovascular Epidemiology Training GrantT32HL007055 · NHLBI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Wayne D. Rosamond · 1986 to 2026
$10.0M
Genetic Epidemiology of Body Mass Index, Adiposity and Weight GainR01DK078150 · NIDDK · UNIV OF NORTH CAROLINA CHAPEL HILL · PI MOHLKE, KAREN L. · 2007 to 2010
$2.3M
Cancer Research UK 14136Chief Scientist Office CZB/4/672Medical Research Council G0401527Medical Research Council G1000143Medical Research Council MC_U106179471Medical Research Council MC_U106179472Medical Research Council MC_UU_12015/1Medical Research Council MC_UU_12015/2Medical Research Council MR/J012165/1Medical Research Council MR/K013351/1Medical Research Council U106179471Medical Research Council U106179472NHLBI NIH HHS R37 HL066289NHLBI NIH HHS T32 HL007055NHLBI NIH HHS T32 HL007427NIDDK NIH HHS DK078150NIDDK NIH HHS R01 DK075787NIDDK NIH HHS R01DK075787NIDDK NIH HHS R01 DK078150Wellcome Trust 097117
6 · The paper itself

Abstract

Rigorous organization and quality control (QC) are necessary to facilitate successful genome-wide association meta-analyses (GWAMAs) of statistics aggregated across multiple genome-wide association studies. This protocol provides guidelines for (i) organizational aspects of GWAMAs, and for (ii) QC at the study file level, the meta-level across studies and the meta-analysis output level. Real-world examples highlight issues experienced and solutions developed by the GIANT Consortium that has conducted meta-analyses including data from 125 studies comprising more than 330,000 individuals. We provide a general protocol for conducting GWAMAs and carrying out QC to minimize errors and to guarantee maximum use of the data. We also include details for the use of a powerful and flexible software package called EasyQC. Precise timings will be greatly influenced by consortium size. For consortia of comparable size to the GIANT Consortium, this protocol takes a minimum of about 10 months to complete.

Indexed as

Meta-Analysis as TopicQuality ControlSoftwareGenome-Wide Association Study

Identifiers

PMID24762786
PMCPMC4083217

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.