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

被引：320

作者：

Winkler, Thomas W. ^{[1
]}

Day, Felix R. ^{[2
]}

Croteau-Chonka, Damien C. ^{[3
,4
,5
]}

Wood, Andrew R. ^{[6
]}

Locke, Adam E. ^{[7
,8
]}

Maegi, Reedik ^{[9
]}

Ferreira, Teresa ^{[10
]}

Fall, Tove ^{[11
,12
]}

Graff, Mariaelisa ^{[13
]}

Justice, Anne E. ^{[13
]}

Luan, Jian'an ^{[2
]}

Gustafsson, Stefan ^{[11
]}

Randall, Joshua C. ^{[14
]}

Vedantam, Sailaja ^{[15
,16
,17
,18
,19
]}

Workalemahu, Tsegaselassie ^{[20
]}

Kilpelainen, Tuomas O. ^{[21
]}

Scherag, Andre ^{[22
,23
]}

Esko, Tonu ^{[9
,15
,16
,17
,18
,19
]}

Kutalik, Zoltan ^{[24
,25
,26
]}

Heid, Iris M. ^{[1
]}

Loos, Ruth J. F. ^{[27
,28
,29
]}

机构：

[1] Univ Regensburg, Inst Epidemiol & Prevent Med, Dept Genet Epidemiol, D-93053 Regensburg, Germany

[2] Addenbrookes Hosp, Inst Metab Sci, MRC, Epidemiol Unit, Cambridge, England

[3] Univ N Carolina, Dept Genet, Chapel Hill, NC USA

[4] Brigham & Womens Hosp, Dept Med, Channing Div Network Med, Boston, MA 02115 USA

[5] Harvard Univ, Sch Med, Boston, MA USA

[6] Univ Exeter, Sch Med, Exeter, Devon, England

[7] Univ Michigan, Dept Biostat, Ann Arbor, MI 48109 USA

[8] Univ Michigan, Ctr Stat Genet, Ann Arbor, MI 48109 USA

[9] Univ Tartu, Estonian Genome Ctr, EE-50090 Tartu, Estonia

[10] Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford, England

[11] Uppsala Univ, Dept Med Sci, Mol Epidemiol & Sci Life Lab, Uppsala, Sweden

[12] Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden

[13] Univ N Carolina, Dept Epidemiol, Chapel Hill, NC USA

[14] Wellcome Trust Sanger Inst, Cambridge, England

[15] Boston Childrens Hosp, Div Endocrinol, Boston, MA USA

[16] Boston Childrens Hosp, Div Genet, Boston, MA USA

[17] Boston Childrens Hosp, Ctr Basic & Translat Obes Res, Boston, MA USA

[18] Broad Inst, Program Med & Populat Genet, Cambridge, MA USA

[19] Harvard Univ, Sch Med, Dept Genet, Boston, MA USA

[20] Harvard Univ, Sch Publ Hlth, Dept Nutr, Boston, MA 02115 USA

[21] Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn, Ctr Basic Metab Res,Sect Metab Genet, Copenhagen, Denmark

[22] Univ Duisburg Essen, Univ Hosp Essen, Inst Med Informat Biometry & Epidemiol, Essen, Germany

[23] Jena Univ Hosp, Ctr Sepsis Control & Care, Integrated Res & Treatment Ctr, Jena, Germany

[24] Univ Lausanne, Dept Med Genet, Lausanne, Switzerland

[25] CHU Vaudois, Inst Social & Prevent Med IUMSP, CH-1011 Lausanne, Switzerland

[26] Swiss Inst Bioinformat, Lausanne, Switzerland

[27] Icahn Sch Med Mt Sinai, Charles Bronfman Inst Personalized Med, New York, NY 10029 USA

[28] Icahn Sch Med Mt Sinai, Mindich Child Hlth & Dev Inst, New York, NY USA

[29] Icahn Sch Med Mt Sinai, Genet Obes & Related Metab Traits Program, New York, NY USA

来源：

NATURE PROTOCOLS | 2014年 / 9卷 / 05期

基金：

欧洲研究理事会; 美国国家卫生研究院; 瑞士国家科学基金会; 英国医学研究理事会;

关键词：

ANALYSES IDENTIFY; GLYCEMIC TRAITS; LOCI; VARIANTS; MASS;

D O I：

10.1038/nprot.2014.071

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1192 / 1212

页数：21

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