Title |
Quality control and conduct of genome-wide association meta-analyses
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Published in |
Nature Protocols, April 2014
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DOI | 10.1038/nprot.2014.071 |
Pubmed ID | |
Authors |
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, Jian'an Luan, Stefan Gustafsson, Joshua C Randall, Sailaja Vedantam, Tsegaselassie Workalemahu, Tuomas O Kilpeläinen, André Scherag, Tonu Esko, Zoltán Kutalik, Iris M Heid, Ruth J F Loos |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 2 | 33% |
India | 2 | 33% |
Norway | 1 | 17% |
Netherlands | 1 | 17% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 3 | 50% |
Scientists | 2 | 33% |
Practitioners (doctors, other healthcare professionals) | 1 | 17% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 4 | <1% |
United Kingdom | 4 | <1% |
Chile | 3 | <1% |
Canada | 3 | <1% |
Australia | 2 | <1% |
Brazil | 2 | <1% |
Spain | 2 | <1% |
Denmark | 2 | <1% |
Finland | 1 | <1% |
Other | 11 | 1% |
Unknown | 764 | 96% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 206 | 26% |
Student > Ph. D. Student | 203 | 25% |
Student > Master | 70 | 9% |
Student > Bachelor | 62 | 8% |
Other | 35 | 4% |
Other | 122 | 15% |
Unknown | 100 | 13% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 219 | 27% |
Biochemistry, Genetics and Molecular Biology | 177 | 22% |
Medicine and Dentistry | 113 | 14% |
Neuroscience | 36 | 5% |
Computer Science | 24 | 3% |
Other | 99 | 12% |
Unknown | 130 | 16% |