Quality control and conduct of genome-wide association meta-analyses Academic Article uri icon

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  • 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.


  • Meyre, David Jean-Claude
  • Winkler, Thomas W
  • Day, Felix R
  • Croteau-Chonka, Damien C
  • Wood, Andrew R
  • Locke, Adam E
  • Mägi, Reedik
  • Ferreira, Teresa
  • Fall, Tove
  • Graff, Mariaelisa
  • Justice, Anne E
  • Luan, Jian'an
  • Gustafsson, Stefan
  • Randall, Joshua C
  • Vedantam, Sailaja
  • Workalemahu, Tsegaselassie
  • Kilpeläinen, Tuomas O
  • Scherag, André
  • Esko, Tonu
  • Kutalik, Zoltán
  • Heid, Iris M
  • Loos, Ruth JF

publication date

  • May 2014