Journal
JOURNAL OF HUMAN GENETICS
Volume 61, Issue 10, Pages 861-866Publisher
SPRINGERNATURE
DOI: 10.1038/jhg.2016.72
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Funding
- Japan Society for the Promotion of Science (JSPS) KAKENHI grant [15H05670, 15H05907, 15H05911, 15K14429]
- Japan Science and Technology Agency (JST)
- Mochida Memorial Foundation for Medical and Pharmaceutical Research
- Takeda Science Foundation
- Gout Research Foundation
- Tokyo Biochemical Research Foundation
- Japan Rheumatism Foundation
- Grants-in-Aid for Scientific Research [15H05907, 15K14429, 15H05670, 15H05911] Funding Source: KAKEN
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To assess the statistical significance of associations between variants and traits, genome-wide association studies (GWAS) should employ an appropriate threshold that accounts for the massive burden of multiple testing in the study. Although most studies in the current literature commonly set a genome-wide significance threshold at the level of P = 5.0 x 10(-8), the adequacy of this value for respective populations has not been fully investigated. To empirically estimate thresholds for different ancestral populations, we conducted GWAS simulations using the 1000 Genomes Phase 3 data set for Africans (AFR), Europeans (EUR), Admixed Americans (AMR), East Asians (EAS) and South Asians (SAS). The estimated empirical genome-wide significance thresholds were P-sig = 3.24 x 10(-8) (AFR), 9.26 x 10(-8) (EUR), 1.83 x 10(-7) (AMR), 1.61 x 10(-7) (EAS) and 9.46 x 10(-8) (SAS). We additionally conducted trans-ethnic meta-analyses across all populations (ALL) and all populations except for AFR (Delta AFR), which yielded P-sig = 3.25 x 10(-8) (ALL) and 4.20 x 10(-8) (Delta AFR). Our results indicate that the current threshold (P = 5.0 x 10(-8)) is overly stringent for all ancestral populations except for Africans; however, we should employ a more stringent threshold when conducting a meta-analysis, regardless of the presence of African samples.
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