The (in)famous GWAS P-value threshold revisited and updated for low-frequency variants

European Journal of Human Genetics

Volumn 24, Issue 8, 2016, Pages 1202-1205

  Fadista, João ^a,b   Manning, Alisa K ^c,d   Florez, Jose C ^c,d,e   Groop, Leif ^b,f  

^a STATENS SERUM INSTITUT   (Denmark)

^b LUND UNIVERSITY DIABETES CENTRE   (Sweden)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

ANCESTRY GROUP; ARTICLE; EUROPEAN; EXOME; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; PRACTICE GUIDELINE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL SIGNIFICANCE; ALLELE; GENETIC HETEROGENEITY; GENETICS; MUTATION RATE; NON INSULIN DEPENDENT DIABETES MELLITUS; PROCEDURES; STANDARDS;

ALLELES; DIABETES MELLITUS, TYPE 2; EXOME; GENETIC HETEROGENEITY; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; MUTATION RATE;

EID: 84953318772     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2015.269     Document Type: Article

References (16)

1. International HapMap Consortium: A haplotype map of the human genome. Nature 2005; 437: 1299-1320.
2. Pe?er I, Yelensky R, Altshuler D, Daly MJ. Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet Epidemiol 2008; 32: 381-385.
3. Welter D, MacArthur J, Morales J, et al. The NHGRI GWAS Catalog, a curated resource of SNP-Trait associations. Nucleic Acids Res 2014; 42: D1001-D1006.
4. Bonferroni CE. Il calcolo delle assicurazioni su gruppi di teste. In Studi in Onore del Professore Salvatore Ortu Carboni. Bardi: Rome, Italy, 1935, pp 13-60.
5. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003; 100: 9440-9445.
6. Wellcome Trust Case Control Consortium: Genome-wide association study of 14000 cases of seven common diseases and 3000 shared controls. Nature 2007; 447: 661-678.
7. The International HapMap Consortium, Frazer KA, Ballinger DG, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449: 851-861.
8. 1000 Genomes Project Consortium, Abecasis GR, Auton A, et al. An integrated map of genetic variation from 1 092 human genomes. Nature 2012; 491: 56-65.
9. Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS: A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 2012; 28: 3326-3328.
10. Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics 2011; 27: 2156-2158.
11. Flicek P, Amode MR, Barrell D, et al. Ensembl 2014. Nucleic Acids Res 2014; 42: D749-D755.
12. Peltonen L, Jalanko A, Varilo T. Molecular genetics of the Finnish disease heritage. Hum Mol Genet 1999; 8: 1913-1923.
13. Service S, DeYoung J, Karayiorgou M, et al. Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies. Nat Genet 2006; 38: 556-560.
14. Wacholder S, Chanock S, Garcia-Closas M, et al. Assessing the probability that a positive report is false: an approach for molecular epidemiology studies. J Natl Cancer Inst 2004; 96: 434-442.
15. Sham PC, Purcell SM. Statistical power and significance testing in large-scale genetic studies. Nat Rev Genet 2014; 15: 335-346.
16. Stephens M, Balding DJ. Bayesian statistical methods for genetic association studies. Nat Rev Genet 2009; 10: 681-690.