Covariate-modulated local false discovery rate for genome-wide association studies

Bioinformatics

Volumn 30, Issue 15, 2014, Pages 2098-2104

  Zablocki, Rong W ^a   Schork, Andrew J ^b   Levine, Richard A ^c   Andreassen, Ole A ^d   Dale, Anders M ^b,e   Thompson, Wesley K ^e  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

^d UNIVERSITY OF OSLO   (Norway)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF VARIANCE; ARTICLE; BAYES THEOREM; BIOLOGY; GENETIC ASSOCIATION; HUMAN; LABORATORY DIAGNOSIS; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANALYSIS OF VARIANCE; BAYES THEOREM; COMPUTATIONAL BIOLOGY; FALSE POSITIVE REACTIONS; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84904959814     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu145     Document Type: Article

References (33)

1. Anderson, C.A. et al. (2011) Meta-Analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat. Genet., 43, 246-252.
2. Andreassen, O.A. et al. (2013) Improved detection of common variants associated with schizophrenia by leveraging pleiotropy with cardiovascular disease risk factors. Am. J. Hum. Genet., 7, 197-209.
3. Andreassen, O.A. et al. (2013) Improved detection of common variants associated with schizophrenia and bipolar disorder using pleiotropy-informed conditional False Discovery Rate method. PLoS Genet., 9, e1003455.
4. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57, 289-300.
5. Brown, L. et al. (2005) Statistical analysis of a telephone call center: A queueingscience perspective. J. Am. Stat. Assoc., 100, 36-50.
6. Carbonetto, P. and Stephens, M. (2013) Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's Disease. PLoS Genet., 9, e1003770.
7. Cho, J.H. and Brant, S.R. (2011) Recent insights into the genetics of inflammatory bowel disease. Gastroenterology, 140, 1704-1712.
8. Collins, F. (2010) Has the revolution arrived? Nature, 464, 674-675.
9. Devlin, B. and Roeder, K. (1999) Genomic control for association studies. Biometrics, 55, 997-1004.
10. Efron, B. (2007) Size, power and false discovery rates. Ann. Stat., 35, 1351-1377.
11. Efron, B. (2010) Large-Scale Inference: Empirical Bayes Methods for Estimation, Testing, and Prediction. Cambridge:Cambridge University Press.
12. Efron, B. and Tibshirani, R. (2002) Empirical bayes methods and false discovery rates for microarrays. Genet. Epidemiol., 23, 70-86.
13. The ENCODE Consortium (2012) An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57-74.
14. Ferkingstad, E. et al. (2008) Unsupervised empirical bayesian multiple testing with external covariates. Ann. Appl. Stat., 2, 714-735.
15. Franke, A. et al. (2010) Genome-wide meta-Analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat. Genet., 42, 1118-1125.
16. Genovese, C.R. et al. (2002) Thresholding of statistical maps in functional neuroimaging using the false discovery rate. Neuroimage, 15, 870-878.
17. Givens, G.H. and Hoeting, J.A. (2005) Computational Statistics. Vol. 483. Wiley-Interscience Press, Hoboken, NJ, USA.
18. Hindorff, L.A. et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362-9367.
19. Hon-Cheong, H. et al. (2010) Estimating the total number of susceptibility variants underlying complex diseases from genome-wide association studies. PloS One, 5, e13898.
20. Lawyer, G. et al. (2009) Local and covariate-modulated false discovery rates applied in neuroimaging. Neuroimage, 47, 213-219.
21. Lewinger, J.P. et al. (2007) Hierarchical Bayes prioritization of marker associations from a genome-wide association scan for further investigation. Genet. Epidemiol., 31, 871-883.
22. Li, H. et al. (2010) A hidden Markov random field model for genome-wide association studies. Biostatistics, 11, 139-150.
23. Manolio, T.A. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
24. Miller, C.J. et al. (2001) Controlling the false discovery rate in astrophysical data analysis. Astron. J., 122, 3492-3505.
25. Ploner, A. et al. (2006) Multidimensional local false discovery rate for microarray studies. Bioinformatics, 22, 556-565.
26. Risch, N. and Merikangas, K. (1996) The future of genetic studies of complex human diseases. Science, 255, 1516-1517.
27. Schork, A.J. et al. (2013) Genetic architecture of the missing heritability for complex human traits and diseases. PLoS Genet., 9, e1003449.
28. Smith, E.N. et al. (2011) Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes. PLoS Genet., 7, e1002134.
29. Sun, L. et al. (2006) Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies. Genet. Epidemiol., 30, 519-530.
30. Torkamani, A. et al. (2011) Annotating individual human genomes. Genomics, 98, 233-241.
31. Tusher, V.G. et al. (2001) Significance analyses of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA, 98, 5116-5121.
32. Yang, B. et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nat. Genet., 42, 565-569.
33. Yang, J. et al. (2011) Genome partitioning of genetic variation for complex traits using common SNPs. Nat. Genet., 43, 519-525. Institutes of Health