Weighted score tests implementing model-averaging schemes in detection of rare variants in case-control studies

PLoS ONE

Volumn 10, Issue 10, 2015, Pages

  Coombes, Brandon ^a   Basu, Saonli ^a   Guha, Sharmistha ^a   Schork, Nicholas ^b  

^a UNIVERSITY OF MINNESOTA   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AVERAGING; CASE CONTROL STUDY; CONTROLLED STUDY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; MAJOR CLINICAL STUDY; RARE VARIANT; STATISTICAL ANALYSIS; STATISTICAL MODEL; STATISTICAL SIGNIFICANCE; WEIGHTED SCORE TEST; ALGORITHM; ALLELE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE FREQUENCY; GENETIC ASSOCIATION STUDY; GENETIC PREDISPOSITION; GENETIC VARIATION; GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

ACYLGLYCEROL LIPASE; AMIDASE; FATTY-ACID AMIDE HYDROLASE;

ALGORITHMS; ALLELES; AMIDOHYDROLASES; CASE-CONTROL STUDIES; COMPUTER SIMULATION; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; HUMANS; MODELS, GENETIC; MONOACYLGLYCEROL LIPASES; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84947288087     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0139355     Document Type: Article

References (33)

1. Manolio T, Collins F, Cox N, Goldstein D, Hindorff L, Hunter D, et al. Finding The Missing Heritability of Complex Diseases. Nature. 2009; 461:747-753. doi: 10.1038/nature08494 PMID: 19812666
2. Zuk O, Hechter E, Sunyaev S, Lander E. The Mystery of Missing Heritability: Genetic Interactions Create Phantom Heritability. Proceedings of the National Academy of Sciences. 2012; 109:1193-1198. doi: 10.1073/pnas.1119675109
3. Lee S, Wray N, Goddard M, Visscher P. Estimating Missing Heritability for Disease from Genome-wide Association Studies. The American Journal of Human Genetics. 2011; 88:294-305. doi: 10.1016/j. ajhg.2011.02.002 PMID: 21376301
4. Slatkin M. Epigenetic Inheritance and The Missing Heritability Problem. Genetics. 2009; 182:845-850. doi: 10.1534/genetics.109.102798 PMID: 19416939
5. Pan W. Asymptotic tests of association with multiple SNPs in linkage disequilibrium. Genetic Epidemiology. 2009; 33(6):497-507. doi: 10.1002/gepi.20402 PMID: 19170135
6. Morgenthaler S, Thilly W. A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutation Research. 2007; 615(1-2):28-56. doi: 10.1016/j.mrfmmm.2006.09.003 PMID: 17101154
7. Li B, Leal S. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. The American Journal of Human Genetics. 2009; 83:311-321. doi: 10. 1016/j.ajhg.2008.06.024
8. Madsen B, Browning S. A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic. PLoS Genetics. 2009; 5(2):e1000384. doi: 10.1371/journal.pgen.1000384 PMID: 19214210
9. Liu D, Leal S. A Novel Adaptive Method for the Analysis of Next-Generation Sequencing Data to Detect Complex Trait Associations with Rare Variants Due to Gene Main Effects and Interactions. PLoS Genetics. 2010; 6(10):1-14. doi: 10.1371/journal.pgen.1001156
10. Ionita-Laza I, Buxbaum J, Laird N, Lange C. A new testing strategy to identify rare variants with either risk or protective effect on disease. PLoS Genetics. 2011; 7(2):e1001289. doi: 10.1371/journal.pgen. 1001289 PMID: 21304886
11. Asimit J, Day-Williams A, Morris A, Zeggini E. ARIEL and AMELIA: testing for an accumulation of rare variants using next-generation sequencing data. Hum Hered. 2012; 73:84-94. doi: 10.1159/000336982 PMID: 22441326
12. Lin D, Tang Z. A general framework for detecting disease associations with rare variants in sequencing studies. Am J Hum Genet. 2012; 89:354-367. doi: 10.1016/j.ajhg.2011.07.015
13. Basu S, Pan W, Oetting WS. A dimension reduction approach for modeling multilocus interaction in case-control studies. Human Heredity. 2011; 71(4):234-245. doi: 10.1159/000328842 PMID: 21734407
14. Basu S, Pan W. Comparison of Statistical Tests for Association with Rare Variants. Genetic Epidemiology. 2011; 35:606-619. doi: 10.1002/gepi.20609 PMID: 21769936
15. Price A, Kryukov G, de Bakker P, Purcell S, Staples J, LJ W, et al. Pooled association tests for rare variants in exon-resequencing studies. The American Journal of Human Genetics. 2010; 86(6):982. doi: 10.1016/j.ajhg.2010.04.005
16. Bhatia G, Bansal V, Harismendy O, Schork N, Topol E, Frazer K, et al. A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes. PLOS Computational Biology. 2010;p. doi: 10.1371/journal.pcbi.1000954 PMID: 20976246
17. Zhang Z, Sha Q, Wang X, Zhang S. Detection of rare variant effects in association studies: extreme values, iterative regression, and a hybrid approach. BMC Proceedings. 2011; 5(9):S112. doi: 10.1186/1753-6561-5-S9-S112 PMID: 22373188
18. Hoffmann T, Marini N, Witte J. Comprehensive Approach to Analyzing Rare Genetic Variants. PLoS One. 2010; 5:e13584. doi: 10.1371/journal.pone.0013584 PMID: 21072163
19. Neale B, Rivas M, Voight B, Altshuler D, Devlin B, Orho-Melander M, et al. Testing for an unusual distribution of rare variants. PLoS Genetics. 2011; 7(3):e1001322. doi: 10.1371/journal.pgen.1001322 PMID: 21408211
20. Wu M, Lee S, Cai T, Li Y, Boehnke M, Lin X. Rare Variant Association Testing for Sequencing Data Using the Sequence Kernel Association Test (SKAT). Am J Hum Genet. 2011; 89:82-93. doi: 10.1016/j.ajhg.2011.05.029 PMID: 21737059
21. Lee S, Wu M, Lin X. Optimal tests for rare variant effects in sequencing association studies. Biostatistics. 2012; 13:762-775. doi: 10.1093/biostatistics/kxs014 PMID: 22699862
22. Derkach A, Lawless J, Sun L. Robust and powerful tests for rare variants using Fisher's method to combine evidence of association from two or more complementary tests. Genet Epidemiol. 2013; 37:110-121. doi: 10.1002/gepi.21689 PMID: 23032573
23. Sun J, Zheng Y, Hsu L. A unified mixed-effects model for rare-variant association in sequencing studies. Genet Epidemiol. 2013; 37:334-344. doi: 10.1002/gepi.21717 PMID: 23483651
24. Lee S, Abecasis G, Boehnke M, Lin X. Rare-Variant Association Analysis: Study Designs and Statistical Tests. Am J Hum Gen. 2014; 95:5-23. doi: 10.1016/j.ajhg.2014.06.009
25. Ionita-Laza I, Lee S, Makarov V, Buxbaum J, Lin X. Sequence Kernel Association Tests for the Combined Effect of Rare and Common Variants. Am J Hum Gen. 2013; 92:841-853. doi: 10.1016/j.ajhg. 2013.04.015
26. Burnham K, Anderson D. In: Model Selection and Multimodel Inference. 2nd ed. Berlin: Springer; 2002. p. 20-23.
27. Raftery A, Madigan D, Hoeting J. Bayesian model averaging for linear regression models. JASA. 1997; 92:179-191. doi: 10.1080/01621459.1997.10473615
28. Hoeting J, Madigan D, Raftery A, Volinsky C. Bayesian Model Averaging: A tutorial (with discussion). Statistical Science. 1999; 14:382-401.
29. Viallefont V, Raftery A, Richardson S. Variable selection and Bayesian model averaging in epidemiological case-control studies. Statistics in Medicine. 2001; 20:3215-3230.
30. Madigan D, Raftery A. Model selection and accounting for model uncertainty in graphical models using Occam's window. JASA. 1994; 89(428):1535-1546. doi: 10.1080/01621459.1994.10476894
31. Bansal V, Libiger O, Torkamani A, Schork N. An application and empirical comparison of statistical analysis methods for associating rare variants to a complex phenotype. Pacific Symposium on Biocomputing Proceedings. 2011;p. 16.
32. Lewontin R. The interaction of selection and linkage. I. General considerations heterotic models. Genetics. 1964; 49(1):49-67. PMID: 17248194
33. Bůžková P, Lumley T, Rice K. Permutation and Parametric Bootstrap Tests for Gene-Gene and Gene-Environment Interactions. Annals of Human Genetics. 2011; 75:36-45. doi: 10.1111/j.1469-1809.2010. 00572.x PMID: 20384625