Sequence kernel association test for survival traits

Genetic Epidemiology

Volumn 38, Issue 3, 2014, Pages 191-197

  Chen, Han ^a,b   Lumley, Thomas ^c   Brody, Jennifer ^d   Heard Costa, Nancy L ^e,f   Fox, Caroline S ^e,g   Cupples, L Adrienne ^a,e   Dupuis, Josée ^a,e  

^a BOSTON UNIVERSITY SCHOOL OF PUBLIC HEALTH   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c UNIVERSITY OF AUCKLAND   (New Zealand)

^d UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^e FRAMINGHAM HEART STUDY   (United States)

^f BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^g BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Cox proportional hazard model; Likelihood ratio test; Rare variant analysis; Variance component test

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENETIC ASSOCIATION; GENETIC PROCEDURES; GENETIC TRAIT; GENETIC VARIABILITY; GENOTYPE; HUMAN; META ANALYSIS (TOPIC); OBESITY; PHENOTYPE; PROPORTIONAL HAZARDS MODEL; SEQUENCE KERNEL ASSOCIATION TEST; SIMULATION; STATISTICAL ANALYSIS; SURVIVAL;

COX PROPORTIONAL HAZARD MODEL; LIKELIHOOD RATIO TEST; RARE VARIANT ANALYSIS; VARIANCE COMPONENT TEST;

COHORT STUDIES; GENETIC ASSOCIATION STUDIES; GENOTYPE; HEART; HUMANS; LOGISTIC MODELS; MODELS, GENETIC; OBESITY; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROPORTIONAL HAZARDS MODELS; RESEARCH DESIGN; SOFTWARE; SURVIVAL; SURVIVAL ANALYSIS; TIME FACTORS;

EID: 84895928909     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21791     Document Type: Article

References (18)

1. Bender R, Augustin T, Blettner M. 2005. Generating survival times to simulate Cox proportional hazards models. Stat Med 24:1713-1723.
2. Cai T, Tonini G, Lin X. 2011. Kernel machine approach to testing the significance of multiple genetic markers for risk prediction. Biometrics 67:975-986.
3. Chen H, Meigs JB, Dupuis J. 2013. Sequence kernel association test for quantitative traits in family samples. Genet Epidemiol 37:196-204.
4. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH. 2010. Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 11:446-450.
5. Fleming TR, Harrington DP, O'Sullivan M. 1987. Supremum Versions of the Log-Rank and Generalized Wilcoxon Statistics. J Am Stat Assoc 82:312-320.
6. Lee S, Emond MJ, Bamshad MJ, Barnes KC, Rieder MJ, Nickerson DA, NHLBI GO Exome Sequencing Project - ESP Lung Project Team, Christiani DC, Wurfel MM, Lin X. 2012. Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. Am J Hum Genet 91:224-237.
7. Lee S, Teslovich TM, Boehnke M, Lin X. 2013. General framework for meta-analysis of rare variants in sequencing association studies. Am J Hum Genet 93:42-53.
8. Li B, Leal SM. 2008. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83:311-321.
9. Lin X, Cai T, Wu MC, Zhou Q, Liu G, Christiani DC, Lin X. 2011. Kernel machine SNP-set analysis for censored survival outcomes in genome-wide association studies. Genet Epidemiol 35:620-631.
10. Lumley T, Brody J, Dupuis J, Cupples LA. 2012. Meta-analysis of a rare-variant association test. http://stattech.wordpress.fos.auckland.ac.nz/files/2012/11/skat-meta-paper.pdf
11. Madsen BE, Browning SR. 2009. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5:e1000384.
12. Morgenthaler S, Thilly WG. 2007. A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat Res 615:28-56.
13. Morris AP, Zeggini E. 2010. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34:188-193.
14. Neale BM, Rivas MA, Voight BF, Altshuler D, Devlin B, Orho-Melander M, Kathiresan S, Purcell SM, Roeder K, Daly MJ. 2011. Testing for an unusual distribution of rare variants. PLoS Genet 7:e1001322.
15. Pan W. 2009. Asymptotic tests of association with multiple SNPs in linkage disequilibrium. Genet Epidemiol 33:497-507.
16. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904-909.
17. Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, Jackson AU, Allen HL, Lindgren CM, Luan J, Mägi R and others. 2010. Association analyses of 249, 796 individuals reveal 18 new loci associated with body mass index. Nat Genet 42:937-948.
18. Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X. 2011. Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 89:82-93.