A generalized genetic random field method for the genetic association analysis of sequencing data

Genetic Epidemiology

Volumn 38, Issue 3, 2014, Pages 242-253

  Li, Ming ^a   He, Zihuai ^b   Zhang, Min ^b   Zhan, Xiaowei ^b   Wei, Changshuai ^c   Elston, Robert C ^d   Lu, Qing ^c  

^a UNIVERSITY OF ARKANSAS FOR MEDICAL SCIENCES   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

^c MICHIGAN STATE UNIVERSITY   (United States)

^d CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Generalized estimating equation; Rare variants; Small scale sequencing studies

Indexed keywords

TRIACYLGLYCEROL;

ARTICLE; CHROMOSOME 22; COMPARATIVE STUDY; CONTROLLED STUDY; DATA ANALYSIS; EXOME; GENE FREQUENCY; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOTYPE; HUMAN; PHENOTYPE; SIMULATION; TRIACYLGLYCEROL BLOOD LEVEL;

GENERALIZED ESTIMATING EQUATION; RARE VARIANTS; SMALL-SCALE SEQUENCING STUDIES;

ANGIOPOIETINS; DISEASE; GENETIC ASSOCIATION STUDIES; GENETIC VARIATION; HEART; HUMANS; MODELS, GENETIC; PHENOTYPE; SEQUENCE ANALYSIS, DNA; TEXAS; TRIGLYCERIDES;

EID: 84895917856     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21790     Document Type: Article

References (33)

1. Adler RJ, Taylor JE. 2007. Random Fields and Geometry. Springer, New York.
2. Almasy L, Dyer TD, Peralta JM, Kent JW, Jr., Charlesworth JC, Curran JE, Blangero J. 2011. Genetic Analysis Workshop 17 mini-exome simulation. BMC Proc 5(Suppl 9):S2.
3. Ansorge WJ. 2009. Next-generation DNA sequencing techniques. N Biotechnol 25(4):195-203.
4. Besag J. 1974. Spatial interaction and statistical analysis of lattice systems. J R Stat Soc B 48:259-302.
5. Bodmer W, Bonilla C. 2008. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40(6):695-701.
6. Davies R. 1980. The distribution of a linear combination of Chi-square random variables. Appl Stat 29:323-333.
7. 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(6):446-50.
8. Han F, Pan W. 2010. A data-adaptive sum test for disease association with multiple common or rare variants. Hum Hered 70(1):42-54.
9. He Z, Zhang M, Zhan X, Lu Q. 2013. Modeling and Testing for Joint Association Using a Genetic Random Field Model. http://arxiv-web3.library.cornell.edu/abs/1302.5493eprintarXiv:1302.5493.
10. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106(23):9362-9367.
11. Kathiresan S, Melander O, Guiducci C, Surti A, Burtt NP, Rieder MJ, Cooper GM, Roos C, Voight BF, Havulinna AS and others. 2008. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet 40(2):189-197.
12. Koster A, Chao YB, Mosior M, Ford A, Gonzalez-DeWhitt PA, Hale JE, Li D, Qiu Y, Fraser CC, Yang DD and others. 2005. Transgenic angiopoietin-like (angptl)4 overexpression and targeted disruption of angptl4 and angptl3: regulation of triglyceride metabolism. Endocrinology 146(11):4943-4950.
13. Kwee LC, Liu D, Lin X, Ghosh D, Epstein MP. 2008. A powerful and flexible multilocus association test for quantitative traits. Am J Hum Genet 82(2):386-397.
14. Lee S, Emond MJ, Bamshad MJ, Barnes KC, Rieder MJ, Nickerson DA, Team NGESP-ELP, 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(2):224-237.
15. 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(3):311-321.
16. Lin DY, Tang ZZ. 2011. A general framework for detecting disease associations with rare variants in sequencing studies. Am J Hum Genet 89(3):354-367.
17. Liu D, Lin X, Ghosh D. 2007. Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics 63(4):1079-1088.
18. Liu K, Fast S, Zawistowski M, Tintle NL. 2013. A geometric framework for evaluating rare variant tests of association. Genet Epidemiol 37(4):345-357.
19. Madsen BE, Browning SR. 2009. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5(2):e1000384.
20. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A and others. 2009. Finding the missing heritability of complex diseases. Nature 461(7265):747-753.
21. McClellan J, King MC. 2010. Genetic heterogeneity in human disease. Cell 141(2):210-217.
22. Morris AP, Zeggini E. 2010. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34(2):188-193.
23. Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR. 2010. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86(6):832-838.
24. Romeo S, Yin W, Kozlitina J, Pennacchio LA, Boerwinkle E, Hobbs HH, Cohen JC. 2009. Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. J Clin Invest 119(1):70-79.
25. Schork NJ, Murray SS, Frazer KA, Topol EJ. 2009. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev 19(3):212-219.
26. Schuster SC. 2008. Next-generation sequencing transforms today's biology. Nat Methods 5(1):16-18.
27. Shimizugawa T, Ono M, Shimamura M, Yoshida K, Ando Y, Koishi R, Ueda K, Inaba T, Minekura H, Kohama T and others. 2002. ANGPTL3 decreases very low density lipoprotein triglyceride clearance by inhibition of lipoprotein lipase. J Biol Chem 277(37):33742-33748.
28. Tzeng JY, Zhang D, Chang SM, Thomas DC, Davidian M. 2009. Gene-trait similarity regression for multimarker-based association analysis. Biometrics 65(3):822-832.
29. Tzeng JY, Zhang D, Pongpanich M, Smith C, McCarthy MI, Sale MM, Worrall BB, Hsu FC, Thomas DC, Sullivan PF. 2011. Studying gene and gene-environment effects of uncommon and common variants on continuous traits: a marker-set approach using gene-trait similarity regression. Am J Hum Genet 89(2):277-288.
30. Wessel J, Schork NJ. 2006. Generalized genomic distance-based regression methodology for multilocus association analysis. Am J Hum Genet 79(5):792-806.
31. Wu MC, Kraft P, Epstein MP, Taylor DM, Chanock SJ, Hunter DJ, Lin X. 2010. Powerful SNP-set analysis for case-control genome-wide association studies. Am J Hum Genet 86(6):929-942.
32. 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(1):82-93.
33. Zawistowski M, Gopalakrishnan S, Ding J, Li Y, Grimm S, Zollner S. 2010. Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. Am J Hum Genet 87(5):604-617.