Sequence Kernel Association Analysis of Rare Variant Set Based on the Marginal Regression Model for Binary Traits

Genetic Epidemiology

Volumn 39, Issue 6, 2015, Pages 399-405

  Wu, Baolin ^a   Pankow, James S ^a   Guan, Weihua ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

GWAS; Score statistic; Sequencing data; SKAT

Indexed keywords

HISTONE ACETYLTRANSFERASE;

ADULT; ANALYTIC METHOD; ARTICLE; ATHEROSCLEROSIS; CONTROLLED STUDY; DATA ADAPTIVE KERNEL ASSOCIATION TEST; ENZYME ACTIVITY; FEMALE; GENE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC TRAIT; GENETIC VARIABILITY; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; MIDDLE AGED; NON INSULIN DEPENDENT DIABETES MELLITUS; PLESIOMORPHY; SEQUENCE KERNEL ASSOCIATION TEST; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; ZZZ3 GENE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETIC ASSOCIATION STUDY; GENETIC SCREENING; GENETICS; RISK FACTOR;

COMPUTER SIMULATION; DIABETES MELLITUS, TYPE 2; FEMALE; GENETIC ASSOCIATION STUDIES; GENETIC TESTING; HUMANS; MALE; MIDDLE AGED; MODELS, GENETIC; RISK FACTORS;

EID: 84939456068     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21913     Document Type: Article

References (32)

1. Berndt SI, Gustafsson S, Magi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR and others. 2013. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nat Genet 45(5):501-512.
2. Bonnefond A, Clement N, Fawcett K, Yengo L, Vaillant E, Guillaume JL, Dechaume A, Payne F, Roussel R, Czernichow S and others. 2012. Rare MTNR1B variants impairing melatonin receptor 1B function contribute to type 2 diabetes. Nat Genet 44(3):297-301.
3. Chen H, Lumley T, Brody J, Heard-Costa NL, Fox CS, Cupples LA, Dupuis J. 2014. Sequence kernel association test for survival traits. Genet Epidemiol 38(3):191-197.
4. Cox DR, Hinkley DV. 1979. Theoretical Statistics. Boca Raton, Florida: CRC Press.
5. 2 random variables. Appl Stat 29(3):323-333.
6. Estrada K, Aukrust I, Bjorkhaug L, Burtt NP, Mercader JM and others. 2014. Association of a low-frequency variant in HNF1A with type 2 diabetes in a latino population. J Am Med Assoc 311(22):2305-2314.
7. Grove ML, Yu B, Cochran BJ, Haritunians T, Bis JC, Taylor KD and others. 2013. Best practices and joint calling of the HumanExome BeadChip: the CHARGE consortium. PloS One 8(7):e68095.
8. Hauck WW, Donner A. 1977. Wald's test as applied to hypotheses in logit analysis. J Am Stat Assoc 72 (360):851-853.
9. Lee S, Wu MC, Lin X. 2012. Optimal tests for rare variant effects in sequencing association studies. Biostatistics 13(4):762-775.
10. 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.
11. 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.
12. 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.
13. Liu H, Tang Y, Zhang HH. 2009. A new chi-square approximation to the distribution of non-negative definite quadratic forms in non-central normal variables. Comput Stat Data Anal 53(4):853-856.
14. Ma C, Blackwell T, Boehnke M, Scott LJ, GoT2D Investigators. 2013. Recommended joint and meta-analysis strategies for case-control association testing of single low-count variants. Genet Epidemiol 37(6):539-550.
15. Madsen BE, Browning SR. 2009. A groupwise association test for rare mutations using a weighted sum statistic. PLOS Genet 5(2):e1000384.
16. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA and others. 2009. Finding the missing heritability of complex diseases. Nature 461(7265):747-753.
17. 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(1-2):28-56.
18. Morris AP, Zeggini E. 2010. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34(2):188-193.
19. Morris AP, Voight BF, Teslovich TM, Ferreira T, Segre AV and others. 2012. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 44(9):981-990.
20. 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(3):e1001322.
21. Pan W. 2009. Asymptotic tests of association with multiple SNPs in linkage disequilibrium. Genet Epidemiol 33(6):497-507.
22. Price AL, Kryukov GV, de Bakker PIW, 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.
23. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, Bakker PIWd, Daly MJ and others. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559-575.
24. Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D. 2005. Calibrating a coalescent simulation of human genome sequence variation. Genome Res 15(11):1576-1583.
25. Steinthorsdottir V, Thorleifsson G, Sulem P, Helgason H, Grarup N and others. 2014. Identification of low-frequency and rare sequence variants associated with elevated or reduced risk of type 2 diabetes. Nat Genet 46(3):294-298.
26. The ARIC Investigators. 1989. The atherosclerosis risk in communities (ARIC) study: design and objectives. Am J Epidemiol 129(4):687-702.
27. Tzeng JY, Zhang D. 2007. Haplotype-based association analysis via variance-components score test. Am J Hum Genet 81(5):927-938.
28. Wang Y, McKay JD, Rafnar T, Wang Z, Timofeeva MN, Broderick P and others. 2014. Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer. Nat Genet 46(7):736-741.
29. 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.
30. 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.
31. Xing G, Lin CY, Wooding SP, Xing C. 2012. Blindly using Wald's test can miss rare disease-causal variants in case-control association studies. Ann Hum Genetics 76(2):168-177.
32. Zhan X, Larson DE, Wang C, Koboldt DC, Sergeev YV, Fulton RS and others. 2013. Identification of a rare coding variant in complement 3 associated with age-related macular degeneration. Nat Genet 45(11):1375-1379.