Haplotype-Based Methods for Detecting Uncommon Causal Variants With Common SNPs

Genetic Epidemiology

Volumn 36, Issue 6, 2012, Pages 572-582

  Lin, Wan Yu ^a   Yi, Nengjun ^b   Zhi, Degui ^b   Zhang, Kui ^b   Gao, Guimin ^c   Tiwari, Hemant K ^b   Liu, Nianjun ^b  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^c VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Haplotype; Linkage disequilibrium; Rare variants; Similarity

Indexed keywords

ANALYTIC METHOD; ARTICLE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC TRAIT; GENETIC VARIABILITY; HAPLOTYPE GLOBAL SCORE TEST; HAPLOTYPE MAP; HAPLOTYPE MAXIMUM SCORE; HUMAN; INTERMETHOD COMPARISON; MINOR ALLELE FREQUENCY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; WEI SIMC MATCHING METHOD;

ANGIOPOIETINS; COMPUTER SIMULATION; GENETIC VARIATION; GENETICS, POPULATION; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84865093332     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21650     Document Type: Article

References (50)

1. Allen AS, Satten GA. 2007. Statistical models for haplotype sharing in case-parent trio data. Hum Hered 64(1):35-44
2. Allen AS, Satten GA. 2009. A novel haplotype-sharing approach for genome-wide case-control association studies implicates the calpastatin gene in Parkinson's disease. Genet Epidemiol 33(8):657-667
3. Barrett JC, Cardon LR. 2006. Evaluating coverage of genome-wide association studies. Nat Genet 38(6):659-662.
4. Besag J, Clifford P. 1991. Sequential Monte Carlo p-values. Biometrika 78:301-304.
5. Bodmer W, Bonilla C. 2008. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40(6):695-701.
6. Dempster AP, Laird NM, Rubin DB. 1977. Maximum likelihood estimation from incomplete data via the EM algorithm. J R Stat Soc 39:1-38.
7. Excoffier L, Slatkin M. 1995. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12(5):921-927.
8. Feng T, Zhu X. 2010. Genome-wide searching of rare genetic variants in WTCCC data. Hum Genet 128(3):269-280.
9. Gusev A, Kenny EE, Lowe JK, Salit J, Saxena R, Kathiresan S, Altshuler DM, Friedman JM, Breslow JL, Pe'er I. 2011. DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation. Am J Hum Genet 88(6):706-717.
10. 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.
11. Hawley ME, Kidd KK. 1995. HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered 86(5):409-411.
12. Imhof JP. 1961. Computing the distribution of quadratic forms in normal variables. Biometrika 48:419-426.
13. Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SF, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, Derohannessian S, de Bakker PI, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CW, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, Fitzgerald GA. 2008. Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS ONE 3(10):e3583.
14. King CR, Rathouz PJ, Nicolae DL. 2010. An evolutionary framework for association testing in resequencing studies. PLoS Genet 6(11):e1001202.
15. Kitsios GD, Zintzaras E. 2010. An NOS3 haplotype is protective against hypertension in a Caucasian population. Int J Hypertens 2010:865031.
16. 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.
17. Li Y, Byrnes AE, Li M. 2010. To identify associations with rare variants, just WHaIT: weighted haplotype and imputation-based tests. Am J Hum Genet 87(5):728-735.
18. Lin DY, Huang BE. 2007. The use of inferred haplotypes in downstream analyses. Am J Hum Genet 80(3):577-579.
19. Lin WY, Lee WC. 2010. Discovering joint associations between disease and gene pairs with a novel similarity test. BMC Genet 11:86.
20. Lin WY, Schaid DJ. 2009. Power comparisons between similarity-based multilocus association methods, logistic regression, and score tests for haplotypes. Genet Epidemiol 33(3):183-197.
21. Lin WY, Tiwari HK, Gao G, Zhang K, Arcaroli JJ, Abraham E, Liu N. 2012. Similarity-based multimarker association tests for continuous traits. Ann Hum Genet 76:246-260.
22. Lin WY, Zhang B, Yi N, Gao G, Liu N. 2011. Evaluation of pooled association tests for rare variant identification. BMC Proc 5 (Suppl 9):S118.
23. Liu PY, Zhang YY, Lu Y, Long JR, Shen H, Zhao LJ, Xu FH, Xiao P, Xiong DH, Liu YJ, Recker RR, Deng HW. 2005. A survey of haplotype variants at several disease candidate genes: the importance of rare variants for complex diseases. J Med Genet 42(3):221-227.
24. Long JC, Williams RC, Urbanek M. 1995. An E-M algorithm and testing strategy for multiple-locus haplotypes. Am J Hum Genet 56(3):799-810.
25. Madsen BE, Browning SR. 2009. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5(2):e1000384.
26. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM. 2009. Finding the missing heritability of complex diseases. Nature 461(7265):747-753.
27. Maxwell TJ, Bendall ML, Staples J, Jarvis T, Crandall KA. 2010. Phylogenetics applied to genotype/phenotype association and selection analyses with sequence data from angptl4 in humans. Int J Mol Sci 11(1):370-385.
28. Morris AP, Zeggini E. 2010. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34(2):188-193.
29. Nelder JA, Wedderburn RWM. 1972. Generalized linear models. J R Stat Soc Ser A 135:370-384.
30. Nolte IM, de Vries AR, Spijker GT, Jansen RC, Brinza D, Zelikovsky A, Te Meerman GJ. 2007. Association testing by haplotype-sharing methods applicable to whole-genome analysis. BMC Proc 1 (Suppl 1):S129.
31. 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.
32. Rinaldo A, Bacanu SA, Devlin B, Sonpar V, Wasserman L, Roeder K. 2005. Characterization of multilocus linkage disequilibrium. Genet Epidemiol 28(3):193-206.
33. Roeder K, Bacanu SA, Sonpar V, Zhang X, Devlin B. 2005. Analysis of single-locus tests to detect gene/disease associations. Genet Epidemiol 28(3):207-219.
34. Romeo S, Pennacchio LA, Fu Y, Boerwinkle E, Tybjaerg-Hansen A, Hobbs HH, Cohen JC. 2007. Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat Genet 39(4):513-516.
35. 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.
36. Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB. 2011. The real cost of sequencing: higher than you think! Genome Biol 12(8):125.
37. 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.
38. Schaid DJ. 2004. Evaluating associations of haplotypes with traits. Genet Epidemiol 27(4):348-364.
39. Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. 2002. Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70(2):425-434.
40. Scheffe H. 1959. The Analysis of Variance. New York: Wiley.
41. Sha Q, Chen HS, Zhang S. 2007. A new association test using haplotype similarity. Genet Epidemiol 31(6):577-593.
42. Tong L, Yang J, Cooper RS. 2010. Efficient calculation of P-value and power for quadratic form statistics in multilocus association testing. Ann Hum Genet 74(3):275-285.
43. Tzeng JY, Devlin B, Wasserman L, Roeder K. 2003. On the identification of disease mutations by the analysis of haplotype similarity and goodness of fit. Am J Hum Genet 72(4):891-902.
44. 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.
45. 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.
46. WTCCC. 2007. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 447(7145):661-678.
47. Yi N, Liu N, Zhi D, Li J. 2011. Hierarchical generalized linear models for multiple groups of rare and common variants: jointly estimating group and individual-variant effects. PLoS Genet 7(12):e1002382.
48. Zeggini E. 2011. Next-generation association studies for complex traits. Nat Genet 43(4):287-288.
49. Zhu X, Fejerman L, Luke A, Adeyemo A, Cooper RS. 2005. Haplotypes produced from rare variants in the promoter and coding regions of angiotensinogen contribute to variation in angiotensinogen levels. Hum Mol Genet 14(5):639-643.
50. Zhu X, Feng T, Li Y, Lu Q, Elston RC. 2010. Detecting rare variants for complex traits using family and unrelated data. Genet Epidemiol 34(2):171-187.