Semiparametric variance-component models for linkage and association analyses of censored trait data

Genetic Epidemiology

Volumn 30, Issue 7, 2006, Pages 570-581

  Diao, G ^a   Lin, Danyu Y ^a  

^a University of North Carolina at Chapel Hill   (United States)

Author keywords

Age at onset; Censoring; Complex diseases; IBD sharing; Linkage disequilibrium; LOD score; Maximum likelihood; Proportional hazards; Quantitative traits; Random effects; Transformation

Indexed keywords

ALCOHOLISM; ALGORITHM; ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS; FAMILY; FOLLOW UP; GENETIC ASSOCIATION; GENETIC LINKAGE; HUMAN; MAXIMUM LIKELIHOOD METHOD; NORMAL DISTRIBUTION; ONSET AGE; PEDIGREE; QUANTITATIVE TRAIT LOCUS; SIMULATION; STATISTICAL MODEL; VARIANCE;

AGE OF ONSET; HUMANS; LIKELIHOOD FUNCTIONS; LINKAGE (GENETICS); LINKAGE DISEQUILIBRIUM; LOD SCORE; MODELS, GENETIC; PROPORTIONAL HAZARDS MODELS; QUANTITATIVE TRAIT, HERITABLE; RANDOM ALLOCATION; TRANSFORMATION, GENETIC;

EID: 33750293950     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20168     Document Type: Article

References (41)

1. Abecasis GR, Cardon LR, Cookson WOC. 2000. A general test of association for quantitative traits in nuclear families. Am J Hum Genet 66:279-292.
2. Almasy L, Blangero J. 1998. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62:1198-1211.
3. American Psychiatric Association. 1987. Diagnostic and Statistical Manual of Mental Disorders, 3rd edition. Washington, DC.
4. Amos CI. 1994. Robust variance-components approach for assessing genetic linkage in pedigrees. Am J Hum Genet 54:535-543.
5. Amos CI, Zhu DK, Boerwinkle E. 1996. Assessing genetic linkage and association with robust components of variance approaches. Ann Hum Genet 60:143-160.
6. Begleiter H, Reich T, Hesselbrock V, Porjesz B, Li TK, Schuckit MA, Edenberg HJ, Rice JP. 1995. The collaborative study on the genetics of alcoholism. Alcohol Health Res World 19:228-236.
7. Bennett S. 1983. Analysis of survival data by proportional odds model. Stat Med 2:273-277.
8. Bickel PJ, Klassen CAJ, Ritov Y, Wellner JA. 1993. Efficient and Adaptive Estimation in Semiparametric Models, Baltimore: Johns Hopkins University Press.
9. Cardon LR, Abecasis GR. 2000. Some properties of a variance components model for fine-mapping quantitative trait loci. Behav Genet 30:235-243.
10. Carter BS, Beaty HB, Steinberg GD, Childs B, Walsh PC. 1992. Mendelian inheritance of familial prostate cancer. Proc Natl Acad Sci USA 89:3367-3371.
11. Claus EB, Risch NJ, Thompson WD. 1990. Using age of onset to distinguish between subforms of breast cancer. Ann Hum Genet 54:169-177.
12. Cox DR. 1972. Regression models and life tables (with discussion). J R Stat Soc B 34:187-220.
13. de Andrade M, Amos CI. 2000. Ascertainment issues in variance components models. Genet Epidemiol 19:333-344.
14. Dempster AP, Laird NM, Rubin DB. 1977. Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc B 39:1-38.
15. Diao G, Lin DY. 2005. A powerful and robust method for mapping quantitative trait loci in general pedigrees. Am J Hum Genet 77:97-111.
16. Diao G, Lin DY. 2006. Improving the power of association tests for quantitative traits in family studies. Genet Epidemiol 30:301-313.
17. Epstein MP, Lin XH, Boehnke M. 2003. A Tobit variance-component method for linkage analysis of censored trait data. Am J Hum Genet 72:611-620.
18. Feighner JP, Robins E, Guze SB et al. 1972. Diagnostic criteria for use in psychiatric research. Arch Gen Psychiatry 26:57-63.
19. Fulker DW, Cherny SS, Sham PC, Hewitt JK. 1999. Combined linkage and association sib-pair analysis for quantitative traits. Am J Hum Genet 64:259-267.
20. Genz A. 1992. Numerical computation of multivariate normal probabilities. J Comput Graph Stat 1:141-149.
21. Higgins M, Province M, Heiss G, Eckfeldt J, Ellison RC, Folsom AR, Rao DC, Sprafka M, Williams R. 1996. NHLBI Family Heart Study: objectives and design. Am J Epidemiol 143:1219-1228.
22. Horvath S, Xu X, Laird NM. 2001. The family based association test method: strategies for studying general genotype-phenotype associations. Eur J Hum Genet 9:301-306.
23. Hsu L. 2003. Genetic association tests with age at onset. Genet Epidemiol 24:118-127.
24. Lange C, Blacker D, Laird NM. 2004. Family-based association tests for survival and times-to-onset analysis. Stat Med 23:179-189.
25. Li H. 1999. The additive genetic gamma frailty model for linkage analysis. Ann Hum Genet 63:455-468.
26. Li H. 2002. The additive genetic gamma frailty model for linkage analysis of diseases with variable age of onset using nuclear families. Lifetime Data Anal 8:315-334.
27. Li H, Zhong X. 2002. Multivariate survival models induced by genetic frailties, with application to linkage analysis. Biostatistics 3:57-75.
28. Lin DY. 2005. An efficient Monte Carlo approach to assessing statistical significance in genomic studies. Bioinformatics 21:781-787.
29. Mokliatchouk O, Blacker D, Rabinowitz D. 2000. Association tests for traits with variable age at onset. Hum Hered 51:46-53.
30. Monks SA, Kaplan NL. 2000. Removing the sampling restrictions from family-based tests of association for a quantitative-trait locus. Am J Hum Genet 66:576-592.
31. Palmer LJ, Katrina JT, Burton PR. 1999. Genome-wide linkage analysis using genetic variance components of alcohol dependency-associated censored and continuous traits. Genet Epdemiol 17(Suppl. 1):S283-S288.
32. Pankratz VS, de Andrade M, Therneau TM. 2005. Random-effect Cox proportional hazards model: general variance components methods for time-to-event data. Genet Epidemiol 28:97-109.
33. Pinheiro JC, Bates DM. 1995. Approximations to the log-likelihood function in the nonlinear mixed-effects model. J Comput Graph Stat 4:12-35.
34. Press WH, Teukolsky SA, Vetterling WT, Flannery BP. 1992. Numerical Recipes in C: The Art of Scientific Computing, 2nd edition. New York: Cambridge University Press.
35. Ripatti S, Palmgren J. 2000. Estimation of multivariate frailty models using penalized partial likelihood. Biometrics 56:1016-1022.
36. Self SG, Liang KL. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J Am Stat Assoc 82:605-610.
37. Shih MC, Whittemore AS. 2002. Tests for genetic association using family data. Genet Epidemiol 22:128-145.
38. Stine OC, Xu J, Koskela R, McMahon FJ, Gschwend M, Friddle C, Clark CD, McInnis MG, Simpson SG, Breschel TS et al. 1995. Evidence for linkage of bipolar disorder to chromosome 18 with a parent-of-origin effect. Am J Hum Genet 57:1384-1394.
39. Valle T, Tuomilehto J, Bergman RN, Ghosh S, Hauser ER, Eriksson J, Nylund SJ, Kohtamaki K, Toivanen L, Vidgren G, Tuomilehto-Wolf E, Ehnholm C, Blaschak J, Langefeld CD, Watanabe RM, Magnuson V, Ally DS, Hagopian WA, Ross E, Buchanan TA, Collins F, Boehnke M. 1998. Mapping genes for NIDDM: design of the Finland-United States Investigation of NIDDM Genetics (FUSION) study. Diab Care 21:949-958.
40. Zeng D, Lin DY, Lin X. 2005. Semiparametric transformation models with random effects for clustered failure time data. Technical Report, Department of Biostatistics, University of North Carolina at Chapel Hill.
41. Zhong X, Li H. 2004. Score tests of genetic association in the presence of linkage based on the additive genetic gamma frailty model. Biostatistics 5:307-327.