Pedigree analysis package vs. MIXD: Fitting the mixed model on a large pedigree

Genetic Epidemiology

Volumn 13, Issue 1, 1996, Pages 91-106

  Olshen, Adam B ^a   Wijsman, Ellen M ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

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

Author keywords

complex segregation analysis; maximum likelihood; Monte Carlo Markov chain; simulation methods

Indexed keywords

ARTICLE; COMPUTER PROGRAM; GENETIC MODEL; GENOTYPE; HERITABILITY; HUMAN; MAJOR CLINICAL STUDY; MAXIMUM LIKELIHOOD METHOD; PEDIGREE ANALYSIS; PROBABILITY; SEGREGATION ANALYSIS; STATISTICAL MODEL; STATISTICAL PARAMETERS; SYSTEM ANALYSIS;

ANALYSIS OF VARIANCE; BIAS (EPIDEMIOLOGY); GENE FREQUENCY; GENOTYPE; HUMANS; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PEDIGREE; REPRODUCIBILITY OF RESULTS; SOFTWARE VALIDATION;

EID: 0029866152     PISSN: 07410395     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1098-2272(1996)13:1<91::AID-GEPI8>3.0.CO;2-9     Document Type: Article

References (32)

1. Bailey-Wilson J, Elston RC (1993): The HGARI familial hypercholesterolemiapedigree. Genet Epidemiol 10:529-531.
2. Boehnke M, Moll PP (1989): Identifying pedigrees segregating at a major locus for a quantitative trait: an efficient strategy for linkage analysis. Am J Hum Genet 44:2126-224.
3. Cannings C. Thompson EA, Skolnick MH (1978): Probability functions on complex pedigrees. Adv Appl Prob 10:26-61.
4. Clerget-Darpoux F, Bonaiti-Pellie C, Hochez J (1986): Effects of misspecifying genetic parameters in lod score analysis. Biometrics 42:393-399.
5. Dempster AP, Laird NM, Rubin DB (1977): Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Ser B 39:1-38.
6. Elston RC, Stewart J (1971): A general model for the genetic analysis of pedigree data. Hum Hered 21:523-542.
7. Falconer DS (1981): "Introduction to Quantitative Genetics, 2nd Ed." New York: Longman, p 150.
8. Faucett C, Gauderman WJ, Thomas D, Ziogas A, Sobel E (1993): Combined segregation and linkage analysis of late-onset Alzheimer's disease in Duke families using Gibbs sampling. Genet Epidemiol 10:489-494.
9. Geman S, Geman D (1984): Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images. IEEE Trans Pattern Anal Mach Intelligence 6:721-741.
10. Greenberg DA, Hodge SE (1989): Linkage analysis under "random" and "genetic" reduced penetrance. Genet Epidemiol 6:259-264.
11. Guo SW (1991): Monte Carlo methods in quantitative genetics. Ph.D. dissertation. Seattle: Department of Biostatistics, University of Washington.
12. Guo SW, Thompson EA (1991): Monte Carlo EM for the estimation of multiple random effects models on large pedigrees. IMA J Math Appl Med Biol 8:171-189.
13. Guo SW, Thompson EA (1992): A Monte Carlo method for combined segregation and linkage analysis. Am J Hum Genet 51:1111-1126.
14. Guo SW, Thompson EA (1994): Monte Carlo estimation of mixed models for large complex pedigrees. Biometrics 50:417-432.
15. Hasstedt SJ, Cartwright P (1981): PAP - Pedigree Analysis Package. Technical report no. 13, Department of Medical Biophysics and Computing, University of Utah.
16. Hasstedt SJ (1982): A mixed-model likelihood approximation on large pedigrees. Computers in Biomed Res 15:295-307
17. Hastings WK (1970): Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109.
18. Kong K, Frigge M, Cox N, Wong WH (1992): Linkage analysis with adjustment for covariates: A method combining peeling with Gibbs sampling. Cytogenet Cell Genet 59:208-210.
19. Jiang OX, Buetow KH (1990): A simulation evaluation of high resolution meiotic gene mapping. Am J Hum Genet 47:A185.
20. Lange K, Sobel E (1991): A random walk method for computing genetic location scores. Am J Hum Genet 49:1320-1334.
21. Lathrop GM, Hooper AB, Huntsman JW, Ward RH (1983): Evaluating pedigree data: I. The estimation of pedigree error in the presence of marker misstyping. Am J Hum Genet 35:241-262.
22. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953): Equation of state calculation by fast computing machines. J Chem Phys 21:1087-1092.
23. Morton NE, MacLean CJ (1974): Analysis of family resemblance. III. Complex segregation of quantitative traits. Am J Hum Genet 26:489-503.
24. Ott J (1979): Maximum likelihood estimation by counting methods under polygenic and mixed models in human pedigrees. Am J Hum Genet 31:161-175.
25. Ott J (1991): Analysis of Human Genetic Linkage. The Johns Hopkins University Press, Baltimore.
26. Sheehan NA (1990): Genetic reconstruction on pedigrees. Ph.D. thesis. Seattle: University of Washington.
27. Thomas D (1992): Fitting genetic data using Gibbs sampling: An application to nevus counts in 38 Utah kindreds. Cytogenet Cell Genet 59:228-230.
28. Thompson EA (1994): Monte Carlo programs for pedigree analysis: 1990-1993. Technical Report no. 267, Department of Statistics, University of Washington.
29. Thompson EA, Guo SW (1991): Evaluation of likelihood ratios for complex genetic models. IMA J Math Appl Med Biol 8:149-169.
30. Thompson EA, Lin S, Olshen AB, Wijsman EM (1993): Monte Carlo analysis on a large pedigree. Genet Epidemiol 10:677-682.
31. Thompson EA, Shaw RG (1990): Pedigree analysis for quantitative traits; variance components without matrices. Biometrics 46:399-414.
32. Wijsman EM (1993): Genetic analysis of Alzheimer's disease: A summary of contributions to GAW8. Genet Epidemiol 10:349-360.