MCMC multilocus lod scores: Application of a new approach

Human Heredity

Volumn 59, Issue 2, 2005, Pages 98-108

  George, Andrew W ^a,b   Wijsman, Ellen M ^a   Thompson, Elizabeth A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF IOWA   (United States)

Author keywords

Alzheimer's disease; Extended pedigrees; Linkage analysis; Markov chain Monte Carlo; Multipoint lod scores

Indexed keywords

ALZHEIMER DISEASE; ARTICLE; CONTROLLED STUDY; GENETIC ANALYSIS; GENETIC LINKAGE; HUMAN; MONTE CARLO METHOD;

ALZHEIMER DISEASE; GENETIC MARKERS; HUMANS; LINKAGE (GENETICS); LOD SCORE; MARKOV CHAINS; MONTE CARLO METHOD; PEDIGREE; SOFTWARE;

EID: 21044459378     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000085224     Document Type: Article

References (37)

1. Ott J: Estimation of the recombination frequency in human pedigrees: Efficient computation of the likelihood for human linkage studies. Am J Hum Genet 1974;26:588-597.
2. Lathrop GM, Lalouel JM, Julier C, Ott J: Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci USA 1984;81:3443-3446.
3. Cottingham RW, Idury RM, Schäffer AA: Faster sequential genetic linkage computations. Am J Hum Genet 1993;53:252-263.
4. O'Connell JR, Weeks DE: The algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nature Genet 1995;11:402-408.
5. Elston RC, Stewart J. A general model for the analysis of pedigree data. Hum Hered 1971;21:523-542.
6. Cannings C, Thompson EA, Skolnick MH: Probability functions on complex pedigrees. Adv Appl Prob 1978;10:26-61.
7. Lander ES, Green P: Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 1987;84:2363-2367.
8. Braverman MS: An algorithm to improve the computational efficiency of genetic linkage analysis. Computers Biomed Res 1985;18:24-36.
9. Schellenberg GD, Bird TD, Wijsman EM, Orr HT, Anderson L, Nemens E, White JA, Bonneycastle L, Weber JL, Alonso ME, et al: Genetic linkage evidence for a familial Alzheimer's disease locus on chromosome 14. Science 1992;258:668-671.
10. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES: Parametric and nonparametric linkage analyses: a unified multipoint approach. Am J Hum Genet 1996;58:1347-1363.
11. Markianos K, Daly M, Kruglyak L: Efficient multipoint linkage analysis through reduction of the inheritance space. Am J Hum Genet 2001;68:963-977.
12. Gudbjartsson DF, Jonasson K, Frigge ML, Kong A: Allegro, a new computer program for multipoint linkage analysis. Nature 2000;25:12-13.
13. Abecasis GR, Cherny SS, Cookson WO, Cardon LR: Merlin - rapid analysis of dense genetic maps using sparse gene flow trees. Nature Genet 2002;30:97-101.
14. Hastings WK: Monte Carlo sampling methods using Markov chains and their applications. Biometrika 1970;57:97-109.
15. Geman S, Geman D: Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images. IEEE Trans Pattern Analysis Machine Intelligence 1984;6:721-741.
16. Lange K, Sobel E: A random walk method for computing genetic location scores. Am J Hum Genet 1991;49:1320-1334.
17. Sobel E, Lange K: Descent graphs in pedigree analysis: Applications to haplotyping, location scores, and marker-sharing statistics. Am J Hum Genet 1996;58:1323-1337.
18. Thompson EA: MCMC estimation of multilocus genome sharing and multipoint gene location scores. Int Stat Rev 2000;68:53-73.
19. Lin S: Multipoint linkage analysis via Metropolis jumping kernels. Biometrics 1996;52:1417-1427.
20. Thompson EA, Guo SW: Evaluation of likelihood ratios for complex genetic models. I.M.A. J Math Appl Med Biol 1991;8:149-169.
21. George AW, Thompson EA: Discovering disease genes: multipoint linkage analysis via a new Markov chain Monte Carlo approach. Stat Science 2003;18:515-531.
22. Geyer CJ, Thompson EA: Annealing Markov chain Monte Carlo with applications to ancestral inference. J Am Stat Assoc 1995;90:909-920.
23. Levy-Lahad E, Wijsman EM, Nemens E, Anderson L, Goddard KA, Weber JL, Bird TD, Schellenberg GD: Familial Alzheimer's disease locus on Chromosome 1. Science 1995;269:970-973.
24. Gelfand AE, Smith AFM: Sampling based approaches to calculating marginal densities. J Am Stat Assoc 1990;85:398-409.
25. Levy-Lahad E, Wasco W, Poorkaj P, Romano DM, Oshima J, Pettingell WH, Yu CE, Jondro PD, Schmidt SD, Wang K, et al: Candidate gene for the Chromosome 1 familial Alzheimer's disease locus. Science 1995;269:973-977.
26. Bird TD, Lampe TH, Nemens EJ, Miner GW, Sumi SM, Schellenberg GD: Familial Alzheimer's disease in American descendants of the Volga Germans: probably genetic founder effect. Ann Neurol 1988;23:25-31.
27. Bird TD, Sumi SM, Nemens EJ, Nochlin D, Schellenberg GD, Lampe TH, Sadovnick A, Chiu H, Miner GW, Tinklenberg J: Phenotypic heterogeneity in familial Alzheimer's disease: a study of 24 kindreds. Ann Neurol1989;25:12-25.
28. Schäffer AA, Gupta SK, Shriram K, Cottingham RW: Avoiding recomputation in linkage analysis. Hum Hered 1994;44:225-237.
29. Thompson EA: Monte Carlo likelihood in genetic mapping. Stat Sci 1994;9:355-366.
30. Heath SC: Markov chain Monte Carlo segregation and linkage analysis for oligogenic models. Am J Hum Genet 1997;61:748-760.
31. Thompson EA, Heath SC: Estimation of conditional multilocus gene identity among relatives. In Statistics in Molecular Biology and Genetics: Selected Proceedings of a 1997 Joint AMS-IMS-SIAM Summer Conference on Statistics in Molecular Biology (edited by F Seillier-Moiseiwitsch), vol. 33 of IMS Lecture Note-Monograph Series. Institute of Mathematical Statistics, Hayward, CA, 1999, pp 95-113.
32. Kong A, Lui JS, Wong WH: Sequential imputations and Bayesian missing data problems. J Am Stat Assoc 1994;89:278-288.
33. Thompson EA: Monte Carlo likelihood in the genetic mapping of complex traits. Philosophical Trans R Soc London (Series B) 1994;344: 345-351.
34. Thompson EA: Statistical Inferences from Genetic Data on Pedigrees, vol. 6 of NSF-CBMS Regional Conference Series in Probability and Statistics. Institute of Mathematical Statistics, Beachwood, OH, 2000.
35. Thomas A, Gutin A, Abkevich V, Bansal A: Multilocus linkage analysis by blocked Gibbs sampling. Stat Computing 2000;10:259-269.
36. Lin S, Thompson EA, Wijsman EM: An algorithm for Monte Carlo estimation of genotype probabilities on complex pedigrees. Ann Hum Genet 1994;58:343-357.
37. Sheehan NA, Thomas AW: On the irreducibility of a Markov chain defined on a space of genotype configurations by a sampling scheme. Biometrics 1993;49:163-175.