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Am J Hum Genet. Sep 1997; 61(3): 748–760.
PMCID: PMC1715966

Markov chain Monte Carlo segregation and linkage analysis for oligogenic models.

Abstract

A new method for segregation and linkage analysis, with pedigree data, is described. Reversible jump Markov chain Monte Carlo methods are used to implement a sampling scheme in which the Markov chain can jump between parameter subspaces corresponding to models with different numbers of quantitative-trait loci (QTL's). Joint estimation of QTL number, position, and effects is possible, avoiding the problems that can arise from misspecification of the number of QTL's in a linkage analysis. The method is illustrated by use of a data set simulated for the 9th Genetic Analysis Workshop; this data set had several oligogenic traits, generated by use of a 1,497-member pedigree. The mixing characteristics of the method appear to be good, and the method correctly recovers the simulated model from the test data set. The approach appears to have great potential both for robust linkage analysis and for the answering of more general questions regarding the genetic control of complex traits.

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Selected References

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  • Blangero J. Genetic analysis of a common oligogenic trait with quantitative correlates: summary of GAW9 results. Genet Epidemiol. 1995;12(6):689–706. [PubMed]
  • Dizier MH, Bonaïti-Pellié C, Clerget-Darpoux F. Conclusions of segregation analysis for family data generated under two-locus models. Am J Hum Genet. 1993 Dec;53(6):1338–1346. [PMC free article] [PubMed]
  • Elston RC, Stewart J. A general model for the genetic analysis of pedigree data. Hum Hered. 1971;21(6):523–542. [PubMed]
  • Guo SW, Thompson EA. A Monte Carlo method for combined segregation and linkage analysis. Am J Hum Genet. 1992 Nov;51(5):1111–1126. [PMC free article] [PubMed]
  • Haley CS, Knott SA. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity (Edinb) 1992 Oct;69(4):315–324. [PubMed]
  • Kruglyak L, Daly MJ, Lander ES. Rapid multipoint linkage analysis of recessive traits in nuclear families, including homozygosity mapping. Am J Hum Genet. 1995 Feb;56(2):519–527. [PMC free article] [PubMed]
  • Lander ES, Green P. Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci U S A. 1987 Apr;84(8):2363–2367. [PMC free article] [PubMed]
  • Lin S, Thompson E, Wijsman E. Achieving irreducibility of the Markov chain Monte Carlo method applied to pedigree data. IMA J Math Appl Med Biol. 1993;10(1):1–17. [PubMed]
  • MacCluer JW, Blangero J, Dyer TD, Kammerer CM. Simulation of a common oligogenic disease with quantitative risk factors. GAW9 problem 2: the answers. Genet Epidemiol. 1995;12(6):707–712. [PubMed]
  • Ott J. Computer-simulation methods in human linkage analysis. Proc Natl Acad Sci U S A. 1989 Jun;86(11):4175–4178. [PMC free article] [PubMed]
  • Satagopan JM, Yandell BS, Newton MA, Osborn TC. A bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. Genetics. 1996 Oct;144(2):805–816. [PMC free article] [PubMed]
  • Sheehan N, Thomas A. On the irreducibility of a Markov chain defined on a space of genotype configurations by a sampling scheme. Biometrics. 1993 Mar;49(1):163–175. [PubMed]
  • Stephens DA, Smith AF. Bayesian inference in multipoint gene mapping. Ann Hum Genet. 1993 Jan;57(Pt 1):65–82. [PubMed]
  • Thomas A. Approximate computation of probability functions for pedigree analysis. IMA J Math Appl Med Biol. 1986;3(3):157–166. [PubMed]

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