Towards linkage analysis with markers in linkage disequilibrium by graphical modelling

Human Heredity

Volumn 64, Issue 1, 2007, Pages 16-26

  Thomas, Alun ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

Conditional independence; Markov chain Monte Carlo integration; Single nucleotide polymorphisms

Indexed keywords

ALLELE; CONFERENCE PAPER; DIPLOIDY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC MODEL; GENOTYPE; HAPLOIDY; LINKAGE ANALYSIS; MATHEMATICAL COMPUTING; MONTE CARLO METHOD; PEDIGREE; PROBABILITY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; STATISTICAL MODEL;

CHILD; DIPLOIDY; FEMALE; GENETIC MARKERS; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL; MONTE CARLO METHOD; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 34247578013     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000101419     Document Type: Conference Paper

References (46)

1. Terwilliger JD, Hiekkalinna T: An utter refutation of the 'Fundamental Theorem of the HapMap'. Eur J Hum Genet 2006;14:426-437.
2. Amos, CI, Chen WV, Lee A, Li W, Kern M, Lundsten R, Batliwalla F, Wener M, Remmers E, Kastner DA, Criswell LA, Seldina MF, Gregersen PK: High density SNP analysis of 642 Caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12 and 2q33. Genet Immun 2006;7:277-286.
3. Schaid DJ, Guenther JC, Christensen GB, Hebbring S, Rosenow C, Hilker CA, McDonnell SK, Cunningham JM, Slager SL, Blute ML, Thibodeau SN: Comparison of microsatellites versus single-nucleotide polymorphisms in a genome linkage screen for prostate cancer-susceptibility loci. Am J Hum Genet 2004;75:948-965.
4. Sellick GS, Webb EL, Allinson R, Matutes E, Dyer MJ, Jonsson V, Langerak AW, Mauro FR, Fuller S, Wiley J, Lyttelton M, Callea V, Yuille M, Catovsky D, Houlston RS: A high-density SNP genomewide linkage scan for chronic lymphocytic leukemia-susceptibility loci. Am J Hum Genet 2005;77:420-429.
5. Abecasis GR, Wigginton JE: Handling marker-marker linkage disequilibrium: Pedigree analysis with clustered markers. Am J Hum Genet 2005;77:754-767.
6. Stephens M, Smith NJ, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001;68:978-989.
7. Morton NE, Collins A: Toward positional cloning with SNPs. Curr Opin Molecular Therapeutics 2002;4:259-264.
8. Lauritzen SL, Spiegelhalter DJ: Local computations with probabilities on graphical structures and their applications to expert systems. J R Stat Soc Ser B 1988;50:157-224.
9. Elston RC, Stewart J: A general model for the genetic analysis of pedigree data. Hum Hered 1971;21:523-542.
10. Cannings C, Thompson EA, Skolnick MH: Probability functions on complex pedigrees. Ann Appl Prob 1978;10:26-61.
11. Lauritzen SL, Sheehan NA: Graphical models for genetic analyses. Stat Sci 2003;18:489-514.
12. Heath SC, Snow GL, Thompson EA, Tseng C, Wijsman EM: MCMC segregation and linkage analysis. Genet Epidemiol 1997;14:1011-1016.
13. Thomas A, Gutin A, Abkevich V, Bansal A: Multipoint linkage analysis by blocked Gibbs sampling. Stat Comput 2000;10:259-269.
14. George AW, Thompson EA: Multipoint linkage analysis for disease mapping in extended pedigrees: A Markov chain Monte Carlo approach. Technical Report 405, Department of Statistice, University of Washington, 2002.
15. Thomas A: GMCheck: Bayesian error checking for pedigree genotypes. Bioinformatics 2005;21:3187-3188.
16. Golumbic MC: Algorithmic Graph Theory and Perfect Graphs. Academic Press, 1980.
17. Højsgaard S, Thiesson B: BIFROST - block recursive models induced from relevant knowledge, observation and statistical techniques. Technical Report R-92-2010, Department of Mathematics and Computer Science, The University of Aalborg, 1992.
18. Thomas A, Camp NJ: Graphical modeling of the joint distribution of alleles at associated loci. Am J Hum Genet 2004;74:1088-1101.
19. Kirkpatrick S, Gellatt CD Jr, Vecchi MP: Optimization by simmulated annealing. Technical Report RC 9353, IBM, Yorktown Heights, 1982.
20. Schwarz G: Estimating the dimension of a model. Annals of Statistics 1978;6:461-464.
21. Tarjan RE, Yannakakis M: Simple lineartime algorithms to test chordality of graphs, test acyclicity of hypergraphs, and selectively reduce acyclic hypergraphs. SIAM J Comput 1984;13:566-579.
22. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH: Equations of state calculations by fast computing machines. J Chem Phys 1953;21:1087-1091.
23. Thomas A: Characterizing allelic associations from unphased diploid data by graphical modeling. Genet Epidemiol 2005;29:23-35.
24. Thomas A: Accelerated gene counting for haplotype frequency estimation. Ann Hum Genet 2003;67:608-612.
25. Dempster AP, Laird NM, Rubin DB: Maximum likelihood estimation from incomplete data via the EM algorithm. J R Stat Soc Ser B 1977;39:1-38.
26. Jensen CS, Kong A: Blocking Gibbs sampling for linkage analysis in large pedigreess with many loops. Technical Report R-96-2048, Department of Computer Science, Aalborg University, 1996.
27. Tavtigian SV, Simard J, Teng DHF, Abtin V, Baumgard M, Beck A, Camp NJ, Carillo AR, Chen Y, Dayananth P, Desrochers M, Dumont M, Farnham JM, Frank D, Frye C, Ghaffari S, Gupte JS, Hu R, Iliev D, Janecki T, Kort EN, Laity KE, Leavitt A, Leblanc G, McArthur-Morrison J, Pederson A, Penn B, Peterson KT, Reid JE, Richards S, Schroeder M, Smith R, Snyder SC, Swedlund B, Swensen J, Thomas A, Tranchant M, Woodland A-M, Labrie F, Skolnick MH, Neuhausen S, Rommens J, Cannon-Albright LA: A candidate prostate cancer susceptibility gene at chromosome 17p. Nature Genet 2001;27:172-180.
28. Thomas A: GCHap: Fast MLEs for haplotype frequencies by gene counting. Bioinformatics 2003;19:2002-2003.
29. Thomas A: Linkage analysis on complex pedigrees by simulation. IMA J Math Appl Med Biol 1994;11:79-93.
30. Heath S: Markov chain Monte Carlo segregation and linkage analysis for oliogenic models. Am J Hum Genet 1997;61:748-760.
31. Kruglyak L, Lander ES: Faster multipoint lankage analysis using Fourier transforms. J Comput Biol 1998;5:1-7.
32. Abecasis GR, Chernay SS, Cookson WO, Cardon Lon R: Merlin - rapid analysis of dense genetic maps using sparse gene flow trees. Nature Genet 2001;30:97-101.
33. Dawid AP: Applications of a general propogation algorithm for probabilistic expert systems. Stat Comput 1992;2:25-36.
34. Thompson EA: Monte Carlo in genetic analysis. Technical Report 294, Department of Statistics, University of Washington, 1995.
35. Thompson EA: Statistical inferences from genetic data on pedigrees. NSF-CBMS Regional Conference Series in Probability and Statistics, IMS, Beachwood, OH, 6, 2000.
36. George AW, Thompson EA: Discoering disease genes: Multipoint linkage analysis via a new markov chain monte carlo approach. Stat Sci 2003;18:515-531.
37. Sheehan N, Thomas A: On the irreducibility of a Markov chain defined on a space of genotype configurations by a sampling scheme. Biometrics 1993;49:163-175.
38. Goldstein DR, Zhao H, Speed TP: The effects of genotyping errors and interference on estimation of genetic distance. Hum Hered 1997;47:86-100.
39. Buetow KH: Influence of aberrent observations on high-resolution linkage analysis outcomes. Am J Hum Genet 1991;49:985-994.
40. Sieberts SK, Wijsman EM, Thompson EA: Relationship inference from trios of individuals, in the presence of typing errors. Am J Hum Genet 2002;70:170-180.
41. Stewart WCL, Thompson EA: Improving estimates of genetic maps: A maximum likelihood approach. Biometrics 2006;62:728-734.
42. Goring HHH, Terwillger JD: Linkage analysis in the presence of errors 1: Complex-valued recombination fractions and complex phenotypes. Am J Hum Genet 2000;66:1095-1106.
43. Abkevich V, Camp NJ, Gutin A, Farnham JM, Cannon-Albright L, Thomas A: A robust multipoint linkage statistic (tlod) for mapping complex trait loci. Genet Epidemiol 2001;21:S492-S497.
44. Verzilli CJ, Stallard N, Whittaker JC: Bayesian graphical models for genomewide association studies. Am J Hum Genet 2006;79:111-112.
45. Marinari E, Parisi G: Simulated tempering: A new Monte Carlo scheme. Europhysics Letters 1992;19:451-458.
46. Geyer CJ, Thompson EA: Annealing Markov chain Monte Carlo with applications to ancestral inference. J Am Stat Ass Soc 1995;90:909-920.