On composite likelihoods in statistical genetics

Statistica Sinica

Volumn 21, Issue 1, 2011, Pages 43-69

  Larribe, F ^a   Fearnhead, P ^b  

^a UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

^b LANCASTER UNIVERSITY   (United Kingdom)

Author keywords

Association; Coalescent process; Composite likelihood; Fine genetic mapping; Linkage disequilibrium

Indexed keywords

EID: 78650319592     PISSN: 10170405     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (68)

1. Auton, A. and McVean, G. (2007). Recombination rate estimation in the presence of hotspots. Genome Res. 17, 1219-1227.
2. Carvajal-Rodriguez, A., Crandall, K. A. and Posada, D. (2006). Recombination estimation under complex evolutionary models with the coalescent composite-likelihood. Mol. Biol. Evol. 23, 817-827.
3. Collins, A. and Morton, N. E. (1998). Mapping a disease locus by allelic association. Proc. Natl. Acad. Sci. USA 95, 1741-1745.
4. Cox, D. R. and Reid, N. (2004). A note on pseudolikelihood constructed from marginal densities. Biometrika 91, 729-737.
5. Crawford, D. C., Bhangale, T., Li, N., Hellenthal, G., Rieder, M. J., Nickerson, D. A. and Stephens, M. (2004). Evidence for substantial fine-scale variation in recombination rates across the human genome. Nature Genetics 36, 700-706.
6. Devlin, B., Risch, N. and Roeder, K. (1996). Disequilibrium mapping: composite likelihood for pairwise disequilibrium. Genomics 36, 1-16.
7. Elston, R. C. (2000). Introduction and overview. Statistical methods in genetic epidemiology. Statist. Meth. Medical Res. 9, 527-541.
8. Fearnhead, P. (2003). Consistency of estimators of the population-scaled recombination rate. Theor. Popul. Biol. 64, 67-79.
9. Fearnhead, P. (2006). SequenceLDhot: detecting recombination hotspots. Bioinformatics 22, 3061-3066.
10. Fearnhead, P. and Donnelly, P. (2001). Estimating recombination rates from population genetic data. Genetics 159, 1299-1318.
11. Fearnhead, P. and Donnelly, P. (2002). Approximate likelihood methods for estimating local recombination rates. J. Roy. Statist. Soc. Ser. A 64, 657-680.
12. Fearnhead, P. and Smith, N. G. C. (2005). A novel method with improved power to detect recombination hotspots from polymorphism data reveals multiple hotspots in human genes. Amer. J. Hum. Genet. 77, 781-794.
13. Garner, C. and Slatkin, M. (2002). Likelihood-based disequilibrium mapping for two-marker haplotype data. Theor. Popul. Biol. 61, 153-161.
14. Gray, M. M., Granka, J. M., Bustamante, C. D., Sutter, N. B., Boyko, A. R., Zhu, L., Ostrander, E. A. and Wayne, R. K. (2009). Linkage disequilibrium and demographic history of wild and domestic canids. Genetics 181, 1493-1505
15. Griffiths, R. C. and Marjoram, P. (1996). Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3, 479-502.
16. Griffiths, R. C. and Marjoram, P. (1997). An ancestral recombination graph. In Progress in Population Genetics and Human Evolution, (Edited by P. Donnelly and S. Tavaré), IMA Volumes in Mathematics and its Applications, 257-270. Springer Verlag, Berlin.
17. Griffiths, R. C. and Tavaré, S. (1994a). Simulating probability distributions in the coalescent. Theor. Popul. Biol. 46, 131-159.
18. Griffiths, R. C. and Tavaré, S. (1994b). Ancestral inference in population genetics. Statist. Sci. 9, 307-319.
19. Griffiths, R. C. and Tavaré, S. (1994c). Sampling theory for neutral alleles in a varying environment. Phil. Trans. R. Soc. Lond. B 344, 403-410.
20. Hein, J., Schierup, M. and Wiuf, C. (2005). Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory. Oxford University Press, Oxford.
21. Hudson, R. R. (2001). Two-locus sampling distributions and their application. Genetics 159, 1805-1817.
22. Jensen, J. D., Kim, Y., DuMont, V. B., Aquadro, C. F. and Bustamante, C. D. (2005). Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170, 1401-1410.
23. Kim, Y. and Nielsen, R. (2004). Linkage disequilibrium as a signature of selective sweeps. Genetics 167, 1513-1524.
24. Kim, Y. and Stephan, W. (2002). Joint effects of genetic hitchhiking and background selection on neutral variation. Genetics 155, 1415-1427.
25. Kingman, J. F. C. (1982a). The coalescent. Stochastic Process. Appl. 13, 235-248.
26. Kingman, J. F. C. (1982b). Exchangeability and the evolution of large populations. In Exchangeability in Probability and Statistics. (Edited by G. Koch and F. Spizzichino ), 97-112. North-Holland, Amsterdam.
27. Kuhner, M. K., Yamato, J. and Felsenstein, J. (1995). Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140, 1421-1430.
28. Kuhner, M. K., Yamato, J. and Felsenstein, J. (1998). Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149, 429-434.
29. Kuhner, M. K., Yamato, J. and Felsenstein, J. (2000). Maximum likelihood estimation of recombination rates from population data. Genetics 156, 1393-1401.
30. Larribe, F. and Lessard, S. (2008). A composite-conditional-likelihood approach for gene mapping based on linkage disequilibrium in windows of marker loci. Statistical Applications in Genetics and Molecular Biology 7, 27.
31. Larribe, F., Lessard, S. and Schork, N. J. (2002). Gene mapping via the ancestral recombination graph. Theor. Popul. Biol. 62, 215-229.
32. Lazzeroni, L. C. (2001). A chronology of fine-scale gene mapping by linkage disequilibrium. Statist. Meth. Medical Res. 10, 57-76.
33. Li, N. (2008). The promise of composite likelihood methods for addressing computationally intensive challenges. Adv. Genetics 60, 637-654.
34. Lindsay, B. G. (1988). Composite likelihood methods. Contemporary Math. 80, 221-239.
35. Liu, J. S., Sabatti, C., Teng, J., Keats, B. J. and Risch, N. (2001). Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res. 11, 1716-1724.
36. McPeek, M. S. and Strahs, A. (1999). Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale gene mapping. Amer. J. Hum. Genet. 65, 858-875.
37. McVean, G., Awadalla, P. and Fearnhead, P. (2002). A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160, 1231-1241.
38. McVean, G., Myers, S., Hunt, S., Deloukas, P., Bentley, D. and Donnelly P. (2004). The fine-scale structure of recombination rate variation in the human genome. Science 304, 581-584.
39. Meligkotsidou, L. and Fearnhead, P. (2007). Postprocessing of genealogical trees. Genetics 177, 347-358.
40. Meiklejohn, C. D., Kim, Y., Hartl, D. L. and Parsh. J. (2004). Identification of a locus under complex positive selection in drosophila simulans by haplotype mapping and compositelikelihood estimation. Genetics 168, 265-279.
41. Morris, A. P., Whittaker, J. C. and Balding, D. J. (2000). Bayesian fine-scale mapping of disease loci, by hidden Markov models. Amer. J. Hum. Genet. 67, 155-169.
42. Myers, S., Bottolo, L., Freeman, C., McVean, G. A. T. and Donnelly, P. (2005). A fine-scale map of recombination rates and hotspots across the human genome. Science 310, 321-324.
43. Myers, S., Freeman, C., Auton, A., Donnelly, P. and McVean, G. A. T. (2008). A common sequence motif associated with recombination hot spots and genome instability in humans. Nature Genetics 40, 1124-1129.
44. Nielsen, R. and Signorovitch, J. (2003). Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor. Popul. Biol. 63, 245-255.
45. Nordborg, M. (2007). Coalescent theory. In Handbook of Statistical Genetics (Edited by D. J. Balding, M. J. Bishop, and C. Cannings), 843-877. John Wiley & Sons, Inc., Chichester, U.K.
46. Nordborg, M. and Tavaré, S. (2002). Linkage disequilibrium: What history has to tell us. Trends in Genetics 18, 83-90.
47. Pickrell, J. K., Coop, G., Novembre, J., Kudaravalli, S., Li, J. Z., Absher, D., Srinivasan, B. S., Barsh, G. S., Myers, R. M., Feldman, M. W. and Pritchard, J. K. (2009). Signals of recent positive selection in a worldwide sample of human populations. Genome Research 19, 826-837.
48. Plagnol, V. and Wall, J. D. (2006). Possible ancestral structure in human populations. PLoS Genetics 2, e105.
49. Rannala, B. and Slatkin, M. (2000). Methods for multipoint disease mapping using linkage disequilibrium. Genet. Epidemiol. 19, S71-S77.
50. Sawyer, S. A. and Hartl, D. L. (1992). Population-genetics of polymorphism and divergence. Genetics 132, 1161-1176.
51. Service, S. K., Temple, D. W., Freimer, N. B. and Sandkuijl, L. A. (1999). Linkage disequilibrium mapping of disease genes by reconstruction of ancestral haplotypes in founder populations. Amer. J. Hum. Genet. 64, 1728-1738.
52. Slatkin, M. and Rannala, B. (2000). Estimating allele age. Annual Review of Genomics and Human Genetics 1, 225-249.
53. Smith, N. G. C. and Fearnhead, P. (2005). A comparison of three estimators of the populationscaled recombination rate: accuracy and robustness. Genetics 171, 2051-2062.
54. Stephens, M. (2007). Inference under the coalescent. In Handbook of Statistical Genetics (Edited by D. J. Balding, M. Bishop and C. Cannings), 878-908. Wiley, Inc., Chichester, U.K.
55. Stephens, M. and Donnelly, P. (2000). Inference in molecular population genetics. J. Roy. Statist. Soc. Ser. B 62, 605-655.
56. Stephens, M., Smith, N. J. and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. Amer. J. Hum. Genet. 68, 978-989.
57. Tavaré, S. and Zeitouni, O. (2004). Lectures on Probability Theory and Statistics: Ecole d'Eté de Probabilités de Saint-Flour XXXI 2001. (Edited by J. Picard), Lecture Notes in Mathematics, Vol. 1837. Springer-Verlag, Berlin and Heidelberg.
58. Terwilliger, J. D. (1995). A powerful likelihood method for the analysis of linkage disequilibrium between trait loci and one or more polymorphic marker loci. Amer. J. Hum. Genet. 56, 777-787.
59. Thompson, E. A. (2000). Statistical inferences from genetic data on pedigrees. NSF-CBMS Regional Conference Series in Probability and Statistics. Volume 6. IMS, Beachwood, OH.
60. Varin, C. (2008). On composite marginal likelihoods. Adv. Statist. Anal. 92, 1-28.
61. Varin, C., Reid, N. and Firth, D. (2011). An overview of composite likelihood methods, Statist. Sinica 21, 5-42.
62. Varin, C. and Vidoni, P. (2005). A note on composite likelihood inference and model selection. Biometrika 92, 519-528.
63. Wakeley, J. (2008). Coalescent Theory: An Introduction. Roberts & Company Publishers, Greenwood Village, Colorado.
64. Wilson, I. J. and Balding, D. J. (1998). Genealogical inference from microsatellite data. Genetics 150, 499-510.
65. Winckler, W., Myers, S. R., Richter, D. J., Onofrio, R. C., McDonald, G. J., Bontrop, R. E., McVean, G. A. T., Gabriel, S. B., Reich, D., Donnelly, P. and Altshuler, D. (2005). Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308, 107-111. (Pubitemid 40471008)
66. Wiuf, C. (2006). Consistency of estimators of population scaled parameters using composite likelihood. J. Math. Biol. 53, 821-841.
67. Xiong, M. and Guo, S. W. (1997). Fine-scale genetic mapping based on linkage disequilibrium: Theory and applications. Amer. J. Hum. Genet. 60, 1513-1531.
68. Zhu, L. and Bustamante, C.D. (2005). A composite-likelihood approach for detecting directional selection from DNA sequence data. Genetics 170, 1411-1421.