Blockwise HMM computation for large-scale population genomic inference

Bioinformatics

Volumn 28, Issue 15, 2012, Pages 2008-2015

  Paul, Joshua S ^a   Song, Yun S ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENOMICS; HAPLOTYPE; HUMAN; METHODOLOGY; POPULATION GENETICS; PROBABILITY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENETICS, POPULATION; GENOMICS; HAPLOTYPES; HUMANS; MARKOV CHAINS; PROBABILITY; SOFTWARE;

EID: 84865132907     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts314     Document Type: Article

References (33)

1. Browning,B.L. and Browning,S.R. (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering. Am. J. Hum. Genet., 81, 1084-1097.
2. Crawford,D.C. et al. (2004) Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat. Genet., 36, 700-706.
3. Davison,D. et al. (2009) An approximate likelihood for genetic data under a model with recombination and population splitting. Theor. Popul. Biol., 75, 331-345.
4. De Iorio,M. and Griffiths,R.C. (2004a) Importance sampling on coalescent histories. I. Adv. Appl. Prob., 36, 417-433.
5. De Iorio,M. and Griffiths,R.C. (2004b) Importance sampling on coalescent histories. II: Subdivided population models. Adv. Appl. Prob., 36, 434-454.
6. Delaneau,O. et al. (2012)Alinear complexity phasing method for thousands of genomes. Nat. Methods, 9, 179-181.
7. Dutheil,J.Y. et al. (2009) Ancestral population genomics: the coalescent hidden markov model approach. Genetics, 183, 259-274.
8. Fearnhead,P. and Donnelly,P. (2001) Estimating recombination rates from population genetic data. Genetics, 159, 1299-1318.
9. Fearnhead,P. and Donnelly,P. (2002) Approximate likelihood methods for estimating local recombination rates. J. Royal Stat. Soc. B, 64, 657-680.
10. Fearnhead,P. and Smith,N.G. (2005) A novel method with improved power to detect recombination hotspots from polymorphism data reveals multiple hotspots in human genes. Am. J. Hum. Genet., 77, 781-794.
11. Gay,J. et al. (2007) Estimating meiotic gene conversion rates from population genetic data. Genetics, 177, 881-894.
12. Griffiths,R.C. et al. (2008) Importance sampling and the two-locus model with subdivided population structure. Adv. Appl. Probab., 40, 473-500.
13. Hellenthal,G. et al. (2008) Inferring human colonization history using a copying model. PLoS Genet., 4, e1000078.
14. Hobolth,A. et al. (2007) Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden markov model. PLoS Genet, 3, e7.
15. Howie,B.N. et al. (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet., 5, e1000529.
16. Hudson,R.R. (2001) Two-locus sampling distributions and their application. Genetics, 159, 1805-1817.
17. Lawson,D. et al. (2012) Inference of population structure using dense haplotype data. PLoS Genet., 8, e1002453.
18. Li,H. and Durbin,R. (2011) Inference of human population history from individual whole-genome sequences. Nature, 475, 493-496.
19. Li,N. and Stephens,M. (2003) Modelling linkage disequilibrium, and identifying recombination hotspots using SNP data. Genetics, 165, 2213-2233.
20. Li,Y. et al. (2010) Mach: Using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet. Epidemiol., 34, 816-834.
21. Marchini,J. et al. (2007)Anew multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet., 39, 906-913.
22. Marjoram,P. and Wall,J.D. (2006) Fast "coalescent" simulation. BMC Genet., 7, 16.
23. McVean,G.A.T. et al. (2004) The fine-scale structure of recombination rate variation in the human genome. Science, 304, 581-584.
24. McVean,G.A. and Cardin,N.J. (2005)Approximating the coalescentwith recombination. Philos. Trans. R. Soc. Lond. B Biol. Sci., 360, 1387-1393.
25. Paul,J.S. and Song,Y.S. (2010) A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination. Genetics, 186, 321-338.
26. Paul,J.S. et al. (2011)An accurate sequentially markov conditional sampling distribution for the coalescent with recombination. Genetics, 187, 1115-1128.
27. Price,A.L. et al. (2009) Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet., 5, e1000519.
28. Scheet,P. and Stephens,M. (2006) A fast and flexible method for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet., 78, 629-644.
29. Stephens,M. and Donnelly,P. (2000) Inference in molecular population genetics. J. R. Stat. Soc. Ser. B Stat. Methodol., 62, 605-655.
30. Stephens,M. and Scheet,P. (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am. J. Hum. Genet., 76, 449-462.
31. Sundquist,A. et al. (2008) Effect of genetic divergence in identifying ancestral origin using HAPAA. Genome Res., 18, 676-682.
32. Wegmann,D. et al. (2011) Recombination rates in admixed individuals identified by ancestry-based inference. Nat. Genet., 43, 847-853.
33. Yin,J. et al. (2009) Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data. Bioinformatics, 25, i231-i239.