Grouping preprocess to accurately extend application of EM algorithm to haplotype inference

Journal of Human Genetics

Volumn 53, Issue 8, 2008, Pages 747-756

  Shindo, Hiroyuki ^a   Chigira, Hiroshi ^a   Tanaka, Junji ^b   Kamatani, Naoyuki ^c   Inoue, Masato ^a  

^a WASEDA UNIVERSITY   (Japan)

^b DaVinci Sakurabashi Bldg   (Japan)

^c TOKYO WOMEN'S MEDICAL UNIVERSITY   (Japan)

Author keywords

Expectation maximization (EM) algorithm; Genome wide association study; Haplotype inference; Haplotype phase; Hardy Weinberg equilibrium (HWE); Single nucleotide polymorphisms (SNPs)

Indexed keywords

ALGORITHM; ARTICLE; GENE LOCUS; HAPLOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; GENETICS, MEDICAL; HAPLOTYPES; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 48549084697     PISSN: 14345161     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10038-008-0308-9     Document Type: Article

References (24)

1. D Altshuler LD Brooks A Chakravarti FS Collins MJ Daly P Donnelly Int HapMap Consortium 2005 A haplotype map of the human genome Nature 437 1299 1320
2. D Brinza A Zelikovsky 2006 2SNP: scalable phasing based on 2-SNP haplotypes Bioinformatics 3 371 373
3. SR Browning BL Browning 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
4. AG Clark 1990 Inference of haplotypes from pcr-amplified samples of diploid populations Mol Biol Evol 7 111 122
5. MJ Daly JD Rioux SE Schaffner TJ Hudson ES Lander 2001 High-resolution haplotype structure in the human genome Nat Genet 29 229 232
6. CM Ding CR Cantor 2003 Direct molecular haplotyping of long-range genomic DNA with M1-PCR Proc Natl Acad Sci USA 100 7449 7453
7. Eronen L, Geerts F, Toivonen H (2006) HaploRec: efficient and accurate large-scale reconstruction of haplotypes. BMC Bioinformatics 7:542
8. L Excoffier M Slatkin 1995 Maximum-likelihood-estimation of molecular haplotype frequencies in a diploid population Mol Biol Evol 12 921 927
9. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM et al (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 7164, 851-U3
10. SE Hodge M Boehnke MA Spence 1999 Loss of information due to ambiguous haplotyping of SNPs Nat Genet 21 360 361
11. GCL Johnson L Esposito BJ Barratt AN Smith J Heward G Di Genova H Ueda HJ Cordell IA Eaves F Dudbridge RCJ Twells F Payne W Hughes S Nutland H Stevens P Carr E Tuomilehto-Wolf J Tuomilehto SCL Gough DG Clayton JA Todd 2001 Haplotype tagging for the identification of common disease genes Nat Genet 29 233 237
12. N Kamatani A Sekine T Kitamoto A Iida S Saito A Kogame E Inoue M Kawamoto M Harigai Y Nakamura 2004 Large-scale single-nucleotide polymorphism (SNP) and haplotype analyses, using dense SNP maps, of 199 drug-related genes in 752 subjects: the analysis of the association between uncommon SNPs within haplotype blocks and the haplotypes constructed with haplotype-tagging SNPs Am J Hum Genet 75 190 203
13. L Kruglyak 1999 Prospects for whole-genome linkage disequilibrium mapping of common disease genes Nat Genet 22 139 144
14. J Marchini D Cutler N Patterson M Stephens E Eskin E Halperin S Lin ZS Qin HM Munro GR Abecasis P Donnelly Intl HapMap Consortium 2006 A comparison of phasing algorithms for trios and unrelated individuals Am J Hum Genet 78 437 450
15. TH Niu ZHS Qin XP Xu JS Liu 2002 Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms Am J Hum Genet 70 157 169
16. ZHS Qin TH Niu JS Liu 2002 Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms Am J Hum Genet 71 1242 1247
17. N Risch K Merikangas 1996 The future of genetics studies of complex human diseases Science 273 1516 1517
18. P Scheet M Stephens 2006 A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase Am J Hum Genet 78 629 644
19. M Stephens P Donnelly 2003 A comparison of Bayesian methods for haplotype reconstruction from population genotype data Am J Hum Genet 73 1162 1169
20. M Stephens NJ Smith P Donnelly 2001 A new statistical method for haplotype reconstruction from population data Am J Hum Genet 68 978 989
21. J Tost O Brandt F Boussicault D Derbala C Caloustian D Lechner IG Gut 2002 Molecular haplotyping at high throughput Nucleic Acids Res 30 e96
22. JC Venter MD Adams EW Myers PW Li RJ Mural GG Sutton HO Smith 2001 The sequence of the human genome Science 291 1304 1351
23. DG Wang JB Fan CJ Siao A Berno P Young R Sapolsky G Ghandour 1998 Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome Science 280 1077 1082
24. EP Xing MI Jordan R Sharan 2007 Bayesian haplotype inference via the dirichlet process J Comput Biol 14 267 284