A dictionary model for haplotyping, genotype calling, and association testing

Genetic Epidemiology

Volumn 31, Issue 7, 2007, Pages 672-683

  Ayers, Kristin L ^a,b   Sabatti, Chiara ^a,b   Lange, Kenneth ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Backward algorithm; Forward algorithm; Gibbs sampling; Linkage disequilibrium

Indexed keywords

DIPEPTIDYL CARBOXYPEPTIDASE;

ALGORITHM; ARTICLE; CHROMOSOME 7; CYSTIC FIBROSIS; DISEASE ASSOCIATION; FRIEDREICH ATAXIA; GENE LINKAGE DISEQUILIBRIUM; GENOTYPE; HAPLOTYPE; HUMAN; LOGISTIC REGRESSION ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MODEL; PROBABILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; ANIMALS; CYSTIC FIBROSIS; FRIEDREICH ATAXIA; HAPLOTYPES; HUMANS; MARKOV CHAINS; MODELS, GENETIC; MUTATION; PEPTIDYL-DIPEPTIDASE A; SEQUENCE ANALYSIS, DNA;

EID: 36248969294     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20232     Document Type: Article

References (27)

1. Akey J, Jin L, Xiong M. 2001. Haplotypes vs single marker linkage disequilibrium tests: what do we gain? Eur J Hum Genet 9:291-300.
2. Ayers KL, Sabatti C, Lange K. 2006. Reconstructing ancestral haplotypes with a dictionary model. J Comput Biol 13:767-785.
3. Bussemaker HJ, Li H, Siggia ED. 2000. Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc Natl Acad Sci USA 97:10096-10100.
4. Campuzano V, Montermini L, Molto MD, Pianese L, Cossee M, Cavalcanti F, Montos E, Rodius F, Duclos F, Monticelli A, Zara F, Canizares J, Koutnikova H, Bidichandani SI, Gellera C, Brice A, Trouillas P, De Michele G, Filla A, De Frutos R, Palau F, Patel PI, Di Donato S, Mandel JL, Cocozza S, Koenig M, Pandolfo M. 1996. Friedreich's ataxia: Autosomal recessive disease caused by an intronic GAA triplet reat expansion. Science 271:1423-1427.
5. Chiano M, Clayton D. 1998. Fine genetic mapping using haplotype analysis and the missing data problem. Ann Hum Genet 62:55-60.
6. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. 2001. High-resolution haplotype structure in the human genome. Nat Genet 29:229-232.
7. Eskin E, Halperin E, Karp R. 2003. Efficient reconstruction of haplotype structure via perfect phylogeny. J Bioinform Comput Biol 1:1-20.
8. Excoffier L, Slatkin M. 1995. Maximum likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927.
9. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, LiuCordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. 2002. The structure of haplotype blocks in the human genome. Science 296:2225-2229.
10. Halperin E, Eskin E. 2004. Haplotype reconstruction from genotype data using imperfect phylogeny. Bioinformatics 20:1842-1849.
11. Hawley ME, Kidd KK. 1995. HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered 86:409-411.
12. Keavney B, McKenzie CA, Connell JM, Julier C, Ratcliffe PJ, Sobel E, Lathrop M, Farrall M. 1998. Measured haplotype analysis of the angiotensin-I converting enzyme gene. Hum Mol Genet 7:1745-1751.
13. Kerem B, Rommens JM, Buchanan JA, Markiewicz D, Cox TK, Chakravarti A, Buchwald M, Tsui LC. 1989. Identification of the cystic fibrosis gene: genetic analysis. Science 245:1073-1080.
14. Lange K, Cantor R, Horvath S, Perola M, Sabatti C, Sinsheimer J, Sobel E. 2001. Mendel version 4.0: a complete package for the exact genetic analysis of discrete traits in pedigree and population data sets. Am J Hum Genet 69(supplement):A1886.
15. Lange K, Sinsheimer J, Sobel E. 2005. Association testing with Mendel. Genet Epidemiol 29:36-50.
16. Lin S, Cutler DJ, Zwick ME, Chakravarti A. 2002. Haplotype inference in random population samples. Am J Hum Genet 71:1129-1137.
17. Liu JS, Sabatti C, Teng J, Keats BJB, Risch N. 2001. Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res 11:1716-1724.
18. Long JC, Williams RC, Urbanek M. 1995. An E-M algorithm and testing strategy for multiple-locus haplotypes. Am J Hum Genet 56:225-232.
19. Marchini J, Cutler D, Patterson N, Stephens M, Eskin E, Halperin E, Lin S, Qin ZS, Munro HM, Abecasis GR, Donnelly P. 2006. A comparision of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 78:437-450.
20. Niu T, Qin ZS, Xu X, Liu JS. 2002. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet 70:157-169.
21. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BT, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SPA, Cox DR. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human Chromosome 21. Science 294:1719-1724.
22. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES. 2001. Linkage disequilibrium in the human genome. Nature 411:199-204.
23. Sabatti C, Lange K. 2002. Genomewide motif identification using a dictionary model. IEEE Proc 90:1803-1810.
24. Sirugo G, Keats B, Fujita R, Duclos F, Purohit K, Kenig M, Mandel JL. 1992. Friedreich ataxia in Lousiana Acadians: demonstration of a founder effect by analysis of microsatellite-generated extended haplotypes. Am J Hum Genet 50:559-566.
25. Stephens M, Smith NJ, Donnelly P. 2001. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989.
26. Xing E, Sharan R, Jordan MI. 2004. Bayesian haplotype inference via the dirichlet process. ICML 69:879-886.
27. Zhang K, Qin ZS, Liu JS, Chen T, Waterman MS, Sun F. 2004. Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res 14:908-916.