Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering
Tóm tắt
Từ khóa
Tài liệu tham khảo
Browning, 2007, Efficient multilocus association mapping for whole genome association studies using localized haplotype clustering, Genet Epidemiol, 31, 365, 10.1002/gepi.20216
The International HapMap Consortium, 2005, A haplotype map of the human genome, Nature, 437, 1299, 10.1038/nature04226
Marchini, 2006, A comparison of phasing algorithms for trios and unrelated individuals, Am J Hum Genet, 78, 437, 10.1086/500808
Excoffier, 1995, Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population, Mol Biol Evol, 12, 921
Long, 1995, An E-M algorithm and testing strategy for multiple-locus haplotypes, Am J Hum Genet, 56, 799
Hawley, 1995, HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes, J Hered, 86, 409, 10.1093/oxfordjournals.jhered.a111613
Scheet, 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, 10.1086/502802
Eronen, 2006, HaploRec: efficient and accurate large-scale reconstruction of haplotypes, BMC Bioinformatics, 7, 542, 10.1186/1471-2105-7-542
Qin, 2002, Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms, Am J Hum Genet, 71, 1242, 10.1086/344207
Stephens, 2001, A new statistical method for haplotype reconstruction from population data, Am J Hum Genet, 68, 978, 10.1086/319501
Halperin, 2004, Haplotype reconstruction from genotype data using imperfect phylogeny, Bioinformatics, 20, 1842, 10.1093/bioinformatics/bth149
Browning, 2006, Multilocus association mapping using variable-length Markov chains, Am J Hum Genet, 78, 903, 10.1086/503876
Kimmel, 2005, GERBIL: genotype resolution and block identification using likelihood, Proc Natl Acad Sci USA, 102, 158, 10.1073/pnas.0404730102
Brinza, 2006, 2SNP: scalable phasing based on 2-SNP haplotypes, Bioinformatics, 22, 371, 10.1093/bioinformatics/bti785
Stephens, 2005, Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation, Am J Hum Genet, 76, 449, 10.1086/428594
Excoffier, 2003, Gametic phase estimation over large genomic regions using an adaptive window approach, Hum Genomics, 1, 7, 10.1186/1479-7364-1-1-7
Ron, 1998, On the learnability and usage of acyclic probabilistic finite automata, J Comput Systems Sci, 56, 133, 10.1006/jcss.1997.1555
Rabiner, 1989, A tutorial on hidden Markov models and selected applications in speech recognition, Proc IEEE, 77, 257, 10.1109/5.18626
Thompson, 2000, Vol 6
Celeux, 1985, The SEM algorithm: a probabilistic teacher algorithm derived from the EM algorithm for the mixture problem, Comput Stat Q, 2, 73
Tregouet, 2004, A new algorithm for haplotype-based association analysis: the stochastic-EM algorithm, Ann Hum Genet, 68, 165, 10.1046/j.1529-8817.2003.00085.x
Schaffner, 2005, Calibrating a coalescent simulation of human genome sequence variation, Genome Res, 15, 1576, 10.1101/gr.3709305
Kong, 2002, A high-resolution recombination map of the human genome, Nat Genet, 31, 241, 10.1038/ng917
Carlson, 2004, Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium, Am J Hum Genet, 74, 106, 10.1086/381000
The Wellcome Trust Case Control Consortium, 2007, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls, Nature, 447, 661, 10.1038/nature05911
Matsuzaki, 2004, Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays, Nat Methods, 1, 109, 10.1038/nmeth718
Rabbee, 2006, A genotype calling algorithm for Affymetrix SNP arrays, Bioinformatics, 22, 7, 10.1093/bioinformatics/bti741
Lin, 2002, Haplotype inference in random population samples, Am J Hum Genet, 71, 1129, 10.1086/344347
Stephens, 2003, A comparison of Bayesian methods for haplotype reconstruction from population genotype data, Am J Hum Genet, 73, 1162, 10.1086/379378
Barrett, 2006, Evaluating coverage of genome-wide association studies, Nat Genet, 38, 659, 10.1038/ng1801
Plagnol, 2007, A method to address differential bias in genotyping in large-scale association studies, PLoS Genet, 3, e74, 10.1371/journal.pgen.0030074