Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

The American Journal of Human Genetics - Tập 81 Số 5 - Trang 1084-1097 - 2007
Sharon R. Browning1,2, Brian L. Browning2
1Department of Statistics, The University of Auckland, Auckland, New Zealand
2Discipline of Nutrition, The University of Auckland, Auckland, New Zealand

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

Lin, 2007, The use of inferred haplotypes in downstream analyses, Am J Hum Genet, 80, 577, 10.1086/512201