rapid haplotype inference for nuclear families快速单体型推断核心家庭.pdfVIP

Williams et al. Genome Biology 2010, 11:R108 /2010/11/10/R108 METHOD Open Access Rapid haplotype inference for nuclear families 1* 2 1 1 Amy L Williams , David E Housman , Martin C Rinard , David K Gifford Abstract Hapi is a new dynamic programming algorithm that ignores uninformative states and state transitions in order to efficiently compute minimum-recombinant and maximum likelihood haplotypes. When applied to a dataset con- taining 103 families, Hapi performs 3.8 and 320 times faster than state-of-the-art algorithms. Because Hapi infers both minimum-recombinant and maximum likelihood haplotypes and applies to related individuals, the haplotypes it infers are highly accurate over extended genomic distances. Background Genome scale haplotypes cannot be discovered using The emergence of high throughput genotyping technol- direct molecular means at present, so computational ogies has enabled rapid, low-cost assays of single methods must be used to infer them. Algorithms for nucleotide polymorphisms (SNPs) in large datasets of inferring haplotypes can be separated into three classes. human subjects. These genotype data provide two unor- One class of haplotyping algorithms applies to unrelated dered allele values at each queried genomic position, individuals, and techniques of this class use probabilistic with each allele derived from the two homologous chro- constraints governed by mathematical models of popula- mosomes in a diploid cell. However, genotype data do tion dynamics to infer haplotypes. Available algori