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BMCBI
2008

Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions

11 years 1 months ago
Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions
Background: The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficulty of determining phase has limited such approaches. Polyploidy is common in plants and is also observed in animals. Partial polyploidy is sometimes observed in humans (e.g. trisomy 21; Down's syndrome), and it arises more frequently in some human tissues. Local changes in ploidy, known as copy number variations (CNV), arise throughout the genome. Here we present a method, implemented in the software polyHap, for the inference of haplotype phase and missing observations from polyploid genotypes. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM) and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty ...
Shu-Yi Su, Jonathan White, David J. Balding, Lachl
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Shu-Yi Su, Jonathan White, David J. Balding, Lachlan J. M. Coin
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