HaplotypeCN: copy number haplotype inference with Hidden Markov Model and localized haplotype clustering.

ABSTRACT: Copy number variation (CNV) has been reported to be associated with disease and various cancers. Hence, identifying the accurate position and the type of CNV is currently a critical issue. There are many tools targeting on detecting CNV regions, constructing haplotype phases on CNV regions, or estimating the numerical copy numbers. However, none of them can do all of the three tasks at the same time. This paper presents a method based on Hidden Markov Model to detect parent specific copy number change on both chromosomes with signals from SNP arrays. A haplotype tree is constructed with dynamic branch merging to model the transition of the copy number status of the two alleles assessed at each SNP locus. The emission models are constructed for the genotypes formed with the two haplotypes.

SUBMITTER: Lin YJ 

PROVIDER: S-EPMC4029584 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature