May 23, 2014

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

PloS One
Yen-Jen LinWen-Ping Hsieh

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. The proposed method can provide the segmentation points of the CNV regions as well as the haplotype phasing for the allelic status on each chromosome. The estimated copy numbers are provided as fractional numbers, which can accommodate the somatic mutation in cancer specimens that usually consist of heterogeneous cell populations. The algorithm is evaluated on simulated data and the previously published regions of CNV of the 270 HapMap individ...Continue Reading

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Citations

Mentioned in this Paper

SNRNP70 gene
Biologic Segmentation
Gene Dosage
Heuristics
DNA Copy Number Changes
Genome
Dopa-Responsive Dystonia
Somatic Mutation
Array-Based Comparative Genomic Hybridization
Neoplasms

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