Journal article

Inferring copy number and genotype in tumour exome data

Kaushalya C Amarasinghe, Jason Li, Sally M Hunter, Georgina L Ryland, Prue A Cowin, Ian G Campbell, Saman K Halgamuge

BMC GENOMICS | BMC | Published : 2014

Abstract

BACKGROUND: Using whole exome sequencing to predict aberrations in tumours is a cost effective alternative to whole genome sequencing, however is predominantly used for variant detection and infrequently utilised for detection of somatic copy number variation. RESULTS: We propose a new method to infer copy number and genotypes using whole exome data from paired tumour/normal samples. Our algorithm uses two Hidden Markov Models to predict copy number and genotypes and computationally resolves polyploidy/aneuploidy, normal cell contamination and signal baseline shift. Our method makes explicit detection on chromosome arm level events, which are commonly found in tumour samples. The methods are..

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