OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes

C Yau - Bioinformatics, 2013 - academic.oup.com
Bioinformatics, 2013academic.oup.com
Recent major cancer genome sequencing studies have used whole-genome sequencing to
detect various types of genomic variation. However, a number of these studies have
continued to rely on SNP array information to provide additional results for copy number and
loss-of-heterozygosity estimation and assessing tumour purity. OncoSNP-SEQ is a statistical
model-based approach for inferring copy number profiles directly from high-coverage whole
genome sequencing data that is able to account for unknown tumour purity and ploidy …
Abstract
Summary: Recent major cancer genome sequencing studies have used whole-genome sequencing to detect various types of genomic variation. However, a number of these studies have continued to rely on SNP array information to provide additional results for copy number and loss-of-heterozygosity estimation and assessing tumour purity. OncoSNP-SEQ is a statistical model-based approach for inferring copy number profiles directly from high-coverage whole genome sequencing data that is able to account for unknown tumour purity and ploidy.
Availability: MATLAB code is available at the following URL: https://sites.google.com/site/oncosnpseq/.
Contact: c.yau@imperial.ac.uk
Supplementary information:  Supplementary data are available at Bioinformatics online.
Oxford University Press