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


BACKGROUND
MATLAB code is available at the following URL: https://sites.google.com/site/oncosnpseq/.
Department of Mathematics, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.
Christopher
C
Yau
D056915:DNA Copy Number Variations; D016678:Genome; D023281:Genomics / Q000379:methods; D006801:Humans; D019656:Loss of Heterozygosity; D009369:Neoplasms / Q000235:genetics*; D011003:Ploidies; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D012985:Software Design