PureCN: copy number calling and SNV classification using targeted short read sequencing View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-12

AUTHORS

Markus Riester, Angad P. Singh, A. Rose Brannon, Kun Yu, Catarina D. Campbell, Derek Y. Chiang, Michael P. Morrissey

ABSTRACT

BACKGROUND: Matched sequencing of both tumor and normal tissue is routinely used to classify variants of uncertain significance (VUS) into somatic vs. germline. However, assays used in molecular diagnostics focus on known somatic alterations in cancer genes and often only sequence tumors. Therefore, an algorithm that reliably classifies variants would be helpful for retrospective exploratory analyses. Contamination of tumor samples with normal cells results in differences in expected allelic fractions of germline and somatic variants, which can be exploited to accurately infer genotypes after adjusting for local copy number. However, existing algorithms for determining tumor purity, ploidy and copy number are not designed for unmatched short read sequencing data. RESULTS: We describe a methodology and corresponding open source software for estimating tumor purity, copy number, loss of heterozygosity (LOH), and contamination, and for classification of single nucleotide variants (SNVs) by somatic status and clonality. This R package, PureCN, is optimized for targeted short read sequencing data, integrates well with standard somatic variant detection pipelines, and has support for matched and unmatched tumor samples. Accuracy is demonstrated on simulated data and on real whole exome sequencing data. CONCLUSIONS: Our algorithm provides accurate estimates of tumor purity and ploidy, even if matched normal samples are not available. This in turn allows accurate classification of SNVs. The software is provided as open source (Artistic License 2.0) R/Bioconductor package PureCN (http://bioconductor.org/packages/PureCN/). More... »

PAGES

13

Journal

TITLE

Source Code for Biology and Medicine

ISSUE

1

VOLUME

11

Author Affiliations

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13029-016-0060-z

DOI

http://dx.doi.org/10.1186/s13029-016-0060-z

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1019667057

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27999612


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