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Inferring structural variant cancer cell fraction

Author(s): Cmero, Marek; Yuan, Ke; Ong, Cheng Soon; Schröder, Jan; PCAWG Evolution and Heterogeneity Working Group; et al

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Abstract: We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number. We assess performance using in silico mixtures of real samples, at known proportions, created from two clonal metastases from the same patient. We find that SVclone’s performance is comparable to single-nucleotide variant-based methods, despite having an order of magnitude fewer data points. As part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we use SVclone to reveal a subset of liver, ovarian and pancreatic cancers with subclonally enriched copy-number neutral rearrangements that show decreased overall survival. SVclone enables improved characterisation of SV intra-tumour heterogeneity.
Publication Date: 5-Feb-2020
Citation: Cmero, Marek, Ke Yuan, Cheng Soon Ong, Jan Schröder, PCAWG Evolution and Heterogeneity Working Group, Niall M. Corcoran, Tony Papenfuss, Christopher M. Hovens, Florian Markowetz, Geoff Macintyre, and PCAWG Consortium. "Inferring structural variant cancer cell fraction." Nature Communications 11, no. 1 (2020). doi:10.1038/s41467-020-14351-8
DOI: 10.1038/s41467-020-14351-8
EISSN: 2041-1723
Language: eng
Type of Material: Journal Article
Journal/Proceeding Title: Nature Communications
Version: Final published version. This is an open access article.
Notes: Supplementary Information:

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