Journal article

SVclone: inferring structural variant cancer cell fraction

Marek Cmero, Cheng Soon Ong, Ke Yuan, Jan Schröder, Kangbo Mo, Niall Corcoran, Anthony Troy Papenfuss, Christopher Hovens, Florian Markowetz, Geoff Macintyre, undefined PCAWG Evolution and Heterogeneity Working Group

Published : 2017


We present SVclone, a computational method for inferring the cancer cell fraction of structural variant breakpoints from whole-genome sequencing data. We validate our approach using simulated and real tumour samples, and demonstrate its utility on 2,778 whole-genome sequenced tumours. We find a subset of liver, breast and ovarian cancer cases with decreased overall survival that have subclonally enriched copy-number neutral rearrangements, an observation that could not be discovered with currently available methods.