Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Level 7 Seminar Room 2, WEHI1

6 June 2017

SVclone: inferring structural variant cancer cell fraction

Marek Cmero
WEHI Bioinformatics

Understanding intra-tumour heterogeneity has fundamental implications for the treatment and prognostication of cancer. Many approaches have arisen for inferring the evolutionary dynamics and clonality of tumour cell populations from point-mutation and copy-number data. However, currently no methods exist that fully incorporate structural variation (SV) and thus balanced rearrangements are not considered, despite being important drivers in particular cancers such as prostate.

To address this gap, 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 2,658 whole-genome sequenced tumours. We find a subset of cases with decreased overall survival that have subclonally enriched copy-number neutral rearrangements, an observation that could not have been discovered with currently available methods.

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