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bioRxiv · 10.1101/172486

SVclone: inferring structural variant cancer cell fraction

Cmero, M.·Ong, C. S.·Yuan, K.·Schröder, J.·Mo, K.·PCAWG Evolution and Heterogeneity Working Group,·Corcoran, N. M.·Papenfuss, A. T.·Hovens, C. M.·Markowetz, F.·Macintyre, G.
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Abstract

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.

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Cmero, M., Ong, C. S., Yuan, K., Schröder, J., Mo, K., PCAWG Evolution and Heterogeneity Working Group,, Corcoran, N. M., Papenfuss, A. T., Hovens, C. M., Markowetz, F., Macintyre, G.. 2017-08-04. SVclone: inferring structural variant cancer cell fraction. https://doi.org/10.1101/172486

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