@article{41aee8b4e98347749020825351f2284d,
title = "Inferring structural variant cancer cell fraction",
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{\textquoteright}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.",
author = "Marek Cmero and Ke Yuan and Ong, {Cheng Soon} and Jan Schr{\"o}der and Adams, {David J.} and Pavana Anur and Rameen Beroukhim and Boutros, {Paul C.} and Bowtell, {David D.L.} and Campbell, {Peter J.} and Shaolong Cao and Christie, {Elizabeth L.} and Yupeng Cun and Dawson, {Kevin J.} and Jonas Demeulemeester and Dentro, {Stefan C.} and Deshwar, {Amit G.} and Nilgun Donmez and Drews, {Ruben M.} and Roland Eils and Yu Fan and Fittall, {Matthew W.} and Garsed, {Dale W.} and Moritz Gerstung and Gad Getz and Santiago Gonzalez and Gavin Ha and Kerstin Haase and Marcin Imielinski and Lara Jerman and Yuan Ji and Clemency Jolly and Kortine Kleinheinz and Juhee Lee and Henry Lee-Six and Ignaty Leshchiner and Dimitri Livitz and Salem Malikic and I{\~n}igo Martincorena and Mitchell, {Thomas J.} and Morris, {Quaid D.} and Ville Mustonen and Layla Oesper and Martin Peifer and Myron Peto and Raphael, {Benjamin J.} and Daniel Rosebrock and Mann, {Graham J.} and Gunnar R{\"a}tsch and Waring, {Paul M.}",
note = "Publisher Copyright: {\textcopyright} 2020, The Author(s).",
year = "2020",
month = dec,
day = "1",
doi = "10.1038/s41467-020-14351-8",
language = "English",
volume = "11",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",
}