TY  - JOUR
AU  - Cmero, Marek
AU  - Yuan, Ke
AU  - Ong, Cheng Soon
AU  - Schröder, Jan
AU  - PCAWG, Evolution
AU  - Heterogeneity Working, Group
AU  - Corcoran, Niall M
AU  - Papenfuss, Tony
AU  - Hovens, Christopher M
AU  - Markowetz, Florian
AU  - Macintyre, Geoff
AU  - PCAWGConsortium
TI  - Inferring structural variant cancer cell fraction.
JO  - Nature Communications
VL  - 11
IS  - 1
SN  - 2041-1723
CY  - [London]
PB  - Nature Publishing Group UK
M1  - DKFZ-2022-01626
SP  - 730
PY  - 2020
N1  - siehe Correction: DKFZ Autoren affiliiert im PCAWG Consortium:https://inrepo02.dkfz.de/record/212436   /   https://doi.org/10.1038/s41467-022-32338-5
AB  - 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.
KW  - Algorithms
KW  - Computational Biology: methods
KW  - Computer Simulation
KW  - DNA Copy Number Variations
KW  - Female
KW  - Gene Frequency
KW  - Genome, Human
KW  - Humans
KW  - Liver Neoplasms: genetics
KW  - Liver Neoplasms: pathology
KW  - Male
KW  - Neoplasms: genetics
KW  - Neoplasms: pathology
KW  - Ovarian Neoplasms: genetics
KW  - Ovarian Neoplasms: pathology
KW  - Pancreatic Neoplasms: genetics
KW  - Pancreatic Neoplasms: pathology
KW  - Prostatic Neoplasms: genetics
KW  - Prostatic Neoplasms: pathology
KW  - Sensitivity and Specificity
KW  - Whole Genome Sequencing
LB  - PUB:(DE-HGF)16
C6  - pmid:32024845
C2  - pmc:PMC7002525
DO  - DOI:10.1038/s41467-020-14351-8
UR  - https://inrepo02.dkfz.de/record/180877
ER  -