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001     180877
005     20240320150835.0
024 7 _ |a 10.1038/s41467-020-14351-8
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037 _ _ |a DKFZ-2022-01626
041 _ _ |a English
082 _ _ |a 500
100 1 _ |a Cmero, Marek
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245 _ _ |a Inferring structural variant cancer cell fraction.
260 _ _ |a [London]
|c 2020
|b Nature Publishing Group UK
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520 _ _ |a 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.
536 _ _ |a 312 - Funktionelle und strukturelle Genomforschung (POF4-312)
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650 _ 2 |a Algorithms
|2 MeSH
650 _ 2 |a Computational Biology: methods
|2 MeSH
650 _ 2 |a Computer Simulation
|2 MeSH
650 _ 2 |a DNA Copy Number Variations
|2 MeSH
650 _ 2 |a Female
|2 MeSH
650 _ 2 |a Gene Frequency
|2 MeSH
650 _ 2 |a Genome, Human
|2 MeSH
650 _ 2 |a Humans
|2 MeSH
650 _ 2 |a Liver Neoplasms: genetics
|2 MeSH
650 _ 2 |a Liver Neoplasms: pathology
|2 MeSH
650 _ 2 |a Male
|2 MeSH
650 _ 2 |a Neoplasms: genetics
|2 MeSH
650 _ 2 |a Neoplasms: pathology
|2 MeSH
650 _ 2 |a Ovarian Neoplasms: genetics
|2 MeSH
650 _ 2 |a Ovarian Neoplasms: pathology
|2 MeSH
650 _ 2 |a Pancreatic Neoplasms: genetics
|2 MeSH
650 _ 2 |a Pancreatic Neoplasms: pathology
|2 MeSH
650 _ 2 |a Prostatic Neoplasms: genetics
|2 MeSH
650 _ 2 |a Prostatic Neoplasms: pathology
|2 MeSH
650 _ 2 |a Sensitivity and Specificity
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650 _ 2 |a Whole Genome Sequencing
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700 1 _ |a Yuan, Ke
|b 1
700 1 _ |a Ong, Cheng Soon
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700 1 _ |a Schröder, Jan
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700 1 _ |a PCAWG, Evolution
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700 1 _ |a Heterogeneity Working, Group
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700 1 _ |a Corcoran, Niall M
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700 1 _ |a Papenfuss, Tony
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700 1 _ |a Hovens, Christopher M
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700 1 _ |a Markowetz, Florian
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700 1 _ |a Macintyre, Geoff
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700 1 _ |a PCAWGConsortium
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773 _ _ |a 10.1038/s41467-020-14351-8
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|t Nature Communications
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