Inferring structural variant cancer cell fraction

• 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.

Subject headings

MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)

MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Medical Genetics (hsv//eng)

Keyword

Algorithms

Computational Biology/methods

Computer Simulation

DNA Copy Number Variations

Female

Gene Frequency

Genome, Human

Humans

Liver Neoplasms/genetics

Male

Neoplasms/genetics

Ovarian Neoplasms/genetics

Pancreatic Neoplasms/genetics

Prostatic Neoplasms/genetics

Sensitivity and Specificity

Whole Genome Sequencing

Publication and Content Type

art (subject category)

ref (subject category)