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Cancer Predisposition Sequencing Reporter



The Cancer Predisposition Sequencing Reporter (CPSR) is a computational workflow that interprets DNA sequence variants identified from next-generation sequencing in the context of cancer predisposition.

CPSR accepts a query file with germline variant calls (SNVs/InDels) from a single sample (i.e. cancer patient), encoded in the VCF format. Through comprehensive gene and variant annotation procedures, CPSR offers the following functionalities to the user:

  1. Flexible selection of cancer predisposition genes that restricts variant classification and reporting - through the use of virtual gene panels
  2. Variant classification (Pathogenic to Benign) through a dedicated and well-performing implementation of ACMG/AMP guidelines
  3. Detection of biomarkers - variants with prognostic, diagnostic, or drug sensitivity/resistance implications in cancer, as well as optional detection of variants related to adverse events/toxicity for common chemotherapies
  4. Optional reporting of secondary/incidental findings (ACMG recommendations)
  5. Interactive HTML output report with detailed variant information, gene annotations, and external links to relevant databases

The CPSR workflow is integrated with the framework that underlies Personal Cancer Genome Reporter - PCGR. While PCGR is intended for reporting and analysis of somatic variants detected in a tumor, CPSR is intended for reporting and ranking of germline variants in protein-coding genes that are implicated in cancer predisposition and inherited cancer syndromes.

Snapshots of sections in the quarto-based cancer predisposition genome report (artificial sample, with more findings than usual):


News

  • March 23rd 2025: 2.2.1 release
    • patch to fix bug with non-standard ClinVar significance levels (Drug Response, Risk Factor)
  • March 22nd 2025: 2.2.0 release
    • more predisposition genes in panel zero
    • optional reporting of pharmacogenomics-related variants (TPMT, DPYD, NUDT15)
    • CHANGELOG
  • October 2024: 2.1.2 release
    • cosmetic fixes in HTML report
    • fix for VEP consequence pick exception
    • CHANGELOG
  • September 2024: 2.1.0 release
    • data bundle upgrade
    • re-calibration of classification tresholds
    • CHANGELOG
  • June 2024: 2.0.0 release
    • New HTML report generation and layout with quarto
    • Excel output supported
    • Data bundle update
    • Singularity/Apptainer support
    • CHANGELOG
  • November 2022: 1.0.1 release

Example report

DOI

Getting started

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