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 main functionalities to the user:

1. Flexible selection of cancer predisposition genes subject to analysis and reporting - through the use of virtual gene panels
2. Variant classification (Pathogenic to Benign) through a dedicated implementation of ACMG/AMP guidelines
3. Detection of germline biomarkers - for prognosis, diagnosis, or drug sensitivity/resistance
4. 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 the 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) are shown below:

News

• July 2024: 2.0.1 release
  • patch with bug fix for mitochondrial input variants (pr245)
  • 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
  • Added CPSR logo (designed by Hal Nakken)
• February 2022: 1.0.0 release
  • Complete restructure of code and Conda installation routines, contributed largely by the great @pdiakumis
  • Updated data bundle
    • ClinVar - Feb 2022
    • CancerMine - Dec 2021
    • UniprotKB - Nov 2021
    • CIViC - Feb 2022
    • GWAS catalog - Dec 2021
  • Software upgrade (VEP 105, R/BioConductor)
  • New documentation site (https://sigven.github.io/cpsr)

Example report

Getting started

• Installation instructions
• Run through an example
• Learn more about
  • Details regarding the CPSR input file, and how it should be formatted
  • The types and contents of CPSR output files
  • ACMG variant classification procedure used in CPSR
  • The list of virtual gene panels available in CPSR

Citation

If you use CPSR, please cite the following publication:

Sigve Nakken, Vladislav Saveliev, Oliver Hofmann, Pål Møller, Ola Myklebost, and Eivind Hovig. Cancer Predisposition Sequencing Reporter (CPSR): a flexible variant report engine for high-throughput germline screening in cancer (2021). Int J Cancer. [doi:10.1002/ijc.33749](https://doi.org/10.1002/ijc.33749)

Contact

sigven@ifi.uio.no