sigven/cpsr

Cancer Predisposition Sequencing Reporter (CPSR)

Cancer Predisposition Sequencing Reporter

The Cancer Predisposition Sequencing Reporter (CPSR) is a computational workflow that interprets and classifies germline DNA variants identified from next-generation sequencing in the context of cancer predisposition and inherited cancer syndromes. The workflow can also report incidental findings (ACMG v3.0) as well as the genotypes of common germline variants associated with cancer risk, as reported in the NHGRI-EBI GWAS catalog.

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.

CPSR accepts a query file from a single case/patient, containing raw germline variant calls encoded in the VCF format (i.e. SNVs/InDels). A comprehensive set of virtual cancer predisposition gene panels harvested from the Genomics England PanelApp allows the user to flexibly put a restriction on which genes and findings are displayed in the cancer predisposition report.

Snapshots of sections in the cancer predisposition genome report:

News

• 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)

• June 30th 2021: 0.6.2 release

  • Updated bundle (ClinVar, CancerMine, UniprotKB, PanelApp, CIViC, GWAS catalog)
  • Software upgrade (VEP, R/BioConductor)
  • CHANGELOG

• November 30th 2020: 0.6.1 release

  • Updated bundle (ClinVar, CancerMine, UniprotKB, CIViC, GWAS catalog)
  • CHANGELOG

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

[email protected]