Repository files navigation

TheCancer Predisposition Sequencing Reporter (CPSR) is a computational workflow thatinterprets DNA sequence variants identified from next-generation sequencingin the context of cancer predisposition.

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

1. Flexibleselection of cancer predisposition genes subject to analysis and reporting - through the use of virtual gene panels
2. Variant classification (Pathogenic toBenign) through a dedicated implementation ofACMG/AMP guidelines
3. Detection of germline biomarkers - for prognosis, diagnosis, or drug sensitivity/resistance in cancer
4. Reporting ofsecondary/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 thePersonal Cancer Genome Reporter - PCGR. WhilePCGR 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 thequarto-based cancer predisposition genome report (artificial sample, with more findings than usual) are shown below:

• 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
• August 2024:2.0.3 release
  • patch with bug fix for copying in quarto templates (pr62)
  • CHANGELOG
• 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 withquarto
  • Excel output supported
  • Data bundle update
  • Singularity/Apptainer support
  • CHANGELOG
• November 2022:1.0.1 release
  • Added CPSR logo (designed byHal Nakken)

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

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)

sigven@ifi.uio.no