Cancer Predisposition Sequencing Reporter (CPSR)
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:
November 2022: 1.0.1 release
February 2022: 1.0.0 release
June 30th 2021: 0.6.2 release
November 30th 2020: 0.6.1 release
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)