sigven/pcgr repository overview

⁠Personal Cancer Genome Reporter (PCGR)

⁠Overview

The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual tumor genomes for precision cancer medicine. It interprets primarily somatic SNVs/InDels and copy number aberrations, and has additional support for interpretation of bulk RNA-seq expression data. The software classifies variants both with respect to oncogenicity, and actionability. Interactive HTML output reports allow the user to interrogate the clinical impact of the molecular findings in an individual tumor.

• Variant classification
  • according to oncogenicity: evaluating the oncogenic potential of somatic DNA aberrations (VICC/CGC/ClinGen guidelines⁠)
  • according to actionability: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations (AMP/ASCO/CAP guidelines⁠)
• Tumor mutational burden (TMB) estimation
• Mutational signature analysis
• Microsatellite instability (MSI) classification
• RNA-seq support - gene expression outlier detection, sample similarity analysis, and immune contexture profiling

PCGR supports both of the most recent human genome assemblies (GRCh37/GRCh38), and accepts variant calls from both tumor-control and tumor-only sequencing assays. Much of the functionality is intended for whole-exome/whole-genome sequencing assays, but you can also apply PCGR to output from targeted sequencing panels. If you are interested in the interrogation of germline variants and their relation to cancer predisposition, we recommend trying the accompanying tool Cancer Predisposition Sequencing Reporter (CPSR)⁠.

⁠News

• March 23rd 2025: 2.2.1 release

  • fix bug in CPSR for ClinVar variants with non-standard significance levels

• March 22nd 2025: 2.2.0 release

  • Data/software updates:
    • Ensembl VEP v113 / GENCODE v47
    • ClinVar (2025-03)
    • CIViC (2025-03-13)
    • and more
  • CHANGELOG⁠

• October 21st 2024: 2.1.2 release

  • CHANGELOG⁠

• October 11th 2024: 2.1.1 release

  • patch to fix bug⁠ with parsing of relative CDS start positions
  • CHANGELOG⁠

• September 29th 2024: 2.1.0 release

  • updated bundle, more oncogenic variants, CNA visualization, improved RNA-seq support, bug fixes, and more
  • CHANGELOG⁠

• August 1st 2024: 2.0.3 release

  • patch to fix purity/ploidy propagation, MAF output for tumor-only runs, and other minor issues
  • CHANGELOG⁠

• July 16th 2024: 2.0.2 release

  • patch to ensure correct reference to actionability guidelines
  • CHANGELOG⁠

• July 7th 2024: 2.0.1 release

  • patch with bug fix for mitochondrial input variants (pr245⁠)
  • CHANGELOG⁠

• June 2024: 2.x.x release

  • Massive reference data bundle upgrade, new report layout, oncogenicity classification++
  • Details at CHANGELOG⁠

• February 2023: 1.3.0 release

  • Details at CHANGELOG⁠
  • proritize protein-coding BIOTYPE csq (pr201⁠)
  • expose --pcgrr_conda option to flexibly activate pcgrr env via a non-default pcgrr name
  • cpsr_validate_input.py: refactor for efficient custom gene egrep

• November 2022: 1.2.0 release

  • Keep only autosomal, X, Y, M/MT chromosomes
  • Import bcftools as dependency

• October 2022: 1.1.0 release

  • Remove Docker command wrappers
  • Deprecate --no_docker and --docker_uid CLI options
  • Merged PRs pr192⁠, pr193⁠, pr194⁠, pr196⁠.
  • See CHANGELOG⁠ for a few more changes.

• May 2022: 1.0.3 release

  • Merged PR #191⁠

• March 2022: 1.0.2 release

  • Fixed CPSR issue #44⁠

• March 2022: 1.0.1 release

  • Fixed bug for huge input sets that cause JSON output crash
    • huge input variant sets (WGS) are now reduced prior to reporting with R, i.e. exclusion of intronic and intergenic variants, as well as upstream/downstream gene variants (#178⁠).
  • Fixed bug for cases where mutational signature analysis reports > 18 different aetiologies after fitting (#187⁠).
  • CHANGELOG⁠

• February 2022: 1.0.0 release

  • Complete restructure of Python and R components. Installation now relies on two separate conda⁠ packages, pcgr (Python component) and pcgrr (R component). Direct Docker support remains, with the Dockerfile simplified to rely exclusively on the installation of the above Conda packages. Significant contributon by the great @pdiakumis⁠
  • VCF validation step removed. Feedback from users suggested that Ensembl's vcf-validator was often too stringent so its use has been deprecated. The --no_vcf_validate option remains for backwards compatibility.
  • New documentation site (https://sigven.github.io/pcgr⁠)
  • Data bundle updates (CIViC, ClinVar, Open Targets Platform, CancerMine, UniProt KB, Pfam)
  • CHANGELOG⁠

⁠Example reports

⁠Getting started

• Installation instructions⁠
• Run through an example⁠
• Learn more about
  • Details regarding PCGR input files⁠, and how they should be formatted
  • How to configure key settings⁠
  • The types and contents of PCGR output files⁠
  • The variant classifications⁠ implemented in PCGR
  • The list of gene and variant annotation resources⁠ used in PCGR annotation
• Frequenty asked questions (FAQ)⁠

⁠Citation

If you use PCGR, please cite the publication:

Sigve Nakken, Ghislain Fournous, Daniel Vodák, Lars Birger Aaasheim, Ola Myklebost, and Eivind Hovig. Personal Cancer Genome Reporter: variant interpretation report for precision oncology (2017). Bioinformatics. 34(10):1778--1780. doi:10.1093/bioinformatics/btx817⁠

⁠Contact

sigven AT ifi.uio.no