From 0cb0d769419541be852ffcc9f15567db22d06c11 Mon Sep 17 00:00:00 2001 From: Sigve Nakken Date: Sun, 29 Sep 2024 18:25:41 +0200 Subject: [PATCH] update README and CHANGELOG --- README.md | 31 +++++++++---------- .../inst/templates/pcgr_quarto_report/msi.qmd | 2 +- pcgrr/pkgdown/index.md | 12 +++---- pcgrr/vignettes/CHANGELOG.Rmd | 2 +- 4 files changed, 22 insertions(+), 25 deletions(-) diff --git a/README.md b/README.md index 3db33068..7220e02a 100755 --- a/README.md +++ b/README.md @@ -24,24 +24,29 @@ Example screenshots from the [quarto](https://quarto.org)-based cancer genome re ![PCGR screenshot 2](pcgrr/pkgdown/assets/img/sc1.png) ![PCGR screenshot 3](pcgrr/pkgdown/assets/img/sc3.png) -PCGR originates from the [Norwegian Cancer Genomics Consortium (NCGC)](http://cancergenomics.no), at the [Institute for Cancer Research, Oslo University Hospital, Norway](http://radium.no). +PCGR originates from the [Norwegian Cancer Genomics Consortium (NCGC)](https://cancergenomics.no), at the [Institute for Cancer Research, Oslo University Hospital, Norway](https://radium.no). ### Top News +- *September 29th 2024*: **2.1.0 release** + - updated bundle, more oncogenic variants, CNA visualization, + improved RNA-seq support, bug fixes, and more + - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) + - *August 1st 2024*: **2.0.3 release** - patch to fix purity/ploidy propagation, MAF output for tumor-only runs, and other minor issues - - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *July 16th 2024*: **2.0.2 release** - patch to ensure correct reference to actionability guidelines - - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *July 7th 2024*: **2.0.1 release** - patch with bug fix for mitochondrial input variants ([pr245](https://github.com/sigven/pcgr/pull/245)) - - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *June 2024*: **2.0.0 release** - - Details in [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - Details in [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - Massive reference data bundle upgrade, new report layout, oncogenicity classification++ - Support for Singularity/Apptainer - Major data/software updates: @@ -52,19 +57,9 @@ PCGR originates from the [Norwegian Cancer Genomics Consortium (NCGC)](http://ca - CancerMine `v50` (2023-03) - UniProt KB `v2024_03` -- *February 2023*: **1.3.0 release** - - Details in [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) - - prioritize protein-coding BIOTYPE csq ([pr201](https://github.com/sigven/pcgr/pull/201)) - - 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 - ### Example reports -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12752833.svg)](https://doi.org/10.5281/zenodo.12752833) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13855988.svg)](https://doi.org/10.5281/zenodo.13855988) ### Why use PCGR? @@ -94,10 +89,12 @@ PCGR integrates a [comprehensive set of knowledge resources](https://sigven.gith ### Citation -If you use PCGR, please cite our publication: +If you use PCGR or CPSR, please cite our publications: 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.org/10.1093/bioinformatics/btx817](https://doi.org/10.1093/bioinformatics/btx817) +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](doi:%5B10.1002/ijc.33749)](https://doi.org/10.1002/ijc.33749) + ## Contact sigven AT ifi.uio.no diff --git a/pcgrr/inst/templates/pcgr_quarto_report/msi.qmd b/pcgrr/inst/templates/pcgr_quarto_report/msi.qmd index 62e8fa87..435f0bbe 100644 --- a/pcgrr/inst/templates/pcgr_quarto_report/msi.qmd +++ b/pcgrr/inst/templates/pcgr_quarto_report/msi.qmd @@ -2,7 +2,7 @@ Microsatellite instability (MSI) is the result of impaired DNA mismatch repair and constitutes a cellular phenotype of clinical significance in many cancer types, most prominently colorectal cancers, stomach cancers, endometrial cancers, and ovarian cancers ([Cortes-Ciriano et al., 2017](https://www.ncbi.nlm.nih.gov/pubmed/28585546)). We have built a statistical MSI classifier that only considers features of the somatic mutation profile (e.g. _fraction of indels_, _load of indels_, _mutations in MMR genes_ etc.) in order to separate _MSI.H_ (MSI-high) from _MSS_ (MS stable) tumors. -he MSI classifier was trained using __N = 1,065__ exome-sequenced TCGA tumor samples with known MSI status (i.e. assayed from mononucleotide markers), and obtained a [positive predictive value](https://en.wikipedia.org/wiki/Positive_and_negative_predictive_values#Positive_predictive_value) of 97.9% and a [negative predictive value](https://en.wikipedia.org/wiki/Positive_and_negative_predictive_values#Negative_predictive_value) of 99.4% on an independent test set of __N = 435 samples__. Details of the MSI classification approach can be found here. +The MSI classifier was trained using __N = 1,065__ exome-sequenced TCGA tumor samples with known MSI status (i.e. assayed from mononucleotide markers), and obtained a [positive predictive value](https://en.wikipedia.org/wiki/Positive_and_negative_predictive_values#Positive_predictive_value) of 97.9% and a [negative predictive value](https://en.wikipedia.org/wiki/Positive_and_negative_predictive_values#Negative_predictive_value) of 99.4% on an independent test set of __N = 435 samples__. Details of the MSI classification approach can be found here.
diff --git a/pcgrr/pkgdown/index.md b/pcgrr/pkgdown/index.md index 12ebb105..8b157f5b 100644 --- a/pcgrr/pkgdown/index.md +++ b/pcgrr/pkgdown/index.md @@ -25,29 +25,29 @@ Example screenshots from the [quarto](https://quarto.org)-based cancer genome re ![PCGR screenshot 2](img/sc1.png) ![PCGR screenshot 3](img/sc3.png) -PCGR originates from the [Norwegian Cancer Genomics Consortium (NCGC)](http://cancergenomics.no), at the [Institute for Cancer Research, Oslo University Hospital, Norway](http://radium.no). +PCGR originates from the [Norwegian Cancer Genomics Consortium (NCGC)](https://cancergenomics.no), at the [Institute for Cancer Research, Oslo University Hospital, Norway](https://radium.no). ### Top News - *September 29th 2024*: **2.1.0 release** - updated bundle, more oncogenic variants, CNA visualization, improved RNA-seq support, bug fixes, and more - - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *August 1st 2024*: **2.0.3 release** - patch to fix purity/ploidy propagation, MAF output for tumor-only runs, and other minor issues - - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *July 16th 2024*: **2.0.2 release** - patch to ensure correct reference to actionability guidelines - - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *July 7th 2024*: **2.0.1 release** - patch with bug fix for mitochondrial input variants ([pr245](https://github.com/sigven/pcgr/pull/245)) - - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *June 2024*: **2.0.0 release** - - Details in [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - Details in [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - Massive reference data bundle upgrade, new report layout, oncogenicity classification++ - Support for Singularity/Apptainer - Major data/software updates: diff --git a/pcgrr/vignettes/CHANGELOG.Rmd b/pcgrr/vignettes/CHANGELOG.Rmd index f4d71cee..6332f29c 100644 --- a/pcgrr/vignettes/CHANGELOG.Rmd +++ b/pcgrr/vignettes/CHANGELOG.Rmd @@ -63,7 +63,7 @@ excluded if setting `--exclude_nonexonic` is used) - Slight change to the default transcript consequence pick order in VEP based on observations of prioritized transcripts (*mane_select > mane_plus_clinical > canonical > biotype > ccds > rank > tsl > appris >length*) - Pulled in known oncogenic variants from ClinVar (assessed through ClinGen/CGC/VICC SOP, oncogenic/likely oncogenic) into the variant oncogenicity assessment algorithm - Added option `--no_html` to disable HTML report generation -- Added option `--input_germline` - re-offering the possibility to integrate CPSR-classified germline variants in the PCGR HTML report +- Added option `--input_cpsr` - re-offering the possibility to integrate CPSR-classified germline variants in the PCGR HTML report - Added `HGVSc_RefSeq` as output column in TSV/HTML - using MANE Select RefSeq transcript identifiers (works primarily for grch38) - Pulled in coding sequence start annotation for protein-coding transcripts from GENCODE, enabling a more useful annotation of promoter variants (e.g. TERT) - Created new column `ALTERATION` in variant tables of HTML report, a combination of `HGVSp`, `HGVSc` (if `HGVSp` not available)