update news, changelog, Zenodo link

sigven · sigven · commit 7e8dcea949d1 · 2025-09-17T08:32:44.000+02:00
diff --git a/README.md b/README.md
@@ -18,7 +18,12 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
 
 ## News
 
-*  *September 8th 2024*: **2.2.4 release**
+*  *September 17th 2025*: **2.2.5 release**
+    -  patch - safeguard against missing data in gnomAD non-cancer variant data
+       using global gnomAD MAF's as fallback
+    -  [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
+
+*  *September 8th 2025*: **2.2.4 release**
     -  patch to avoid duplicate matching of PVS1 criteria
 
 *  *March 23rd 2025*: **2.2.1 release**
@@ -51,7 +56,7 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
 
 ## Example report
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15050542.svg)](https://doi.org/10.5281/zenodo.15050542)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17117326.svg)](https://doi.org/10.5281/zenodo.17117326)
 
 
 ## Getting started
diff --git a/pkgdown/index.md b/pkgdown/index.md
@@ -25,7 +25,10 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
 
 ### News
 
-*  *September 8th 2024*: **2.2.4 release**
+*  *September 17th 2025*: **2.2.5 release**
+    -  patch - safeguard against missing data in gnomAD non-cancer variant data
+
+*  *September 8th 2025*: **2.2.4 release**
     -  patch to avoid duplicate matching of PVS1 criteria
 
 *  *March 23rd 2025*: **2.2.1 release**
@@ -59,7 +62,7 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
 
 ### Example report
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15050542.svg)](https://doi.org/10.5281/zenodo.15050542)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17117326.svg)](https://doi.org/10.5281/zenodo.17117326)
 
 ### Getting started
 
diff --git a/vignettes/CHANGELOG.Rmd b/vignettes/CHANGELOG.Rmd
@@ -3,9 +3,20 @@ title: "Changelog"
 output: rmarkdown::html_document
 ---
 
+## v2.2.5
+
+- Date: **2025-09-17**
+- Patch to safeguard missing gnomAD frequencies in the non-cancer subset, 
+  using the general/global gnomAD frequencies as a fallback - improved
+  assignment of ACMG criteria BA1/BS1/PM2
+  - Supplement gnomAD exome AFs with genome-based AF's when running in VEP, 
+    i.e. adding the `--af_gnomadg` by default
+  - Added interactive filtering for global gnomAD frequencies in HTML datatables
+  - Added `gnomADg_AF` (global gnomAD MAF) column in TSV output files
+
 ## v2.2.4
 
-- Date: **2025-09-28**
+- Date: **2025-09-08**
 - Patch to avoid duplicate matches of PVS1 criteria
 
 ## v2.2.1
diff --git a/vignettes/output.Rmd b/vignettes/output.Rmd
@@ -223,15 +223,25 @@ MES|<SCORE_DIFF>|SCORE_REF>|<SCORE_ALT>|EFFECT (MaxEntScan). |
 
 | Tag | Description |
 |-----|-------------|
-| `gnomADe_AFR_AF` | African/American germline allele frequency ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
-| `gnomADe_AMR_AF` | American germline allele frequency ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
-| `gnomADe_AF` | Adjusted global germline allele frequency ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
-| `gnomADe_SAS_AF` | South Asian germline allele frequency ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
-| `gnomADe_EAS_AF` | East Asian germline allele frequency ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
-| `gnomADe_FIN_AF` | Finnish germline allele frequency ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
-| `gnomADe_NFE_AF` | Non-Finnish European germline allele frequency ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
-| `gnomADe_OTH_AF` | Other germline allele frequency ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
-| `gnomADe_ASJ_AF` | Ashkenazi Jewish allele frequency ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADe_AFR_AF` | African/American germline allele frequency - exome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADe_AMR_AF` | Latino/Admixed American germline allele frequency - exome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADe_AF` | Adjusted global germline allele frequency - exome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADe_SAS_AF` | South Asian germline allele frequency - exome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADe_EAS_AF` | East Asian germline allele frequency - exome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADe_FIN_AF` | Finnish germline allele frequency - exome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADe_NFE_AF` | Non-Finnish European germline allele frequency - exome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADe_OTH_AF` | Other germline allele frequency - exome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADe_ASJ_AF` | Ashkenazi Jewish allele frequency - exome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADg_AFR_AF` | African/American germline allele frequency - genome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADg_AMR_AF` | Latino/Admixed American germline allele frequency - genome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADg_AF` | Adjusted global germline allele frequency - genome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADg_SAS_AF` | South Asian germline allele frequency - genome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADg_EAS_AF` | East Asian germline allele frequency - genome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADg_FIN_AF` | Finnish germline allele frequency - genome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADg_NFE_AF` | Non-Finnish European germline allele frequency - genome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADg_MID_AF` | Middle Eastern germline allele frequency - genome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADg_OTH_AF` | Other germline allele frequency - genome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
+| `gnomADg_ASJ_AF` | Ashkenazi Jewish allele frequency - genome set ([gnomAD release 4.1](http://gnomad.broadinstitute.org/)) |
 | `gnomADe_non_cancer_ASJ_AF` | Alternate allele frequency for samples of Ashkenazi Jewish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
 | `gnomADe_non_cancer_EAS_AF` | Alternate allele frequency for samples of East Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
 | `gnomADe_non_cancer_AFR_AF` | Alternate allele frequency for samples of African-American/African ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
@@ -398,12 +408,13 @@ The following variables are included in the tiered TSV file (VCF tags in the que
 | 61. `N_INSILICO_SPLICING_NEUTRAL` | Number of algorithms with splicing neutral prediction from dbscSNV |
 | 62. `N_INSILICO_SPLICING_AFFECTED` | Number of algorithms with splicing affected prediction from dbscSNV |
 | 63. `gnomADe_AF` | Global MAF in gnomAD (exome samples) |
-| 64. `FINAL_CLASSIFICATION` | Final variant classification, using either `CLINVAR_CLASSIFICATION` if variant is ClinVar-classified, or `CPSR_CLASSIFICATION` for novel variants. _Note_: ClinVar-classified
+| 64. `gnomADg_AF` | Global MAF in gnomAD (genome samples) |
+| 65. `FINAL_CLASSIFICATION` | Final variant classification, using either `CLINVAR_CLASSIFICATION` if variant is ClinVar-classified, or `CPSR_CLASSIFICATION` for novel variants. _Note_: ClinVar-classified
 variants annotated with _Drug Response_ or _Risk Factor_ clinical significance are provided a `VUS` final classification |
-| 65. `CPSR_CLASSIFICATION` | Variant clinical significance by CPSR's classification algorithm (P/LP/VUS/LB/B) |
-| 66. `CPSR_PATHOGENICITY_SCORE` | Aggregated pathogenicity score by CPSR's algorithm |
-| 67. `CPSR_CLASSIFICATION_CODE` | Combination of CPSR classification codes assigned to the variant (ACMG) |
-| 68. `<CUSTOM_POPULATION_GNOMAD`> | Population specific MAF in gnomAD control (non-cancer, population configured by user) |
+| 66. `CPSR_CLASSIFICATION` | Variant clinical significance by CPSR's classification algorithm (P/LP/VUS/LB/B) |
+| 67. `CPSR_PATHOGENICITY_SCORE` | Aggregated pathogenicity score by CPSR's algorithm |
+| 68. `CPSR_CLASSIFICATION_CODE` | Combination of CPSR classification codes assigned to the variant (ACMG) |
+| 69. `<CUSTOM_POPULATION_GNOMAD`> | Population specific MAF in gnomAD control (non-cancer, population configured by user) |
 
 **NOTE**: The user has the possibility to append the TSV file with data from other INFO tags in the input VCF (i.e. using the *--retained_info_tags* option)
 
diff --git a/vignettes/variant_classification.Rmd b/vignettes/variant_classification.Rmd
@@ -37,7 +37,7 @@ while(i <= NROW(cpsr::acmg$evidence_codes)){
 ```
 
 <br>
-Currently (as of March 2025), based on a calibration against ClinVar-classified variants (minimum two review status stars) in n = 105 core cancer predisposition genes, the clinical significance (**CPSR_CLASSIFICATION**) is determined based on the following ranges of pathogenicity scores:
+As of September 2025, based on a calibration against ClinVar-classified variants (minimum two review status stars) in n = 105 core cancer predisposition genes, the clinical significance (**CPSR_CLASSIFICATION**) is determined based on the following ranges of pathogenicity scores:
 
 <br>
 
