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update README/CHANGELOG
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sigven committed Oct 11, 2024
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2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -18,6 +18,8 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos

## News

- *October 2024*: **2.1.1 release**
- cosmetic fixes in HTML report
- *September 2024*: **2.1.0 release**
- data bundle upgrade
- re-calibration of classification tresholds
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2 changes: 2 additions & 0 deletions pkgdown/index.md
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Expand Up @@ -25,6 +25,8 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos

### News

* *October 2024*: **2.1.1 release**
- cosmetic fixes in HTML report

* *September 2024*: **2.1.0 release**
- data bundle upgrade
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12 changes: 9 additions & 3 deletions vignettes/CHANGELOG.Rmd
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output: rmarkdown::html_document
---

## v2.1.1

- Date: **2024-10-11**

- Cosmetic fixes in HTML report

## v2.1.0

- Date: **2024-09-29**
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* Classifications of genes as tumor suppressors/oncogenes are now based on a combination of CancerMine citation count and presence in Network of Cancer Genes

##### Added
* Missing ACMG criterion for classification of silent and intronic variants outside of splice regions (_ACMG_BP7_)
* Missing ACMG criterion for classification of variants in promoter and untranslated regions (_ACMG_BP3_)
* Missing ACMG/AMP criterion for classification of silent and intronic variants outside of splice regions (_ACMG_BP7_)
* Missing ACMG/AMP criterion for classification of variants in promoter and untranslated regions (_ACMG_BP3_)
* Possibility to create custom virtual panel - any combination of genes from panel 0 provided as a single-column text file with argument `--custom_list`
* Ensured that non-empty datatables pr. tier (__ClinVar__ and __Non-ClinVar__) are set as the active tab
* Improved documentation of variant classification in the __References__ section
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* Date: **2019-09-23**

##### Fixed
* Bug in implementation of ACMG criteria; genes without a known loss-of-function mechanism were handled inappropriately
* Bug in implementation of ACMG/AMP criteria; genes without a known loss-of-function mechanism were handled inappropriately
* Bug in assignment of heterozygous/homozygous states (input VCF)
* Bug in implementation of ACMG_PS1 - Same amino acid change as previously pathogenic variant
* Improved consequence prioritisation for variants with transcript consequences in multiple, distinct cancer predisposition genes
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