v2.3.3

Changes

🐛 Bug Fixes

• Fix TERT Promoter issue @zhx828 (#94)

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• v2.3.2...v2.3.3

v2.3.2

Changes

🐛 Bug Fixes

• Do not duplicate counting for the same mutation under ACTIONABLE_MUTATIONS column @zhx828 (#92)

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• v2.3.1...v2.3.2

v2.3.1

Changes

👷‍♀️ Testing, Configuration & Deployment

• Separate dependencies for python 2.7 and 3 & Add test for 2.7 and windows/macos @zhx828 (#91)

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• v2.3.0...v2.3.1

v2.3.0

Changes

🧬 Features

• Use POST methods for annotation to improve the performance @zhx828 @darasanchez (#87)

🐛 Bug Fixes

• Remove the default tumor type & Standardize the oncokb column names @zhx828 (#88)

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• v2.2.2...v2.3.0

v2.2.2

Changes

🐛 Bug Fixes

• Avoid author name SyntaxError @zhx828 (#90)
• Fix overflow bug on Win OS @Leowisd (#84)

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• v2.2.1...v2.2.2

v2.2.1

🧬 Features

• Add examples for atypical alterations @zhx828 (#64)
• Support 3 Letter Code on HGVSP Column @darasanchez (#65)

🧰 Maintenance

• Add Action to run all tests @zhx828 (#66)

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• v2.2.0...v2.2.1

v2.2.0

Changes

🧬 Features

• Give option to annotate Gain/Loss CNA events @zhx828 (#58)
• Include Gene in OncoKB and Variant in OncoKB columns @zhx828 (#53)
• Do not make API calls for genes are note curated in OncoKB @zhx828 (#55)
• Allow user uploads SV name format REGEX @zhx828 (#54)

🐛 Bug Fixes

• Give option to not upper case column name when reading file header @zhx828 (#56)
• Shorten the example MAF to include essential columns only @zhx828 (#45)

🧰 Maintenance

• Bump requests from 2.11.1 to 2.20.0 @dependabot (#40)

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• v2.1.1...v2.2.0

Turn off unnecessary log from the libraries

Merge pull request #44 from victoria34/turn-off

Turn off requests additional log mesaages

Make oncokb-annotator compatible with Python3

v2.1.0

Merge pull request #41 from victoria34/compatible-python3

Support V2 Levels of Evidence

Introducing Simplified OncoKB Levels of Evidence:

• New Level 2, defined as “Standard care biomarker recommended by the NCCN or other expert panels predictive of response to an FDA-approved drug in this indication” (formerly Level 2A).
• Unified Level 3B, defined as “Standard care or investigational biomarker predictive of response to an FDA-approved or investigational drug in another indication” (combination of previous Levels 2B and 3B).

We have implemented these changes for 2 reasons:

• To be consistent with the Joint Consensus Recommendation by AMP, ASCO and CAP and the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT)
• To reflect the clinical data that demonstrates patients with investigational predictive biomarkers for a specific tumor type based on compelling clinical evidence (currently Level 3A) are more likely to experience clinical benefit compared to patients with predictive biomarkers that are considered standard care in a different tumor type (previously Level 2B, now combined into Level 3B).

If you want to annotate your files with previous Levels of Evidence, please git checkout v1.