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NCATS-Tangerine / cq-notebooks

Notebooks for answering competency questions
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QB1.7 variant compensatory changes notebook status #23 #38

Open stuppie opened 7 years ago

stuppie commented 7 years ago

Notebook Folder Link:

https://github.com/NCATS-Tangerine/cq-notebooks/tree/master/Orange_QB1_Benchmark_CQs/QB1.7_compensatory_mutations

Implementors:

(* = notebook lead)

Status:

Primary Knowledge Sources Used:

APIs Used:

Notes: See Readme

mbrush commented 7 years ago

Quick note here - the original CQ asked "What compensatory mutations in FA core genes confer resistance to chemotherapeutic drugs (e.g. cisplatin)?" Maureen has clarified that 'compensatory mutation' means some second mutation in a gene that make a cancer previously susceptible to drug x become resistant. This 'compensatory' mutation can be in the same gene as the original causal mutation, or another gene. Such compensatory mutations are of interest because what is gained back by the compensatory mutation can tell us about mechanism of drug action and/or disease parthenogenesis.

There are no data sources that curate/provide such data - so the notebook here does the next best thing which is to answer the simpler question "What mutations in FA core genes confer resistance of some cancer to some treatment?".

stuppie commented 6 years ago

@mbrush That is correct

Also, I just added a second notebook that explores this same question using PharmGKB and Clinvar. The end result is that there is one such variant curated by PharmGKB (https://www.pharmgkb.org/rsid/rs1799801) and none found in clinvar (unless I made some mistakes in analyzing this...)