CYP2D6 diplotypes with activity score `≥3.75` are not correctly annotated in CPIC JSON data resource

[kuanyili]

More specifically, diplotypes

• *1x≥3/*41x3
• *2x≥3/*41x3

currently have

• "generesult": "Indeterminate"
• "lookupkey": "n/a"
• "activityScore": "n/a"
• "phenotype": "Indeterminate"

in src/main/resources/org/pharmgkb/pharmcat/phenotype/cpic/CYP2D6.json.

But instead they shall have

• "generesult": "Ultrarapid Metabolizer"
• "lookupkey": "≥3.75"
• "activityScore": "≥3.75"
• "phenotype": "Ultrarapid Metabolizer"

according to

• CYP2D6 Phenotype Table
• CYP2D6 Diplotype-Phenotype Table
• CPIC API
  • curl --silent 'https://api.cpicpgx.org/v1/diplotype?genesymbol=eq.CYP2D6&diplotype=eq.*1x≥3/*41x3'
  • curl --silent 'https://api.cpicpgx.org/v1/diplotype?genesymbol=eq.CYP2D6&diplotype=eq.*2x≥3/*41x3'

Activity score ≥3.75 is also consequently missing in docs/Phenotypes-List.md.

Is the JSON data resource generated by a program so I should start from there to ensure future correctness? Or is the file maintained manually so I can just submit a PR by directly editing the file?

[whaleyr]

Thanks for letting us know. The data will be updated in the next release.

[markwoon]

What you get via the API is real time.

Whenever we release we update the data as well, so what you're seeing now is a snapshot of what was available at release.

[kuanyili]

What you get via the API is real time.

Whenever we release we update the data as well, so what you're seeing now is a snapshot of what was available at release.

This was also what I thought, but I checked cpic_db_dump-v1.35.0.sql.gz, which was released on Dec. 19, 2023. The ≥3.75 annotation was there, and the JSON stated that it uses CPIC version v1.35. Am I missing something?

[whaleyr]

@markwoon There was a mismatch between DB's that caused what's in the CPIC DB to not match what was pulled in DataManager. We can talk specifics later, but I will fix this immediate problem in the next release.

[whaleyr]

The fix has been pushed into development branch and will be in the next release.

[kuanyili]

Thank you for the support! 😄

[kuanyili]

@whaleyr @markwoon Hi! This issue kind of resurfaced since commit a57b955b3f42e0786154093a437e74393f89b4c0. Any idea?

[whaleyr]

Looking into it, thanks for pointing it out.

We changed how we handle diplotype data so must have re-introduced a bug.

[whaleyr]

Found the problem and pushed an updated phenotype file in cae0f8c6da998b0abc5ca2fc78aa7fa69767d600 that should address this issue.

[kuanyili]

Cool! Many thanks!