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PreMedKB / PAnno

PAnno is a Pharmacogenomics Annotation tool for clinical genomic testing.
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Great tool - Few questions #1

Open Pharmacogenetecist opened 2 years ago

Pharmacogenetecist commented 2 years ago

Hi I was wondering if you could provide some documentation/link to which shown which genes are being interrogated?

In the report generated - My suggestion would be to remove the below and only show it when an IM/PM or related alleles are found. The below could be quite confusing and could make a clinician think that "action" or "dose adjustment" is required.

"mercaptopurine Related Gene: NUDT15 Detected Alleles: *1

DPWG: Select an alternative drug or reduce the initial dose of mercaptopurine for patients that are NUDT15 poor metabolizers and reduce initial dose for patients that are NUDT15 intermediate metabolizers. CPIC: Consider an alternate agent or extreme dose reduction of mercaptopurine for patients who are TPMT or NUDT15 poor metabolizers. Start at 30-80% of target dose for patients who are TPMT or NUDT15 intermediate metabolizers. Related Gene: TPMT Detected Alleles: *1

CPIC: Consider an alternate agent or extreme dose reduction of mercaptopurine for patients who are TPMT or NUDT15 poor metabolizers. Start at 30-80% of target dose for patients who are TPMT or NUDT15 intermediate metabolizers. DPWG: Select an alternative drug or reduce the initial dose of mercaptopurine for patients that are TPMT poor metabolizers and reduce initial dose for patients that are TPMT intermediate metabolizers. RNPGx: The French National Network of Pharmacogenetics (Réseau national de pharmacogénétique (RNPGx)) recommends testing for TPMT."

Also, both hyperlinks appear to lead to dead links: (The VCF files are available at https://github.com/PreMedKB/PAnno-analysis/tree/main/vcf. The PAnno reports are available at https://github.com/PreMedKB/PAnno-analysis/tree/main/report.)

Using the GIAB VCF, I am getting incorrect outputs for multiple genes.

Thank you, Simran.

sigven commented 2 years ago

Following up on the comments by @Pharmacogenetecist: I would really like to see the dead hyperlinks (i.e. https://github.com/PreMedKB/PAnno-analysis/tree/main/vcf and https://github.com/PreMedKB/PAnno-analysis/tree/main/report) working again.

kind regards, Sigve