Star alleles from PharmGKB

Dear Team,

I want to learn more details about the plan on Star alleles from PharmGKB

The Platform only showcases records of high confidence (1A, 1B, 2A and 2B in PharmGKB’s categorisation system). In future releases, we will focus on streamlining the integration of variants reported as star alleles, ensuring our pharmacogenetics data aligns with the common notation used by clinicians and researchers in the field.

I am wondering whether we can have a planning with more details so that we can fully understanding the future update for this direction.

Thanks.

Shicheng

Hi @Shicheng_Guo,

I’m happy to see you are enjoying our new release! If you’re interested in staying updated on our developments in this area, I recommend following this thread on our issue tracker:

We will be posting updates about our intentions and progress there.

Best regards,
Irene

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Hello Shicheng,

As Irene mentioned, we are working on the best way to represent the * allele annotations into the Platform and hope to provide these in the next release.

Just to expand a little bit on this…we represent variants in the Platform as rsIDs or using the mapping Chrom_position_ref_alt. As you mentioned, the * nomenclature is the way the Pharmacogenetics community represents these multi-variant alleles, however they pose a challenge for implementation using standard variant representation and mapping. This is why we started initially with all the Level 1/2 clinical annotations for variants with rsIDs.

Because of the complicated nature of many of these * alleles, our initial thought is to simply link to the allele page on PharmGKB, so that users are able to see all the relevant variant mappings and also the useful functional annotation information that has been curated. For example, in the Genotype ID column of the PGx data widget we would add CYP2D6*4.

It would be great to get your thoughts on this - and anyone else in the community following this thread! Thank you.

(We raised some of these challenges in the guidelines we published for how to help in the curation and incorporation of your PGx study into knowledgebases: Enabling the curation of your pharmacogenetic study - PMC).