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SBIMB / StellarPGx

Calling star alleles in highly polymorphic pharmacogenes (e.g. CYP450 genes) by leveraging genome graph-based variant detection.
MIT License
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Genotype explanation #19

Closed krukanna closed 2 years ago

krukanna commented 2 years ago

Hi, what does it mean if the program output looks like this:

CYP2D6 Star Allele Calling with StellarPGx Initially computed CN = 17 Sample core variants: 42126611C>G1/1;42127941G>A0/1;42128945C>T0/1;42130692G>A0/1;42130761C>T0/1 Candidate alleles: ['35.v1_4.v2'] Result: 35/4x16 Activity score: 1.0 Metaboliser status: Intermediate metaboliser (IM)

The main problem is with copy numbers in genotype. I use StellarPGx on WES, but expanded to relevant pharmacogenomic regions. Can I do something to change that copy number computation? Or my data cannot be used to solve CYP2D6 genotype?

Thanks in advance

twesigomwedavid commented 2 years ago

@krukanna,

Thanks. At present, we strongly advise against using StellarPGx for WES data as we haven't configured the parameters to handle data other than high coverage whole-genome sequence data.

David

krukanna commented 2 years ago

Thanks, Do you have any plans to develop the tool? And could you correct me, if I undestand it wrong: that genotype say we got *4 on one chromosome, but multiplied 16 times?

twesigomwedavid commented 2 years ago

@krukanna,

Yes, we have plans to add support for WES but likely for next year.

Regarding the diplotype interpretation: Yes, 4x16 would mean having 16 copies of 4 on one chromosome. But as I mentioned earlier, this would be inaccurate for your WES data as the parameters set in StellarPGx currently are for high-coverage WGS. WES data presents different problems especially regarding CNV analysis.

krukanna commented 2 years ago

ok, thank you! now I'm waiting for the release :)