CFTR outside calls diplotype

[Bioinf-usr]

Hi,

What is the accepted genotype for CFTR while supplying from an outside calls file? I am trying with Reference/Reference but somehow pharmcat is unable to translate into the respective phenotype. I am using the latest version of pharmcat 2.8.3.

Whereas when I try to call the phenotype directly using pharmcat by providing the vcf, it is showing the same genotype Reference/Reference but now it is translated into the corresponding phenotype.

Please let me know if I'm missing something here?

[whaleyr]

Hi, thanks for bringing this up. Two things to know:

1) The list of valid allele and phenotype names for all genes can be found on the Phenotypes List page and there is a section for CFTR that lists ivacaftor non-responsive CFTR sequence as a valid allele. 2) You ran into a bug in the system which prevented ivacaftor non-responsive CFTR sequence from working properly in outside calls. The system was "helpfully" stripping gene symbols from allele names to help normalize them before attempting to match. However, in this case it caused a valid allele name to break and not match properly. I've removed the code to strip the gene symbol and now it will work properly.

CFTR is a bit of an odd duck due to CPIC not using an allele with the name Reference. We do reassign ivacaftor non-responsive CFTR sequence to Reference for the final report since we believe that's a more intuitive value to display for people reading it.

This fixed on the development branch and will be included in the next release of PharmCAT.

[Bioinf-usr]

Thanks for looking into it. Regarding point 1, I have also noticed it and tried changing the Reference to ivacaftor non-responsive CFTR sequence as described in the documentation. However, due to the bug mentioned in point 2, I still didn't manage to generate the correct phenotype.

Looking forward to the next release :)

[markwoon]

This should be fixed now.