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→Chosing the correct variants to include in the PGx alleles
The allele definitions from PharmGKB and PharmVar are not always one-to-one, and some background knowledge about why this is, is required.
Additional prefiltering of PharmGKB or PharmVar allele definitions by domain experts may be needed. * Prefiltering was performed by the [[PGx in Estonia|PGx pipeline of the University of Tartu]], and a list of the resulting variants were published in the supplementary material to [https://www.biorxiv.org/content/early/2018/07/04/356204 ''Reisberg et al.'']. The variants per star allele are, however, not written out explicitly.* Prefiltering was performed on allele definitions in Aldy and the [https://github.com/inumanag/aldy/tree/master/aldy/resources/genes result published in their code].
An example that illustrates many definition problems is CYP2C19*19:
The main problem with the changes in definitions is that the same patient may be given different PGx-advice depending on the build version of the pipeline (unless of course that the haplotype is always conserved)
Comparisons between PGx genotyping tools can give some insight into the accuracy of allele definitions. In Aldy they have [https://github.com/inumanag/aldy-paper-resources compared their method to targeted sequencing] with good results.
==How to define PGx alleles for next generation sequencing==
