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→Which definition should we stick to?
* PGx alleles on Excel-style formats, also accessible through the PharmGKB API (seems to be hidden from the Swagger documentation, but direct links when searching for haplotype definitions at the pharmgkb.org website)
* [https://github.com/PharmGKB/PharmCAT/tree/master/src/main/resources/org/pharmgkb/pharmcat/definition/alleles PGx alleles for use in PharmCAT] are included in their source code. It is reasonable to suspect that these files are parsed from the Excel files.
* [https://github.com/inumanag/aldy/tree/master/aldy/resources/genes PGx alles for use in Aldy] are included in their source code. Due to the lack of GRCh37 variant definitions for CYP2D6, Aldy has likely lifted over GRCh38 variants to GRCh37. The Aldy developers have also added new star alleles with (non functional) variants that are often observed together with the main star allele.
* PGx alleles as VCF files from [https://www.pharmvar.org PharmVar]
==How to chose the correct PGx allele definitions==
===Chosing an appropriate genomic reference build===
PGx allele definitions are given in either GRCh37 or GRCh38 reference coordinates. * PharmCAT, CPIC and PharmGKB as a rule use build GRCh38. * Aldy uses GRCh37. * The process of changing from PharmGKB API as a rule is using GRCh37 to GRCh38 alleles, but not for the PharmGKB API seems to be only partially completedall variants. For instance, in the PharmGKB API JSON-LD dataMoreover, the build is given as "hg38", but even when the actual coordinates are mostly GRCh37 (hg19). In the PharmGKB and CPIC Excel sheets, however, the move to GRCh38 is completed. As is evident from liftOver, hg19 is not equal to GRCHh37, nor hg38 to GRCHh38. Are we sure that there are no errors here?This could also be a source of error.
===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==
*But whenever we have additional variants, no PGx alleles will be reported
(Note that in practice PharmCAT lets the user decide which allele definitions to use in their [https://github.com/PharmGKB/PharmCAT/wiki/NamedAlleleMatcher-101 NamedAlleleMatcher])
===The Aldy method===
The Aldy method is similar to the PharmCAT method, but with some important notes
- The method takes into account the copy number of each variant
- The method introduces additional PGx variants in order to avoid no-calls. The additional variants have been interpreted and curated by the Aldy team.
- The method uses BAM-files instad of VCF files.
===Which definition should we stick to?===
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| PharmCAT method || One PGx allele per patient || Less compatible with previous SNP array methods. Some patients are no longer assigned to a known PGx allele
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| Aldy method || One PGx allele per patient, detection of new variants || [https://github.com/inumanag/aldy-paper-resources Test data sets for Aldy] shows that the method performs well, also with respect to targeted methods
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