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Allele definition

411 bytes added, 11:15, 30 August 2018
How to obtain PGx allele definitions from literature
* [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.
* 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. The process of changing from GRCh37 to GRCh38 for the PharmGKB API seems to be only partially completed (at least . For instance, in the PharmGKB API JSON-LD data, the build is given as "hg38", but the actual coordinates are mostly GRCh37 (hg19). In the PharmGKB and CPIC Excel sheets, the move to GRCh38 is completed.===Chosing the correct variants to include in the PGx alleles===The allele definitions from the three sources PharmGKB and PharmVar are not always one-to-one, and some background knowledge about why this is, is required. Prefiltering of PharmGKB allele definitions were performed by the [[PGx in Estonia|PGx pipeline of the University of Tartu]] as shown in [https://www.biorxiv.org/content/early/2018/07/04/356204 ''Reisberg et al.''].
==How to define PGx alleles for next generation sequencing==