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==How to define PGx alleles==
PGx alleles are defined as collections of one or more SNPs, INDELs or structural variants. When a patient is sequenced by next generation sequencing (NGS) we may typically observe more variants than those which are included in any individual PGx allele definitions.
[[File:Variant tree outline.png|miniaturethumb|The 16 possible haplotypes for a four loci, decomposed variant calling]]
This means that
*Patients may have a large, ambiguous number of matching PGx alleles
==The SNP array method==
[[File:Variant tree allele snp definition.png|miniaturethumb|PGx alleles defined as collections of variants, with no requirement on loci that are not part of the definition, will assign the same PGx allele to several different haplotypes]]
This definition only requires matches for variants explicitly included in PGx allele definitions.
==The PharmCAT method==
This definition requires matches also for variants not explicitly included in PGx allele definitions.
[[File:Variant tree allele pharmcat definition.png|miniaturethumb|PGx alleles defined as complete haplotypes classifies the patient uniquely]]
This means that
*Only one PGx allele can exist simultaneously for the same patient