Allele definition

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. This means that

• Patients may have a large, ambiguous number of matching PGx alleles
• Patients may have additional variants that may modify the effect of a known PGx allele

The SNP array method

This definition requires matches only for variants explicitly included in PGx allele definitions. This means that

• Several PGx alleles may match to the patient
• But the presence of additional variants will have no effect on reported PGx alleles

The PharmCAT method

Require matches also for variants not explicitly included in PGx allele definitions