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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.
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
We illustrate some of the problems that we encountered when trying to match patient haplotypes to the PGx allele definitions, by an imagined four loci PGx gene
The SNP array method
This definition only requires matches for variants explicitly included in PGx allele definitions.
This means that
- Several PGx alleles may match the patient
- But the presence of additional variants will have no effect on reported PGx alleles
The PharmCAT method
This definition requires matches also for variants not explicitly included in PGx allele definitions.
This means that
- Only one PGx allele can exist simultaneously for the same patient
- But whenever we have additional variants, no PGx alleles will be reported
Which definition should we stick to?
| Method | Advantages | Disadvantages |
|---|---|---|
| SNP array method | Compatible with previous SNP array methods. Assigns PGx alleles to the maximum number of patients | Multiple PGx alleles are possible |
| PharmCAT method | One PGx allele per patient | Less compatible with previous SNP array methods. Many patients are not assigned to a known PGx allele |