Difference between revisions of "Allele definition"

m (The PharmCAT method)
(The SNP array method)
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==The SNP array method==
 
==The SNP array method==
This definition requires matches only for variants explicitly included in PGx allele definitions. This means that
+
This definition only requires matches for variants explicitly included in PGx allele definitions. This means that
 
*Several PGx alleles may match to the patient
 
*Several PGx alleles may match to the patient
 
*But the presence of additional variants will have no effect on reported PGx alleles
 
*But the presence of additional variants will have no effect on reported PGx alleles

Revision as of 14:05, 12 July 2018

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 only requires matches 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

This definition require matches also for variants not explicitly included in PGx allele definitions. This means that

  • Several PGx alleles may not be simultaneously reported for the same patient
  • But whenever we have additional variants, no PGx alleles will be reported