Difference between revisions of "Allele definition"
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==The PharmCAT method== | ==The PharmCAT method== | ||
This definition require matches also for variants not explicitly included in PGx allele definitions. | This definition require matches also for variants not explicitly included in PGx allele definitions. | ||
| − | [[Fil:Variant tree allele pharmcat definition.png|miniatyr]] | + | [[Fil:Variant tree allele pharmcat definition.png|miniatyr|PGx alleles defined as complete haplotypes classifies the patient uniquely]] |
This means that | This means that | ||
*Several PGx alleles may not be simultaneously reported for the same patient | *Several PGx alleles may not be simultaneously reported for the same patient | ||
*But whenever we have additional variants, no PGx alleles will be reported | *But whenever we have additional variants, no PGx alleles will be reported | ||
Revision as of 14:45, 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. miniatyr|All possible haplotypes for a four loci, decomposed varinant calling 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 can illustrate all the possible PGx allele definitions for a four loci PGx haplotype as
The SNP array method
This definition only requires matches for variants explicitly included in PGx allele definitions. miniatyr|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 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. miniatyr|PGx alleles defined as complete haplotypes classifies the patient uniquely 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
