I'm a newbie in the field of pharmacogenetics and I'm a bit confused by CYP genes star alleles.
Most of the star alleles are defined by official nomenclature (https://www.pharmvar.org) as haplotypes based on a combination of SNPs. For example CYP2D6*10 is defined as a combiantion of 3 SNPs (100C>T, 1662G>C, 4181G>C).
However I've noticed that most available pharmacogenetic testing kits only use one SNP to define the *10 allele (rs1065852 100C>T). The same apply for several other star alleles. Since we are interesting in developing our own genotyping solution, I'm wondering how to define the list of SNPs for our star alleles of interest.
Do I have to test all the SNPs for a given star haplotype or there is a reference to define a single SNPs that identify each star allele?
Moreover, how can a genotyping kit possibly test for the full haplotypes anyway?
Hi Edoardo. I'm also a newbie in this field. However, I think that you can choose the SNPs according their frequencies, the effect in the gene and/or their relevance. For example, the SNP most studied for the CYP2D6*10, as you noticed, is the rs1065852 C100T, which is associated with reduced metabolism of various CYP2D6 substrates. Another possibility would be, investigate all the SNPs of the CYP2D*10 and then, create haplotypes derived from these SNPs after linkage disequilibrium analysis.