An Inexpensive and Quick Method for Genotyping of HLA Variants Included in the Spanish Pharmacogenomic Portfolio of National Health System

The possibility of using the same genotyping technology (TaqMan) for all the genetic tests included in the new Spanish pharmacogenomics portfolio should enable the application of a multigenotyping platform to obtain a whole pharmacogenomics profile. However, HLA-typing is usually performed with other technologies and needs to be adapted to TaqMan assays. Our aim was to establish a set of TaqMan assays for correct typing of HLA-A*31:01, HLA-B*15:02, HLA-B*57:01, and HLA-B*58:01. Therefore, we searched for and selected SNVs described in different populations as surrogate markers for these HLA alleles, designed TaqMan assays, and tested in a set of samples with known HLA-A and HLA-B. HLA-A*31:01 was correctly typed with a combination of rs1061235 and rs17179220 (PPV 100%, 95% CI 84.6-100-%; NPV 100%, 95% CI 96.5-100.0%), HLA-B*15:02 with rs10484555 (PPV 100%, 95% CI 69.2-100.0%; NPV 100%, 95% CI 96.8-100.0%) and rs144012689 (PPV 100%, 95% CI 69.2-100.0%; NPV 100%, 95% CI 96.8-100.0%), and HLA-B*57:01 with rs2395029 (PPV 99.5%, 95% CI 72.9-99.3%; NPV 99.5%, 95% CI 98.3-100.0%). HLA-B*58:01 was typed using two allele-specific TaqMan probes mixed with a ß-Globin reference and treated as a genotyping assay (PPV 100.0%, 95% CI 81.5-100.0%; NPV 100%, 95% CI 96.8-100.0%). In conclusion, we demonstrated a clinically useful way to type HLA-A and HLA-B alleles included in the Spanish pharmacogenomics portfolio using TaqMan assays.