As PHASE was not able to distinguish the diplotypes *A1 *B1a vs *A3 *B2, we established a reliable PCR-based genotyping method. Forward GSTA1-F-1336BP 5′-TGGATCCCTCAGTTTTGTAAGG-3′ and reverse GSTA1-R-1336BP 5′-TAAACGCTGTCACCGTCC-3′ oligos were used to specifically amplify the promoter region of GSTA1 using Platinum SuperFi II PCR Master Mix (ThermoFisher, USA) and the following cycling conditions: initiation for 3 min at 95 °C followed by 38 cycles at 95 °C for 30 s, 64 °C for 30 s and 72 °C for 45 s. PCR products were genotyped using forward and reverse PCR primers and Sanger sequencing service (Fasteris, Switzerland). In the case of ambiguous diplotype, PCR products were TOPO TA cloned using linearized pMiniT 2.0 vector (E1202S, New England Biolabs, USA) according to manufacturer’s recommendations. Several colonies were picked for sequencing using standard SP6 and T7 oligo and E. coli NightSeq Sanger sequencing service (Microsynth, Switzerland). This method was validated on a patient showing ambiguous genotype from Ansari et al.27 (link) cohort (Table 2) and eight 1000 Genomes Project samples (Supplementary Fig. 2).
Free full text: Click here