Genotyping of eight thiopurine methyltransferase mutations: Three-color multiplexing, "two-color/shared" anchor, and fluorescence-quenching hybridization probe assays based on thermodynamic nearest-neighbor probe design

Background: The inherited deficiency of thiopurine methyltransferase (TPMT) leads to severe myelosuppression in homozygous patients treated with thiop urine derivatives. One in 300 Caucasians has a homozygous TPMT deficiency w ith no measurable enzyme activity. To date, eight single-point mutations ha ve been characterized; one group (TPMT*3) accounts for 75% of these. Methods: We used four LightCycler(TM) capillaries to investigate all eight mutations. The three mutations on exon 10 were detected in one capillary wi th a single "shared" anchor labeled 5' with Cy5.5 and 3' with fluorescein. A wild-type-compatible 3'-fluorescein-labeled probe 5' adjacent to the anch or covered the TPMT*7 mutation, and a 5'-LC-RED640-labeled probe 3' adjacen t to the anchor covered the TPMT*3C mutation. For TPMT*4, the forward ampli fication primer was internally labeled with a fluorescence quencher [6-carb oxytetramethylrhodamine (TAMRA), and a 3'-fluorescein-labeled antisense wil d-type-compatible probe was placed at the mutation. For TPMT*2 and TPMT*3D, Located on exon 5, a shared anchor approach was chosen. TPMT*3B and TPMT*6 were detected in multiplex technique and TPMT*5 in conventional manner. An chors and probes were designed using a thermodynamic nearest-neighbor model . Results: All mutations were detected using four capillaries with one amplif ication protocol in 40 min. The concentrations of the shared anchors had to be decreased to reduce their intrinsic fluorescence resonance energy trans fer signals. The quenching approach using TAMRA produced a very reproducibl e upside-down-shaped melting curve in channel 1 of the LightCycler. Deviati ons from wild type were easily detected because the smallest melting point shift for any possible mutation under the core of the probes was 1.5 degree sC. Conclusions: This total TPMT genotyping approach shows that it is possible to use double site-labeled anchor oligonucleotides, that channel 1 of the L ightCycler can be used as detection channel for mutations using a quenching design, and that the designed probes enable detection of wild types with 1 00% likelihood. (C) 2000 American Association for Clinical Chemistry.