The Pharmacogenetics Resource for Enhanced Education and Monitoring of Pharmacological Therapy (PREEMPT) Project will provide easy access to evidence-based pharmacogenetic testing and education for clinicians and patients in Alberta. 

As a first step toward achieving this aim, we are conducting a pilot study to establish a pharmacogenetic testing pipeline that could be adopted by Alberta Precision Laboratories and be made available to all clinicians in Alberta. The focus of the pilot will be on thiopurine S-methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15) testing. This testing was selected because the clinical impact is high and guidelines for dosing of thiopurines (azathioprine, mercaptopurine, and thioguanine) have been established based on TPMT/NUDT15 genotype results. Once therapy is initiated, we plan to measure both parent drug and its metabolites by LC-MS/MS to assess the role of phenotype testing in pharmacogenetics. 

Rationale and Relevance for TPMT/NUDT15 testing:

TPMT is an enzyme that metabolizes thiopurines, immunosuppressive drugs prescribed in childhood leukemias, inflammatory bowel disease, dermatological conditions and in transplant recipients. TPMT deficiency significantly increase the risk for serious adverse reactions (i.e. myelosuppression, anemia, bleeding, leukopenia, infection or death) in individuals receiving thiopurines. NUDT15 is an enzyme that catalyzes the conversion of cytotoxic thioguanine triphosphate metabolites to the non-toxic thioguanine monophosphate. Thus, deficiency in NUDT15 can increase thioguanine triphosphate metabolites and result in severe myelosuppression. Importantly, risk alleles in TPMT are the primary genetic cause of thiopurine intolerance in Europeans and Africans, whereas risk alleles in NUDT15 explain the majority of thiopurine-related myelosuppression in Asians and are also common in Hispanics. Given Alberta is home to individuals from all of these ethnic backgrounds, TPMT and NUDT15 genetic testing is strongly advised prior to thiopurine use. We estimate 7%, 13%, and 16% of individuals with European, Asian, and African ancestry will carry an actionable TPMT or NUDT15 allele requiring thiopurine dose reductions. 

Outline of Methods:

We plan to test the feasibility of a TPMT/NUDT15 testing workflow in a stepwise fashion. 

1.     TPMT and NUDT15 genotyping assay development and validation: There are 33 known TPMT alleles but it has been shown that five alleles (*2, *3A, *3B, *3C, *4) account for >90% of TPMT deficiency, with excellent sensitivity (90%) and specificity (99%). Nine alleles in NUDT15 have been identified but only six alleles (*1 - *6) have actionable recommendations.  We will create a genotyping assay capable of detecting these TPMT and NUDT15 alleles and then validate the assay using reference samples from the Genetic Testing Reference Materials Coordination Program housed at the Coriell Institute for Medical Research. To further externally validate our assay all requests for TPMT genetic testing will also be sent out as per current protocol to the referral laboratory and concordance between our assay results and that of the referral laboratory will be calculated. 

2.     TPMT and NUDT15 phenotype assay development: A companion therapeutic drug monitoring assay via LC-MS/MS will also be developed to measure thiopurine and metabolites after patients start taking the medication. 

3.     Pilot of the TPMT and NUDT15 assay in the clinical setting: In collaboration with Clinical Pharmacology Consultation Service and clinicians who routinely prescribe thiopurines at Foothills Medical Centre, we will pilot our TPMT/NUDT15 testing service in 50 adult patients. The pilot will follow the current dosing algorithm published by the Clinical Pharmacogenetics Implementation Consortium (Figure). 

4.     Collect performance indicators: Performance indicators related to service process, service utilization and satisfaction will be collected throughout the duration of the project. Service process indicators will include: turnaround time monitoring for both genotype and phenotype results (from order to results). Service utilization indicators will include: consult volume (per month and by medical service) and number of TPMT genotype and phenotype tests ordered per number of patients on drug in participating medical services. Satisfaction indicators will include overall satisfaction of providers with the TPMT testing service by survey.

Figure. Clinical Pharmacogenetics Implementation Consortium (CPIC) Recommended Starting Doses of Thiopurines by TPMT and NUDT15 genotype-predicted phenotype. 

Research Team:

Dr. Chad Bousman PhD, Departments of Medical Genetics, Physiology and Pharmacology, and Psychiatry, University of Calgary, Calgary, Alberta

Dr Mark Yarema MD FRCPC, Poison and Drug Information Service, Alberta Health Services, Calgary, Alberta

Dr. Hossein Sadrzadeh PhD DABCC FACB, Department of Pathology and Laboratory Medicine, University of Calgary and Alberta Precision Laboratories, Calgary, Alberta

Dr. Jessica Boyd, PhD FCACB, Department of Pathology and Laboratory Medicine, University of Calgary and Alberta Precision Laboratories, Calgary, Alberta

Dr. Tim Pollak  MD PhD FRCPC, Departments of Medicine and Cardiac Sciences, University of Calgary and Calgary Laboratory Services, Calgary, Alberta

Dr. Dennis Orton PhD, Department of Pathology and Laboratory Medicine, University of Calgary and Alberta Precision Laboratories, Calgary, Alberta

Funding Partner: