Page 329 - Personalised medicine of fluoropyrimidines using DPYD pharmacogenetics Carin Lunenburg

genotyped with current genotyping techniques, and more expensive genotyping techniques need to be used, it is uncertain if DPYD genotyping remains cost-neutral. For example, at this moment sequencing the entire DPYD gene is too expensive to be used in a daily clinical care setting. Also, reimbursement for DPYD genotyping costs in the Netherlands is not (yet) covered by nationwide health care insurances. Therefore, hospitals in the Netherlands will cover costs in different ways, which leads to differences in health care between patients.
In chapter 9 we describe the dilemma of required confirmation practice as a quality control aspect of PGx testing.56 Implementation of DPYD genotyping will benefit from the inexpensiveness of current genotyping arrays. Yet, as PGx tests are usually only executed once in a lifetime, it is of utmost importance to have a correct genotyping result. When applying the most adequate, but comprehensive, confirmation method, i.e. executing a second, independent genotyping assay, erroneous results can be discovered. In this study we discovered that, even after extensive validation, erroneous results can still occur due to misclassification of a genotype, e.g. caused by allele dropout. Despite the increase in costs and labour, a confirmation method is useful for genetic tests with a high clinical impact, such as DPYD testing. We also showed substantial variability between laboratories in the use of a second, independent technique for PGx testing. As is the case for applying DPYD genotyping in the first place, clear guidelines are required to align confirmatory laboratory practices for PGx as well.
Currently, mostly assays testing single variants are used to genotype DPYD. In case of a compound heterozygous DPYD variant carrier, a patient who carries multiple different DPYD variants, the genotyping result cannot be translated into a dose recommendation when phasing information (the allelic location of variants) is missing. Compound heterozygous DPYD variant allele carriers are at increased risk of severe fluoropyrimidine-induced toxicity when dose reductions cannot be applied. In chapter 11, we describe seven cases and examine diagnostic and therapeutic strategies for fluoropyrimidine treatment of patients carrying multiple DPYD variants.57 The additional genotyping methods investigated in this study are still in early phases of development or currently too expensive to implement in clinical care, compared to a well-established DPD-phenotyping test. Therefore, we concluded to execute a phenotype test in these patients in order to determine a safe starting dose. When genotyping techniques which can determine the phasing of variants, such as long-read sequencing, will become less expensive in the future and are implemented in clinical care, phasing of variants of compound heterozygous DPYD variant allele carriers will be known directly and these patients can be treated according to dosing guidelines.
The probability of identifying a compound heterozygous DPYD variant carrier is low, yet while completing this chapter, five other patients were discovered in several genotyping facilities in the Netherlands, showing that this is a clinically relevant issue. Some of these patients were identified prospectively, after which the advice was given to determine the DPD enzyme activity. One patient was a carrier of three DPYD variants (DPYD*2A, c.2846A>T and c.1236G>A) and was treated safely with a 40% dose based on the results of an executed DPD enzyme activity measurement. The other patients were carriers of two DPYD variants in different combinations (DPYD*2A + c.2846A>T, c.2846A>T + c.1236G>A and DPYD*13 + c.2846A>T).
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