Pharmacogenetics refers to the influence of DNA variants on drug response, the knowledge of which can facilitate selection of the optimal drug, dose, and treatment duration and avert adverse drug reactions [1
]. Several demonstrations have been given on the differences in response to drugs between children and adults [2
]. These include differences in drug metabolism and gene expression, the latter being a highly dynamic process functioning from the neonatal period over childhood into adult life. Though the number of studies specifically devoted to the pediatric population is still limited compared to adults, an increasing number of genes are being identified in which variants have an influence on pharmacological treatment of childhood diseases [3
]. The identification of variants in novel genes as well as the validation of their functional effects will further increase our ability to predict drug treatment response in children; at the same time, the clinical implementation of this knowledge will demand an efficient diagnostic approach to first identify a pharmacogenomic profile in an individual patient in a short period of time, next to evidence-based clinical guidelines to facilitate decision making based on the genotype [4
The current golden standard for detecting pathogenic variants—single nucleotide variations or small indels—is Sanger sequencing [5
]. Developed in the late 70s by Frederick Sanger, an English biochemist, the technique has currently been optimized to evaluate variations in PCR-amplified DNA fragments with high sensitivity and specificity. The major disadvantages of Sanger sequencing—particularly in a domain such as pharmacogenetics where for a specific drug variants in multiple genes can be, either independent of or in interaction with each other, involved—are that each novel genetic test needs optimization and turn-around times for each gene analysis can be relatively long, certainly if therapeutic decisions would be based on these results. Together with the sometimes ambiguous evidence for the effect of certain variants and the lack of robust validation and clinical guidelines, this technical hurdle has been one of the reasons that genotyping to inform clinical decisions regarding pharmacological treatment is not widely practiced to date.
The introduction of next generation sequencing (NGS) brought about a technological revolution among genetic screening tools, as it now becomes possible to screen the whole exome—the coding regions of our DNA—and even the complete genome in a single experiment [7
]. The increase of technological capacities and decrease of costs involved in such analysis have resulted in successful implementation of exome sequencing as a research tool, particularly to identify novel genes for rare disorders [10
]. Causal genes for, for example, the Freeman-Sheldon (OMIM no. 193700) or the Kabuki syndrome (OMIM no. 147920) were identified by combining whole exome sequencing data from different patients with a typical phenotype of these conditions [12
]. They demonstrate that it is possible to capture exomic variation and identify pathogenic variants using bioinformatic tools. Since then, several other examples have been reported.
Because of this success, these screening techniques are slowly starting to make their way as a diagnostic tool. Certainly for complex diseases for which several genes have been identified—the sequence analysis of which is laborious, time consuming, and expensive—the idea of sequencing all 23.000 genes in the exome in a single reaction is an alluring alternative. Similarly, in a field such as pharmacogenetics, with different variants in different genes influencing the final drug response in an individual patient, such parallel sequencing techniques can provide the promptness which would be required in a clinical setting. This shift to the more extensive screening assays has induced an evolution from pharmacogenetics to pharmacogenomics [3
]. Besides the excitement surrounding these technical innovations, it has become clear that NGS applications also present several challenges. These include not only the quantity of data which is generated, its analysis, and interpretation but also ethical and legal aspects. In the pediatric population, the latter have very particular properties as a consequence of the incapacity of the child to give informed consent himself and of the predictive character of the interpreted sequence data which may go beyond the initial clinical question.
In this paper, we will consider the characteristics of NGS, the different means by which NGS technology can be applied, and set out a concept that we think would be feasible to use NGS-based pharmacogenetics in a present-day clinical pediatric setting.