Development and validation of a next-generation sequencing panel for clinical pharmacogenetics

Abstract

The rapid clinical implementation of next generation sequencing techniques is due to its ability to sequence a large number of genetic regions at lower costs than conventional techniques. However, its use in the field of pharmacogenetics is still very limited. ObjectiveDesign, development, implementation and validation of a clinical pharmacogenetics next-generation sequencing panel. MethodWe developed a panel of hybrid capture probes (SureSelect®) for the analysis of the genetic regions of clinical interest collected by literature search and using Illumina HiSeq 1500® sequencing platform. We developed a bioinformatic algorithm for variant annotation, haplotype inference and determination of structural variants in the genes of interest. The results obtained were validated with Coriell® reference material from the pharmacogenetic repositories. ResultsThe developed panel allows the study of a total of 12,794 regions comprised in 389 genes. Validation results showed a sensitivity greater than 99% for single nucleotide variants and small INDELs. Haplotype imputation was consistent with the consensus results in the characterized reference materials. Furthermore, the developed tool was able to correctly identify different types of CYP2D6 copy number variations as well as a wide variety of HLA-B alleles. ConclusionsThis technology represents an appropriate alternative for its clinical use with advantages over conventional techniques in its throughput and complex gene study capabilities (CYP2D6, HLA-B).