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

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.

Design, development, implementation and validation of a clinical  pharmacogenetics next-generation sequencing panel.

We 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.

The 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.

This 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).