Combining familial hypercholesterolemia and statin genetic studies as a strategy for the implementation of pharmacogenomics. A multidisciplinary approach

The diagnostic process of familial hypercholesterolemia frequently involves the use of genetic studies. Patients are treated with lipid-lowering drugs, frequently statins. Although pharmacogenomic clinical practice guidelines focusing on genotype-based statin prescription have been published, their use in routine clinical practice remains very modest.We have implemented a new NGS strategy that combines a panel of genes related to familial hypercholesterolemia with genomic regions related to the pharmacogenomics of lipid-lowering drugs described in clinical practice guidelines and in EMA and FDA drug labels. A multidisciplinary team of doctors, biologists, and pharmacists creates a clinical report that provides diagnostic and therapeutic findings using a knowledge management and clinical decision support system, as well as an algorithm for treatment selection.For 12 months, a total of 483 genetic diagnostic studies for familial hypercholesterolemia were carried out, of which 221 (45.8%) requested a complementary pharmacogenomic test. Of these 221 patients, 66.5% were carriers of actionable variants in any of the studied pharmacogenomic pathways: 46.6% of patients in one pathway, 19.0% in two pathways, and 0.9% in three pathways. 45.7% of patients could have a response to atorvastatin different from that of the reference population, 45.7% for simvastatin and lovastatin, 29.0% for fluvastatin, and 6.7% patients for pitavastatin.This implementation approach facilitates the incorporation of pharmacogenomic studies in clinical care practice, it does not add complexity nor additional steps to laboratory processes, and improves the pharmacotherapeutic process of patients.

Results of the implementation of a pharmacogenomics platform based on NGS technologies. Combining clinical and research approaches

OBJECTIVE

As more genes are incorporated into pharmacogenomic care  processes and more importance is given to rare variants, the use of targeted  capture sequencing panels has been proposed as a very efficient alternative  due to their affordability, high throughput, and deep coverage, all of them  characteristics of high-quality next-generation sequencing data. The purpose of  this study is to describe the prevalence of clinically actionable  pharmacogenetic variants previously described in the scientific literature, as  well as that of new variants identified by next-generation sequencing  technologies, and to evaluate the drugs potentially affected by such variants.

METHOD

A panel of 18 clinically actionable pharmacogenomics-related genes  was evaluated in 41 subjects diagnosed with breast cancer undergoing  neoadjuvant treatment. The prevalence of previously descri- bed clinically  actionable variants as well as of phenotypes classified according to current  interpretation standards was studied. The pharmacological treatments  potentially affected by the identified variants were also evaluated. An  estimation was made of the prevalence of not previously described, possibly  deleterious, variants selected using bioinformatics criteria.

RESULTS

All subjects carried clinically actionable variants, with a mean of 4.02  genes affected by each variant per individual. VKORC1, CYP4F2, CYP2C19,  CYP2D6 and CYP2B6 were the most polymorphic genes and were present with  actionable phenotypes in more than 50% of patients; 15-50% had actionable  phonotypes in UGT1A1, SLCO1B1, CYP2C9 and TPMT and 2-15% in HLA-B,  CYP3A5, HLA-A and DPYD. No actionable variants were identified in RYR1,  CACNA1S, G6PD, F5 and NUDT15. These variants had the potential to affect  response to 84% of the drugs described in the leading pharmacogenetic  guidelines. Possibly deleterious variants not previously described accounted for  11.4% of all clinically actionable variants and were present in 12.2% of  patients.

CONCLUSIONS

The results obtained show a high prevalence of clinically actionable variants, both common, i.e., previously described in the  literature, and rare, i.e., not previously studied with conventional technological  approaches. The latter are candidates for a more exhaustive  molecular and/or clinical characterization.

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.

OBJECTIVE

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

METHOD

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.

RESULTS

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.

CONCLUSIONS

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).

Study of cases of abiraterone discontinuation due to toxicity in pre-chemotherapy after 1 year’s experience

Abiraterone acetate is a potent and irreversible inhibitor of cytochrome p450 17A1 that suppresses androgen synthesis. It is approved for chemotherapy-naive and docetaxel-treated patients with metastatic castration-resistant prostate cancer. We describe the protocol for use of abiraterone in metastatic castration-resistant prostate cancer chemotherapy naive patients has been implanted in our centre and we review the cases of those patients whose adverse effects have forced the discontinuation of treatment. The side effects fit the safety profile of abiraterone, speed of their appearance and severity indicate that you should perform a thorough follow-up of these patients especially in the early phases of treatment.