Development and Analytical Validation of a 29 Gene Clinical Pharmacogenetic Genotyping Panel: Multi‐Ethnic Allele and Copy Number Variant Detection

Abstract

To develop a novel pharmacogenetic genotyping panel, a multidisciplinary team evaluated available evidence and selected 29 genes implicated in interindividual drug response variability, including 130 sequence variants and additional copy number variants (CNVs). Of the 29 genes, 11 had guidelines published by the Clinical Pharmacogenetics Implementation Consortium. Targeted genotyping and CNV interrogation were accomplished by multiplex single‐base extension using the MassARRAY platform (Agena Biosciences) and multiplex ligation‐dependent probe amplification (MRC Holland), respectively. Analytical validation of the panel was accomplished by a strategic combination of > 500 independent tests performed on 170 unique reference material DNA samples, which included sequence variant and CNV accuracy, reproducibility, and specimen (blood, saliva, and buccal swab) controls. Among the accuracy controls were 32 samples from the 1000 Genomes Project that were selected based on their enrichment of sequence variants included in the pharmacogenetic panel (VarCover.org). Coupled with publicly available samples from the Genetic Testing Reference Materials Coordination Program (GeT‐RM), accuracy validation material was available for the majority (77%) of interrogated sequence variants (100% with average allele frequencies > 0.1%), as well as additional structural alleles with unique copy number signatures (e.g., CYP2D6*5 , *13 , *36 , *68 ; CYP2B6*29 ; and CYP2C19*36 ). Accuracy and reproducibility for both genotyping and copy number were > 99.9%, indicating that the optimized panel platforms were precise and robust. Importantly, multi‐ethnic allele frequencies of the interrogated variants indicate that the vast majority of the general population carries at least one of these clinically relevant pharmacogenetic variants, supporting the implementation of this panel for pharmacogenetic research and/or clinical implementation programs.

Discovery of Targetable Genetic Alterations in NSCLC Patients with Different Metastatic Patterns Using a MassARRAY-Based Circulating Tumor DNA Assay

“…Despite these limitations, the benefits of this assay include its cost effectiveness and low turnaround time combined without the need for complex data analysis, bioinformatics pipelines or large data storage capacity. Furthermore, the MassARRAY system is a flexible platform allowing a broad range of different clinical applications such as HPV detection [47], tumor profiling [48], pharmacogenetics (SNP) analyses [49], sample qualification [50], and SARS-CoV-2 testing [51], thus being well suitable and accessible for a various medical laboratories with clearly lower running costs compared to NGS based analyses.…”

The Clinical Pharmacogenetics Implementation Consortium Guideline for SLCO1B1, ABCG2, and CYP2C9 genotypes and Statin‐Associated Musculoskeletal Symptoms

“…rs2231142 can be genotyped alone (e.g., polymerase chain reaction–based single SNP assay) or multiplexed on a variety of array‐based platforms. Various commercial genotyping platforms include rs2231142 in panels of pharmacogenetic variants 12 …”

Pharmacogenomic education among genetic counseling training programs in North America

“…In the United States, ~20% of all medications have response phenotypes associated with pharmacogenomic variants involved in drug metabolism (Relling & Evans, 2015). Multi-ethnic allele frequency studies have determined that the vast majority of the general population carries a clinically actionable pharmacogenomic variant, with most people having multiple actionable variants (Scott et al, 2020). As such, pharmacogenomic testing is increasingly being utilized in clinical practice, which is supported by the availability of reimbursable tests from clinical laboratories, published clinical pharmacogenomic practice guidelines (e.g., Clinical Pharmacogenomics Implementation Consortium [CPIC] (Relling et al, 2020),] Dutch Pharmacogenomics Working Group (Swen et al, 2011), Food and Drug Administration (Cheng et al, 2020)), and other implementation resources (e.g., American College of Medical Genetics and Genomics (Lyon et al, 2012), Association for Molecular Pathology (Pratt et al, 2020), PharmGKB (Barbarino et al, 2018), PharmVar (Gaedigk et al, 2020)).…”