Validation of a Large Custom-Designed Pharmacogenomics Panel on an Array Genotyping Platform
Autor: | David L. George, Kiang-Teck J. Yeo, Keith Danahey, Xander M R van Wijk, Xun Pei, Larry House, Elizabeth Lipschultz, Peter H. O'Donnell, Mark J. Ratain, Nga Yeung Tang |
---|---|
Jazyk: | angličtina |
Rok vydání: | 2021 |
Předmět: |
Genotype
Single sample Computational biology 030226 pharmacology & pharmacy Polymorphism Single Nucleotide law.invention 03 medical and health sciences symbols.namesake 0302 clinical medicine law Drug response Medicine Humans Genotyping Polymerase chain reaction Sanger sequencing Reproducibility business.industry High-Throughput Nucleotide Sequencing Reproducibility of Results General Medicine Articles Pharmacogenetics 030220 oncology & carcinogenesis Pharmacogenomics symbols business |
Zdroj: | J Appl Lab Med |
Popis: | BackgroundPharmacogenomics has the potential to improve patient outcomes through predicting drug response. We designed and evaluated the analytical performance of a custom OpenArray® pharmacogenomics panel targeting 478 single-nucleotide variants (SNVs).MethodsForty Coriell Institute cell line (CCL) DNA samples and DNA isolated from 28 whole-blood samples were used for accuracy evaluation. Genotyping calls were compared to at least 1 reference method: next-generation sequencing, Sequenom MassARRAY®, or Sanger sequencing. For precision evaluation, 23 CCL samples were analyzed 3 times and reproducibility of the assays was assessed. For sensitivity evaluation, 6 CCL samples and 5 whole-blood DNA samples were analyzed at DNA concentrations of 10 ng/µL and 50 ng/µL, and their reproducibility and genotyping call rates were compared.ResultsFor 443 variants, all samples assayed had concordant calls with at least 1 reference genotype and also demonstrated reproducibility. However, 6 of these 443 variants showed an unsatisfactory performance, such as low PCR amplification or insufficient separation of genotypes in scatter plots. Call rates were comparable between 50 ng/µL DNA (99.6%) and 10 ng/µL (99.2%). Use of 10 ng/µL DNA resulted in an incorrect call for a single sample for a single variant. Thus, as recommended by the manufacturer, 50 ng/µL is the preferred concentration for patient genotyping.ConclusionsWe evaluated a custom-designed pharmacogenomics panel and found that it reliably interrogated 437 variants. Clinically actionable results from selected variants on this panel are currently used in clinical studies employing pharmacogenomics for clinical decision-making. |
Databáze: | OpenAIRE |
Externí odkaz: |