High-throughput genotyping system as a robust and useful tool in oncology: Experience from a single institution

Abstract

Background and aim: Single nucleotide polymorphisms (SNPs) are substitutions of one base for another in the gene sequence and conforms the basis for pharmacogenetics and the development of personalized medicine. Many methods have been developed for SNP genotyping. The aim of the present study was to validate the use of a novel high-throughput genotyping system.Methods: Five SNPs (rs25487, rs25489, rs1799782, rs13181, and rs11615) were genotyped in 118 cancer patients using the classical method PCR restriction fragment length polymorphism (RFLP) and the high-throughput, automated assay Biotrove OpenArray (R) NT Cycler, trying to explore the feasibility and reproducibility of the OpenArray system in the context of oncology.Results: The call rates obtained ranged from 95.7 to 100% for both techniques. The percentage of overlapping ranged from 96.2 to 100% among both assays, showing a high reproducibility between the techniques.Conclusion: These findings, together with the low-cost and the simple and fast work flow, suggest that the OpenArray system is a robust and easy methodology for genotyping in the field of oncology. (C) 2013 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.