Performance evaluation of three DNA sample tracking tools in a whole exome sequencing workflow

Abstract

IntroductionNext-generation sequencing applications are becoming indispensable for clinical diagnostics. These experiments require numerous wet and dry lab steps, each one increasing the probability of a sample swap or contamination. Therefore, an identity confirmation at the end of the process is recommended to ensure the right data is used for each patient. MethodsWe tested three commercially available, SNP based sample tracking kits in a diagnostic workflow to evaluate their ease of use and performance. The coverage uniformity, on-target specificity, sample identification and genotyping performance were determined to assess the reliability and the cost-effectiveness of each kit. Results and discussionHands-on time and manual steps are almost identical for the kits from pxlence and Nimagen. The Swift kit has an extra purification step, making it the longest and most demanding protocol. Furthermore, the Swift kit failed to correctly genotype 26 out of the 46 samples. The Nimagen kit identified all but one sample and the pxlence kit unambiguously identified all samples, making it the most reliable and robust kit of this evaluation. The Nimagen kit showed poor on-target mapping rates, resulting in deeper sequencing needs and higher sequencing costs compared to the other two kits. Our conclusion is that the Human Sample ID kit from pxlence is the most cost-effective of the three tested tools for DNA sample tracking and identification. Key pointsO_LIKits from pxlence and Nimagen are easy to use. C_LIO_LIUnambiguous identification of all samples possible with the pxlence kit. C_LIO_LIOnly 20 out of 46 samples were correctly identified with the Swift kit. C_LIO_LIPoor on-target rates for the Nimagen kit results in higher sequencing costs. C_LI