Multiplexed High Resolution Melting Assay for Versatile Sample Tracking in a Diagnostic and Research Setting

Development of a coding SNP panel for tracking the origin of whole-exome sequencing samples

Whole-exome sequencing (WES) is widely used to diagnose complex genetic diseases and rare conditions. The implementation of a robust and effective quality control system for sample identification and tracking throughout the WES process is essential. We established a multiplex panel that included 22 coding single-nucleotide polymorphism (cSNP) loci. The personal identification and paternity identification abilities of the panel were evaluated, and a preliminary validation of the practical feasibility of the panel was conducted in a clinical WES case. These results indicate that the cSNP panel could be a useful tool for sample tracking in WES.

Performance Evaluation of Three DNA Sample Tracking Tools in a Whole Exome Sequencing Workflow

INTRODUCTION

Next-generation sequencing applications are becoming indispensable for clinical diagnostics. These experiments require numerous wet- and dry-laboratory steps, each one increasing the probability of a sample swap or contamination. Therefore, identity confirmation at the end of the process is recommended to ensure the right data are used for each patient.

METHODS

We tested three commercially available, single nucleotide polymorphism (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 cost effectiveness of each kit.

RESULTS AND DISCUSSION

Hands-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 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 with the other two kits.

CONCLUSION

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.