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

Area of Science:

• Clinical diagnostics
• Genomics
• Molecular biology

Background:

• Next-generation sequencing (NGS) is crucial for clinical diagnostics.
• NGS workflows involve multiple steps, increasing risks of sample mix-ups and contamination.
• Ensuring sample identity is vital for accurate patient data and diagnostic outcomes.

Purpose of the Study:

• To evaluate the performance and usability of three commercial single nucleotide polymorphism (SNP)-based sample tracking kits.
• To determine the reliability and cost-effectiveness of each kit for DNA sample identification in a diagnostic setting.

Main Methods:

• Three commercially available SNP-based kits were tested within a diagnostic workflow.
• Evaluated parameters included coverage uniformity, on-target specificity, sample identification accuracy, and genotyping performance.
• Assessed ease of use, hands-on time, and protocol complexity.

Main Results:

• The pxlence and Nimagen kits had similar hands-on times; the Swift kit required an additional purification step.
• The Swift kit failed to genotype 26 out of 46 samples correctly.
• The pxlence kit identified all samples unambiguously, while the Nimagen kit identified all but one.
• The Nimagen kit exhibited poor on-target mapping rates, potentially increasing sequencing costs.

Conclusions:

• The pxlence Human Sample ID kit is the most reliable and robust option for DNA sample tracking.
• The pxlence kit offers the best cost-effectiveness among the evaluated tools for sample identification in diagnostic NGS workflows.