A TaqMan-compatible 44-SNP barcode for robust sample tracking in research and clinical settings

The adoption of next-generation sequencing (NGS) into research and clinical routine has deeply transformed precision medicine. However, it has also introduced significant challenges in sample tracking and authentication across increasingly complex analytical workflows. While the frequency of sample misidentification may be low, potential negative outcomes are worrying. Existing SNP-based quality control solutions rely on non-coding genetic markers or require advanced technologies. There is a gap for small, robust panels that are portable across technologies, compatible with diagnostic panels, applicable across diverse populations and that have straightforward wet-lab implementation. We applied a stringent filtering pipeline to identify a set of highly discriminant, cross-platform compatible genetic markers supported by predesigned TaqMan assays, prioritizing broad applicability across world populations. We prioritized SNPs present in clinical sequencing panels. The panel was validated using whole-genome sequencing (WGS) data from 150 neuropathology samples in the NAGENDATA cohort and cross-validated with qPCR genotyping. We identified and validated a TaqMan-compatible 44-SNP panel for cross-platform sample authentication. The full panel demonstrates exceptional discriminatory power, with theoretical cumulative random match probabilities (CRMPs) ranging from 2.43 × 10⁻¹⁹ (European) to 9.37 × 10⁻¹⁸ (East Asian). We validated the panel in the NAGENDATA cohort using both NGS and qPCR-based methods. Cross-platform comparison revealed 99% concordance between NGS and qPCR profiles. Combined within-platform and cross-platform analyses successfully identified three cases of sample mislabelling in the NAGENDATA collection. We present a robust, ready-to-deploy SNP barcode bridging NGS and wet-lab workflows, enabling retrospective sample authentication across sequencing platforms and qPCR systems. Our solution is specifically designed for clinical settings, offering cross-platform compatibility and cost-effective implementation.