Single-cell deoxyribonucleic acid typing for forensic mixtures and trace evidence: Opportunities, validation requirements, and reporting limits

Abstract

Forensic deoxyribonucleic acid (DNA) interpretation is limited less by genotyping technology than by the biochemical and inferential effects of mixed, low-template, and environmentally complex traces. Single-cell and single-molecule strategies, including the United Kingdom Research and Innovation-funded single-cell and single-molecule analysis for DNA identification (SCAnDi) program, aim to preserve cellular resolution. They allow investigators to isolate and type individual cells or defined small-cell pools before heterogeneous evidence is converted into a bulk lysate. In selected validation settings, this approach has yielded near-complete diploid short tandem repeat (STR) profiles from small pools, credible genotype sets tightly concentrated on the true genotype across high-order mixtures, and improved access to donor-specific profiles from sexual assault and other complex samples. However, these studies also show important limits. Many operationally successful “single-cell” workflows are, in practice, single-cell-plus-consensus or few-cell workflows. Stochastic effects remain intrinsic, and cell capture itself becomes a probabilistic sampling step. This opinion review explicitly adopts an evaluative stance: It synthesizes recent validation studies and guidance documents to identify the performance thresholds and reporting boundaries that should be met before targeted forensic deployment of SCAnDi-like workflows. We argue that casework entry should require measured cell-recovery probabilities, phenotype-misclassification rates, locus- and cell-type-specific dropout and stutter models, quantified contamination and drop-in rates, validated minimum cell counts for consensus generation, and explicit database-upload criteria. It should also require strict separation between sub-source reporting and activity-level propositions. If those conditions are met, single-cell typing can complement, rather than replace, bulk STR analysis and probabilistic genotyping in a narrow but important set of high-value forensic scenarios.

Keywords: Forensic genetics; Single-cell genomics; DNA mixtures; Laser capture microdissection; Digital cell sorting; Whole-genome amplification; Short tandem repeats; Activity-level propositions; DNA transfer

Core Tip: Single-cell forensic deoxyribonucleic acid typing has moved beyond speculation, but present evidence supports targeted use only in validated niches. Its forensic value lies in reducing mixture complexity before computation, preserving cell-of-origin information, and rescuing contributor profiles that bulk analysis may not resolve. Its forensic risk lies in selective cell capture, single-template stochasticity, contamination at near-single-copy sensitivity, and the temptation to over-read cellular context as activity-level proof. The appropriate translational question is therefore not whether single-cell short tandem repeat typing works in principle, but which minimum validation thresholds and reporting limits are necessary before it enters accredited casework.