Shotgun DNA sequencing evidence: Sample-specific and unknown genotyping error probabilities

Overview

This research extends a statistical framework for interpreting shotgun DNA sequencing evidence in forensic genetics contexts. The extension addresses asymmetric genotyping error probabilities arising from samples of differential quality, such as highly degraded trace samples compared to high-quality reference samples. The work develops methods to handle unknown genotyping error rates through maximum profile likelihood estimation and Bayesian approaches, implementing these advances in the wgsLR software package.

Methods and approach

The study extends the wgsLR model previously established for single-source contribution analysis. Two primary methodological extensions are implemented: accommodation of asymmetric genotyping error probabilities between trace and reference samples, and estimation of unknown error probabilities via profile likelihood maximization and prior distribution specification. The robustness of the model against overdispersion was empirically evaluated. Implementation occurred through extension of the existing R package wgsLR, enabling computational application of the theoretical framework.

Key Findings

The analysis demonstrates that unknown genotyping error probabilities from low-quality trace samples can be effectively estimated when sufficient independent markers are available. The methodology proved robust across different prior distribution specifications. Additionally, the extended wgsLR model demonstrates resilience to overdispersion, indicating stability of the statistical framework under departures from model assumptions.

Implications

These methodological extensions enhance the applicability of shotgun sequencing in forensic genetic casework, particularly for low-quality or degraded samples where nuclear DNA profiling via conventional STR methods is infeasible. By accounting for differential error rates and enabling estimation of unknown error parameters, the model facilitates more accurate assessment of evidentiary strength in comparisons between trace and reference samples.

Scope and limitations

This summary is based on the study abstract and available metadata. It does not include a full analysis of the complete paper, supplementary materials, or underlying datasets unless explicitly stated. Findings should be interpreted in the context of the original publication.