Evaluation of Massively Parallel Sequencing Technology for Routine Forensic Casework

The basis of individual identification in modern forensics is DNA typing by short tandem repeats (STRs). This technique has brought a standardized, quantitative method with strong statistical underpinnings to the criminal justice system that has dramatically improved just and impartial outcomes. While the fundamental principles behind STR typing have not changed, newly developed instrumentation and informative biological markers have the potential to address the limitations of current techniques as well as to improve throughput at lower cost.
Current DNA analysis methods for individual identification have technical, cost and throughput limitations. These methods are based on capillary electrophoretic sizing of selected amplicons, some of which would not be accepted today due to poor population frequency distributions or PCR amplification problems. Capillary electrophoresis (CE) itself has inherent limitations. It is a single reaction detection method without capabilities for multiplexing and is consequently slow. It can only measure amplicon lengths and consequently fails to detect sequence specific information that could improve STR analysis. Finally, it is approaching the maximum number of STRs it can process, thus effectively abandoning improvements from new STRs and single nucleotide polymorphisms (SNPs) that could improve individual identification, mixture deconvolution and hereditary analysis.
The forensic community is beginning to evaluate massively parallel sequencing (MPS) as a means to overcome these problems. Such instruments not only add additional sequencing information, but have a nearly unlimited capacity for additional STRs as well as SNP markers, thereby enhancing individual identification. These instruments also have the potential for significant improvements in throughput at lower costs.
The goal of this application is to evaluate Thermo Fisher’s Precision ID GlobalFiler MPS STR chemistry on their Ion S5 System for forensic casework. To achieve this goal five Specific Aims are proposed: i) determine accuracy and sensitivity using single source samples, ii) assess reliability, barcoding, and contamination, iii) test challenging samples, including degraded samples from bones, blood cards and teeth as well as mixed samples in various ratios from two to six persons, iv) establish a high throughput liquid handling system for consistent library preparations, and v) calculate costs and time from preparation through analysis in comparison to currently used CE technology.
We believe this application directly addresses the specific goals of this solicitation - by “evaluating emerging methods”, having “a direct and immediate impact on laboratory efficiency” and assisting in “making laboratory policy decisions.”
Note: This project contains a research and/or development component, as defined in applicable law, and complies with Part 200 Uniform Requirements - 2 CFR 200.210(a)(14).

CA/NCF