Evaluation of Target Enrichment for SNP Genotyping of Skeletal Remains

Proposed Start Date: January 1, 2024

Proposed End Date: December 31, 2025

Funding Amount Request: $659,287.00

Project Title: Evaluation of Target Enrichment for SNP Genotyping of Skeletal Remains

Solicitation Name: NIJ FY23 Research and Development in Forensic Science for Criminal Justice Purposes

Bode Technology (Bode) proposes to implement the project entitled Evaluation of Target Enrichment for SNP Genotyping of Skeletal Remains. The purpose of this project is to investigate methods to improve high-density SNP genotyping of degraded or compromised human bone samples for forensic investigative genetic genealogy (FIGG) investigations. Ancient DNA techniques and targeted SNP enrichment hybridization capture prior to sequencing will be assessed for their ability to develop useful profiles, improve human identification, extended kinship analysis, and allow for searching in law enforcement-accessible direct-to-consumer genealogical databases. A workflow for library preparation and hybridization capture that can be implemented in a standard forensic laboratory will be optimized. Project activities will include the following: evaluate the sensitivity, accuracy, and reproducibility of a commercially developed genotype-by-sequencing hybridization capture panel targeting over 595,000 population diversity SNPs to improve recovery of human content from bone samples with high quantities of exogenous microbial DNA; evaluate the genotype-by-sequencing panel in combination with a “spike-in” forensic-specific target enrichment hybridization capture panel used to generate supplemental forensically relevant data; assess the feasibility of performing “in-house” processing of skeletal remains through library prep with target enrichment hybridization capture and analysis in a forensics laboratory without needing to submit the library to a service laboratory for high-depth sequencing; and determine the limitations of the panel by applying the workflow to laboratory-created compromised samples and human bones that had previously demonstrated poor genotyping ability with microarrays. Expected outcomes will include the following: improved recovery of human DNA from bone samples compromised by degradation and exogenous microbial DNA; determination of best practices for FIGG investigations involving compromised human bone samples; and dissemination of the study results to the forensic community through publications in peer-reviewed journals and presentations at scientific meetings. Crime laboratories, law enforcement, the FIGG community, victims, and victims’ families are the intended beneficiaries of the project. Subrecipient activities by the University of Tennessee Forensic Anthropology Center will include delivery of bone powder and blood card punches from ten skeletonized human donors to Bode; provision of subject matter expertise for processing and analysis of human remains; and contribution to writing/drafting of semi-annual progress reports, the Final Research Report, and peer-reviewed publications. CA/NCF