This paper reports on the efforts of a research team consisting of experts in forensic anthropology, bioarchaeology, evolutionary genetics, forensic genetics, and ancient DNA in order to accomplish the following: examine the success rate of two DNA extraction methods for CODIS STR analysis; investigate how different methods of extraction, preparation, and targeted enrichment affect DNA recovery; and to assess read count and unique reads post-sequencing with NGS computational pipelines designed for degraded samples.
This technical report summarizes the preliminary findings and outcomes of a project that tested new genomic methodologies to understand and optimize the capacity to generate DNA profiles while using extremely low quantities of DNA. The project’s major goals sought to answer three specific questions: if the Dabney et al. (2013) ancient DNA extraction method recovers more DNA from bones that have undergone high degrees of charring or burning compared to the Loreille et al. (2010) protocol for both traditional (CODIS) and NGS analyses; if the single-stranded DNA library construction improves the ability to increase the proportion of unique molecules from highly burned samples for subsequent mtDNA and nuclear SNP capture, and if it is more effective than current double-stranded DNA library build protocols; and what the extent of fragmentation and damage in DNA recovered from bones and teeth with different levels of burning is, and how that impacts CODIS and NGS results after capture when using single- and double-stranded DNA library preparation protocols that are specifically designed for ancient samples. To achieve their goals, the authors sampled skeletal elements from fire death causes in Maricopa County, investigated by the Maricopa Office of the Medical Examiner, and from individuals subjected to controlled burning at the University of Tennessee’s Forensic Anthropology Center (FAC) over the course of three years. This paper reports on the study, which was designed to augment the researchers’ previous research where most samples were obtained from hand and foot bones, and discusses progress towards publication of the final results.