Impact of DNA Degradation on Massively Parallel Sequencing-based Autosomal STR, iiSNP, and Mitochondrial DNA Typing Systems

• NCJ Number: 254116
• Journal: International Journal of Legal Medicine Volume: 133 Issue: 5 Dated: 2019 Pages: 1369-1380
• Author(s): Elena I. Zavala; Swetha Rajagopal; George H. Perry; Ivana Kruzie; Zeljana Basic; Thomas J. Parsons; Mitchell M. Holland
• Date Published: 2019
• Length: 12 pages
• Grant Number(s): 2015-DN-BX-K025
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical); Report (Study/Research); Report (Grant Sponsored); Program/Project Description
• Award: Assessing the Effects of DNA Damage on Next Generation mtDNA Sequencing

Annotation

This project performed a modeling study that demonstrated SNPs can increase the significance of an identification when analyzing DNA down to an average size of 100 bps for input amounts between 0.375 and 1 ng of nuclear DNA; and observations from this study were then compared with 14 human skeletal material results (ninth to eighteenth centuries), which further demonstrated the utility of the ForenSeq kit for degraded samples.

Abstract

Biological samples, including skeletal remains exposed to environmental insults for extended periods of time, exhibit increasing levels of DNA damage and fragmentation. Human forensic identification methods typically use a combination of mitochondrial (mt) DNA sequencing and short tandem repeat (STR) analysis, which target segments of DNA ranging from 80 to 500 base pairs (bps). Larger templates are often unavailable as skeletal samples age and the associated DNA degrades. Single-nucleotide polymorphism (SNP) loci target shorter templates and may serve as a solution to the problem. Recently developed assays for STR and SNP analysis using a massively parallel sequencing approach, such as the ForenSeq kit (Verogen, San Diego, CA), offer a means for generating results from degraded samples, since they target templates down to 60 to 170 bps. The robustness of the Promega PowerSeq Mito System was also tested with 70 human skeletal remains (ninth to eighteenth centuries), resulting in successful coverage of 99.29 percent of the mtDNA control region at 50 coverage or more. This was accompanied by modifications to a mainstream DNA extraction technique for skeletal remains that improved recovery of shorter templates. (publisher abstract modified)