Development of Probe Capture Next-Generation Sequencing Assays for Degraded DNA

• NCJ Number: 251820
• Author(s): Cassandra D. Calloway
• Date Published: March 2017
• Length: 17 pages
• Grant Number(s): 2013-MU-MU-K044
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical); Report (Study/Research); Report (Grant Sponsored); Program/Project Description

Annotation

This report summarizes findings and methodology for a project that aimed to 1) develop and optimize a probe capture enrichment assay for deep sequencing the entire mitochondrial genome; 2) analyze highly degraded and limited forensically relevant samples using the mtDNA probe capture Next Generation Sequencing (NGS) assay; 3) develop a custom software for analyzing mtDNA mixture data; and 4) design and test a nuclear SNP probe capture assay to show proof-of-principle of analysis of limited, degraded, and mixed DNA samples.

Abstract

The project succeeded in showing that NGS coupled with a probe capture enrichment system can be used for deep sequencing the entire mitochondrial genome and nSNP markers. This procedure can be applied to both nuclear and mtDNA analysis of degraded samples, including bone specimens, and limited DNA amounts (1-100 pg). Thus, these assays can significantly improve discriminatory power compared to current mitochondrial HVI/HVII sequences analysis; and they increase the success rate of genotyping degraded and limited samples. 3 figures and listings of names and descriptions of protocols, probe capture panel, and software programs