CODIS STR Template Enrichment by Affinity Bead Capture and Its Application in Forensic DNA Analysis

• NCJ Number: 236431
• Author(s): Diane J. Rowold, Ph.D.; Rachel E. Balsam, M.S.; Michael C. Jablecki, Ph.D.
• Date Published: November 2011
• Length: 39 pages
• Grant Number(s): 2009-DN-BX-K181
• Agencies: NIJ-Sponsored
• Publication Type: Report (Study/Research)
• Award: Next Generation Sequencing-based STR Mixture Deconvolution and STR Profiling of Degraded Samples

Annotation

This project's objective was to adapt and explore a technical application as a potential front-end treatment of a forensic sample, particularly a DNA sample that is not currently amenable to conventional methods, so as to improve the probability that such samples could be evaluated with currently validated approaches.

Abstract

This effort was occasioned by the fact that forensic investigations which involve sub-optimal evidentiary DNA samples are often hampered by incomplete and/or ambiguous Combined DNA Index System (CODIS) STR profiles that arise from low-template quantity, degradation (from age and exposure), mixed human source composition, and/or the presence of PCR inhibitors. This project developed a biotinylated oligonucleotide-streptavidin coated magnetic bead capture process that allows for the multiplex capture and PCR amplification of CODIS specific STR loci. Recovered DNA materials from highly degraded DNA samples or significantly fragmented DNA samples were assessed by a comparative analysis of the 13 established CODIS STR loci plus the amelogenin and D2S1338 STR loci. Head-to head comparisons at single to multiple loci were used to determine whether the process impacted fragment-length bias, two-contributor proportion analysis, and eukaryotic versus prokaryotic specificity. Initial results with a minimally optimized system/process indicate that despite the loss of sizeable quantities (from 30-70 percent) of the specific sequence, there were no locus dropouts, minimal allelic dropouts (less than 1 percent), and statistically relevant CODIS STR profiles were generated. In addition, PCR amplification/CE analysis of captured DNA samples did not introduce additional artifacts that might complicate CODIS STR analysis. The process was also successful at quantitatively extracting eukaryotic STR specific alleles from a five-fold excess prokaryotic background. 10 tables, 9 figures, and 29 references