An Instrument for Automated Purification of Nucleic Acids from Contaminated Forensic Samples

Abstract

Forensic crime scene sample analysis, by its nature, often deals with samples in which there are low amounts of nucleic acids, on substrates that often lead to inhibition of subsequent enzymatic reactions such as PCR amplification for STR profiling. Common substrates include denim from blue jeans, which yields indigo dye as a PCR inhibitor, and soil, which yields humic substances as inhibitors. These inhibitors frequently co-extract with nucleic acids in standard column or bead-based preps, leading to frequent failure of STR profiling. We present a novel instrument for DNA purification of forensic samples that is capable of highly effective concentration of nucleic acids from soil particulates, fabric, and other complex samples including solid components. The novel concentration process, known as SCODA, is inherently selective for long charged polymers such as DNA, and therefore is able to effectively reject known contaminants. We present an automated sample preparation instrument based on this process, and preliminary results based on mock forensic samples.

Development of internal amplification controls for DNA profiling with the AmpFℓSTR® SGM Plus® kit

“…Challenging samples containing degraded DNA or contaminated with PCR inhibitors may yield partial profiles or negative results. Broemeling et al [2] estimated that 10% or more of crime scene samples fail to generate a profile due to insufficient DNA or co-extraction of PCRinhibiting contamination.…”

DNA/RNA Preparation for Molecular Detection

“…A new technology can purify large amounts of NA from almost any sample. In a spin on gel purification, a method called synchronous coefficient of drag alteration (SCODA) is used for clean concentrated NA preparation from any sample (69 ). A rotating electric field is used to focus NA in a spot that can be removed and purified.…”

Novel Tissue Types for the Development of Genomic Biomarkers

“…However, the extraction and purification of nucleic acids in feces is quite challenging due to its low abundance and the high level of contaminants like humic acid. Thankfully, there are a number of commercial kits available for fecal DNA isolation, and new techniques such as synchronous coefficient of drag alteration (SCODA) show promise in further purifying and concentrating this rare DNA (Broemeling et al, 2008;Marziali et al, 2005). Interestingly, both the amount and integrity of DNA in feces have been shown to identify colorectal cancer patients (Klaassen et al, 2003;Osborn & Ahlquist, 2005).…”