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Open Access Methodology

Purification of crime scene DNA extracts using centrifugal filter devices

Lina Norén1, Ronny Hedell12, Ricky Ansell13 and Johannes Hedman14*

Author Affiliations

1 Swedish National Laboratory of Forensic Science (SKL), Linköping, SE, 581 94, Sweden

2 Department of Mathematical Sciences, Chalmers University of Technology, Göteborg, SE, 412 96, Sweden

3 Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, SE, 581 83, Sweden

4 Division of Applied Microbiology, Lund University, Lund, SE, 221 00, Sweden

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Investigative Genetics 2013, 4:8  doi:10.1186/2041-2223-4-8

Published: 24 April 2013

Abstract

Background

The success of forensic DNA analysis is limited by the size, quality and purity of biological evidence found at crime scenes. Sample impurities can inhibit PCR, resulting in partial or negative DNA profiles. Various DNA purification methods are applied to remove impurities, for example, employing centrifugal filter devices. However, irrespective of method, DNA purification leads to DNA loss. Here we evaluate the filter devices Amicon Ultra 30 K and Microsep 30 K with respect to recovery rate and general performance for various types of PCR-inhibitory crime scene samples.

Methods

Recovery rates for DNA purification using Amicon Ultra 30 K and Microsep 30 K were gathered using quantitative PCR. Mock crime scene DNA extracts were analyzed using quantitative PCR and short tandem repeat (STR) profiling to test the general performance and inhibitor-removal properties of the two filter devices. Additionally, the outcome of long-term routine casework DNA analysis applying each of the devices was evaluated.

Results

Applying Microsep 30 K, 14 to 32% of the input DNA was recovered, whereas Amicon Ultra 30 K retained 62 to 70% of the DNA. The improved purity following filter purification counteracted some of this DNA loss, leading to slightly increased electropherogram peak heights for blood on denim (Amicon Ultra 30 K and Microsep 30 K) and saliva on envelope (Amicon Ultra 30 K). Comparing Amicon Ultra 30 K and Microsep 30 K for purification of DNA extracts from mock crime scene samples, the former generated significantly higher peak heights for rape case samples (P-values <0.01) and for hairs (P-values <0.036). In long-term routine use of the two filter devices, DNA extracts purified with Amicon Ultra 30 K were considerably less PCR-inhibitory in Quantifiler Human qPCR analysis compared to Microsep 30 K.

Conclusions

Amicon Ultra 30 K performed better than Microsep 30 K due to higher DNA recovery and more efficient removal of PCR-inhibitory substances. The different performances of the filter devices are likely caused by the quality of the filters and plastic wares, for example, their DNA binding properties. DNA purification using centrifugal filter devices can be necessary for successful DNA profiling of impure crime scene samples and for consistency between different PCR-based analysis systems, such as quantification and STR analysis. In order to maximize the possibility to obtain complete STR DNA profiles and to create an efficient workflow, the level of DNA purification applied should be correlated to the inhibitor-tolerance of the STR analysis system used.

Keywords:
Amicon Ultra; DNA purification; DNA recovery; Forensic DNA analysis; Microsep; PCR inhibition; PCR inhibitors