Using Centrifugal Filter Devices for Purification of Crime Scene DNA

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.

Biological samples from crime scenes are heterogeneous, as any human cell type deposited on any material or surface can be recovered and used as evidence. Forensic DNA analysis is limited by the size, quality and purity of these samples. Efficient sample treatment protocols are needed to release and concentrate the nucleic acids and remove PCR-inhibitory compounds, thus maximizing the analytical success rate.

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Crime Scene
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Crime Scene DNA

Sample treatment generally includes i) eluting cells from evidence item, swab or mini-tape, ii) cell lysis, and iii) DNA purification. In this process, there is generally a trade-off between yield and purity. Physical separation of cells from the background material prior to lysis, for example, by laser microdissection or differential centrifugation methods, can improve sample purity. However, these methods are time-consuming, laser microdissection is very costly and differential centrifugation generally gives poor recovery rates (below 50%). Direct lysis is more straightforward and generates higher yields, and has therefore become the most common approach in forensics.

Cell lysis can be chemical (for example, using detergents), enzymatic (for example, proteinase K treatment), physical (for example, heating) or mechanical (for example, bead-beating). Direct lysis involves the obvious risk of co-extracting disturbing substances with physicochemical properties similar to DNA. Extensive DNA purification can therefore be needed to generate PCR-compatible extracts. DNA purification, however, inevitably leads to DNA loss . The level of loss is dependent on both sample type and purification method. Recovery rates spanning from 10 to 85% have been reported when comparing different methods for a certain sample type. Visit this directory for more on this subject.

Post-extraction DNA purification of crime scene samples is generally performed using kits based on silica-coated magnetic beads or silica membranes in manual or automated protocols or applying centrifugal filter devices. Centrifugal filter devices, or microdialysis, have been applied in forensics since the early days of PCR-based DNA analysis.

Lately, the forensic application of the Amicon Ultra (Millipore, Billerica, MA, USA) filter device has been reported in several studies, for purification as well as for concentration of DNA extracts. However, there is a lack of studies investigating the recovery rate and general performance of this and other centrifugal devices for common crime scene sample types. The recent introduction of new short tandem repeat (STR) DNA typing kits with increased PCR inhibitor tolerance also make it relevant to update the view on DNA purification. We have evaluated the recovery rate and purification capacity of the centrifugal filter devices Amicon Ultra 30 K and Microsep 30 K (Pall, Port Washington, NY, USA) and compared their respective performance in long-term routine use.

Amicon Ultra 30 K and Microsep 30 K were evaluated using dilution series of extracted DNA and mock crime scene DNA extracts from various sample types and extraction procedures. The non-purified DNA extracts were first quantified and in some cases STR-analyzed (see below) and used as references for calculation of recovery rates. Each extract was split between the two devices, Amicon Ultra 30 K and Microsep 30 K, and purified in parallel to achieve the most accurate comparison regarding recovery rate and general performance. Additionally, the performance of the two filter devices was compared in long-term use in routine casework. In total, 7,869 casework DNA extracts were evaluated with respect to level of PCR inhibition and STR results, of which 4,883 were purified using Amicon Ultra 30 K and 2,986 using Microsep 30 K. Read this article for additional information.

Pure DNA was prepared for the recovery rate study. DNA extracted from whole blood using BioRobot M48 (Qiagen, Hilden, Germany) was quantified (see below) and diluted to 2.0, 0.5, and 0.2 ng/μL. Five 200 μL replicates per concentration and type of filter device (Amicon Ultra 30 K and Microsep 30 K) were analyzed. One wash cycle was applied in the filter purification (see below). All extracts were quantified before and after centrifugal filter purification.

DNA extracts were prepared for various mock crime scene sample types. All extractions were performed using Chelex, except where other methods are indicated. The samples were quantified and STR-analyzed (see below). For blood on denim, blood (20 μL of diluted blood corresponding to 2 μL of whole blood) was placed on 0.5 × 0.5 cm pieces of denim fabric and left to dry (three samples). For blood on paper, 10 samples of blood on kitchen paper (30 μL of diluted blood corresponding to 3 μL whole blood on 0.5 × 0.5 cm pieces of paper) were left to dry before performing organic (phenol) extraction. For hair, 10 anagen hairs were cut 0.5 cm from the root and each hair was placed in a 1.5 mL microcentrifuge tube with hair buffer for Chelex extraction. For rape case samples, 24 samples with both semen (1 μL of semen in 30 μL water) and saliva (80 μL of mouth rinse, from 5 mL of tap water rinsed for one minute, added to mimic the epithelial fraction of sex-crime samples) were prepared on cotton swabs and left to dry before extraction using Chelex-based differential lysis extraction, generating 24 semen and 24 epithelial cell fractions.

For saliva on envelopes, the envelopes were sealed with saliva and left to dry, and 1 × 1.5 cm pieces of the adhesive edges were cut and divided into six equally sized strips prior to extraction (three samples). For touch stains, 10 pieces of mini-tape were used for collection of cells from a pair of tights that had been worn for a couple of days prior to sample collection. For inhibitory samples, DNA (100 μL of 0.2 ng/μL DNA, from the recovery rate study, see above) was mixed with moist snuff extract (100 μL), corresponding to one portion of moist snuff. Three replicates were purified using Amicon Ultra 30 K. For the moist snuff samples, one wash cycle was applied in filter purification.

For more information on this topic see the full article at its source at the Investigative Genetics website.