Automated Extraction of DNA from Forensic Sample Types Using the PrepFiler Automated Forensic DNA Extraction Kit

Brevnov, Maxim G.; Mundt, Janna M.; Benfield, Jacki; Treat-Clemons, Lynda; Kalusche, Geert; Meredith, Jason; Porter, Greg; Furtado, Manohar R.; Shewale, Jaiprakash G.

doi:10.1016/j.jala.2009.06.006

Cited by 15 publications

(4 citation statements)

References 10 publications

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“…The Prepfiler™ Kit is based on a unique chemistry wherein DNA from the lysate binds to the magnetic particles by formation of a complex that remains stable during the washing steps for effective removal of inhibitors and is ultimately dissociated in the elution buffer conditions. The PrepFiler™ Kit was designed specifically to support both manual and automated extraction of DNA from forensic samples (8,9).…”

mentioning

confidence: 99%

AutoMate Express™ Forensic DNA Extraction System for the Extraction of Genomic DNA from Biological Samples*

Liu¹,

Zhong²,

Holt³

et al. 2012

Journal of Forensic Sciences

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The AutoMate Express™ Forensic DNA Extraction System was developed for automatic isolation of DNA from a variety of forensic biological samples. The performance of the system was investigated using a wide range of biological samples. Depending on the sample type, either PrepFiler™ lysis buffer or PrepFiler BTA™ lysis buffer was used to lyse the samples. After lysis and removal of the substrate using LySep™ column, the lysate in the sample tubes were loaded onto AutoMate Express™ instrument and DNA was extracted using one of the two instrument extraction protocols. Our study showed that DNA was recovered from as little as 0.025 μL of blood. DNA extracted from casework-type samples was free of detectable PCR inhibitors and the short tandem repeat profiles were complete, conclusive, and devoid of any PCR artifacts. The system also showed consistent performance from day-to-day operation.

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mentioning

confidence: 99%

AutoMate Express™ Forensic DNA Extraction System for the Extraction of Genomic DNA from Biological Samples*

Liu¹,

Zhong²,

Holt³

et al. 2012

Journal of Forensic Sciences

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“…gram positive and acid fast bacilli), or complex clinical sample types (e.g., blood, nasopharyngeal aspirate [NPA], and nasopharyngeal swabs [NPS]) (Sin et al, 2014; Dineva et al, 2007). Commercially-available, automated workstations provide users the procedural flexibility to develop and validate extraction protocols for a wide range of sample types, but may still require off-line (manual) sample pretreatment (Brenov et al, 2009). Perhaps more limiting is that the automated systems themselves require significant capital investment and laboratory space, either of which may not be available at all institutions interested in performing molecular diagnostics.…”

Section: Introductionmentioning

confidence: 99%

A bench-top automated workstation for nucleic acid isolation from clinical sample types

Thakore

Garber

Bueno

et al. 2018

Journal of Microbiological Methods

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Systems that automate extraction of nucleic acid from cells or viruses in complex clinical matrices have tremendous value even in the absence of an integrated downstream detector. We describe our bench-top automated workstation that integrates our previously-reported extraction method - TruTip - with our newly-developed mechanical lysis method. This is the first report of this method for homogenizing viscous and heterogeneous samples and lysing difficult-to-disrupt cells using "MagVor": a rotating magnet that rotates a miniature stir disk amidst glass beads confined inside of a disposable tube. Using this system, we demonstrate automated nucleic acid extraction from methicillin-resistant Staphylococcus aureus (MRSA) in nasopharyngeal aspirate (NPA), influenza A in nasopharyngeal swabs (NPS), human genomic DNA from whole blood, and Mycobacterium tuberculosis in NPA. The automated workstation yields nucleic acid with comparable extraction efficiency to manual protocols, which include commercially-available Qiagen spin column kits, across each of these sample types. This work expands the scope of applications beyond previous reports of TruTip to include difficult-to-disrupt cell types and automates the process, including a method for removal of organics, inside a compact bench-top workstation.

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“…Common methods of DNA extraction, as an instance, Chelex and organic phenol-chloroform, have been widely and consistently used in forensic laboratories for a long time, and are still the favored methods for some sample types (Lee & Shewale, 2006), while EZ (advanced and biorobot) has succeded in removing several inhibitors of PCR, which are often alongside with the organic method of DNA extraction (Brevnov et al, 2009;Frégeau et al, 2006Frégeau et al, , 2008Haak et al, 2008;Montpetit et al, 2005;Scherer et al, 2009;Witt et al, 2012). Many laboratories still depend on Chelex (Walsh et al, 2013) or organic methods (Sambrook, 1989), especially for the extraction of DNA from forensic trace evidence.…”

Section: Introductionmentioning

confidence: 99%

Carrier RNA is a key factor affecting fully integrated short tandem repeats profiling in challenging forensic samples models

El-Shorbagy

El-Liethy

Moussa

et al. 2022

JoBAZ

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Background Short tandem repeats (STRs) are used today to provide discriminatory power for DNA fingerprinting. The present results showed that different factors may affect STR profiles in challenging samples including DNA quantity, DNA quality, PCR inhibitors and storage time. In the present study, blood stain samples were applied on two types of fabrics (black cotton and denim) to compare the efficiency of two different DNA-extraction methods (automated magnetic based beads method (EZ1), and manual organic method), with and without adding carrier RNA molecules, and to assess the quality and quantity of the extracted DNA and their capabilities for producing reportable STR-profiles in the presence of PCR inhibitors at two different storage times. Results Carrier RNA caused a dramatic increase in DNA recovery from black cotton or denim using EZ1 in contrast to organic method. EZ1 was found to be preferred than organic, especially when a time passed over, while organic method was preferred when samples are available in small quantities. In addition, using carrier RNA within the organic method steps showed no improvement in STR profiling. EZ1 with carrier RNA was preferred for bloodstained samples on fabrics with textile dyes (black dye or denim indigo), especially when stored for a long time. Conclusions Denim was found to be more problematic than black cotton due to presence of challenging inhibitors (indigo dye). DNA concentration, storage time and types of fabrics are key factors for choosing the appropriate extraction method for reportable STR profile. Using EZ1 with carrier RNA gives less dropout profile than not using it, or when using organic method even in presence or absence of carrier RNA. Anyway, innovation of more sensitive, more robust analytical protocols could result in a better understanding of these inhibitory samples.

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Automated Extraction of DNA from Forensic Sample Types Using the PrepFiler Automated Forensic DNA Extraction Kit

Cited by 15 publications

References 10 publications

AutoMate Express™ Forensic DNA Extraction System for the Extraction of Genomic DNA from Biological Samples*

AutoMate Express™ Forensic DNA Extraction System for the Extraction of Genomic DNA from Biological Samples*

A bench-top automated workstation for nucleic acid isolation from clinical sample types

Carrier RNA is a key factor affecting fully integrated short tandem repeats profiling in challenging forensic samples models

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