Establishing a novel automated magnetic bead-based method for the extraction of DNA from a variety of forensic samples

Extraction of DNA from trace forensic samples with a modified lysis buffer and chitosan coated magnetic beads

The trace amounts of human tissue cells or body fluids left at the crime scene are often mixed with inhibitors such as rust, pigments, and humic acid. The extraction of the DNA from the trace cells is crucial for the investigation of cases. Usually, specially designed magnetic nanoparticles were chosen by the case investigators to enrich and elute DNA, which was then used for polymerase chain reaction (PCR) and short tandem repeat (STR) analysis. The traditional approach often had the following problems, such as low DNA enrichment efficiency, possible DNA breakage, and complex operations. Here, the 1%(w/v) of chitosan (75% deacetylation degree) was used to modify the 50 nm magnetic nanoparticles to gain the Chitosan@Beads, which theoretically carried positively charged in the pH = 5 of lysis buffer so as to adsorb negatively charged DNA through electrostatic interactions. The XPS and FT-IR results demonstrated that chitosan was successfully attached to the surface of magnetic nanoparticles. A set of simulated samples, containing 20 mg/μL of humic acid, pigments, iron ions (Fe2+, Fe3+), and the coexistence of the above three substances, were prepared to simulate the case scene. Human bronchial epithelial cells were mixed with the 200 μL of the above simulated samples for DNA extraction. 400 μL of lysis buffer, 20 μL of proteinase K (10 mg/mL) and 20 μL of Chitosan@Beads solution (20 mg/mL) was used for cell disruption and DNA enrichment. The extraction sensitivity of Chitosan@Beads was confirmed to be 10 cells, superior to commercial reagent kits. The Chitosan@Beads@DNA can directly use for "In-situ PCR" with elution-free operations. The STR loci rate of DNA extracted by Chitosan@Beads was around 97.9%, higher than the commercial kit (66.7%). In short, we foresee here developed novel Chitosan@Beads and modified lysis buffer could provide a new model for the DNA extraction of forensic trace evidence.

Programmable magnetic robot (ProMagBot) for automated nucleic acid extraction at the point of need

Upstream sample preparation remains the bottleneck for point-of-need nucleic acid testing due to its complexity and time-consuming nature. Sample preparation involves extracting, purifying, and concentrating nucleic acids from various matrices. These processes are critical for ensuring the accuracy and sensitivity of downstream nucleic acid amplification and detection. However, current sample preparation methods are often laboratory-based, requiring specialized equipment, trained personnel, and several hours of processing time. As a result, sample preparation often limits the speed, portability, and cost-effectiveness of point-of-need nucleic acid testing. A universal, field-deployable sample preparation device is highly desirable for this critical need and unmet challenge. Here we reported a handheld, battery-powered, reconfigurable, and field-deployable nucleic acid sample preparation device. A programmable electromagnetic actuator was developed to drive a magnetic robot (ProMagBot) in X/Y 2D space, such that various magnetic bead-based sample preparations can be readily translated from the laboratory to point-of-need settings. The control of the electromagnetic actuator requires only a 3-phase unipolar voltage in X and Y directions, and therefore, the motion space is highly scalable. We validated the ProMagBot device with a model application by extracting HIV viral RNAs from plasma samples using two widely used magnetic bead kits: ChargeSwitch and MagMAX beads. In both cases, the ProMagBot could successfully extract viral RNAs from 50 μL plasma samples containing as low as 102 copies of viral RNAs in 20 minutes. Our results demonstrated the ability of ProMagBot to prepare samples from complex mediums at the point of need. We believe such a device would enable rapid and robust sample preparation in various settings, including resource-limited or remote environments, and accelerate the development of next-generation point-of-need nucleic acid testing.

Robotic DNA Extraction Utilizing Qiagen BioSprint® 96 Workstation

After an examination of evidentiary or reference samples has been performed, the next step is DNA extraction. This crucial step allows for deoxyribonucleic acid (DNA) to be released from a substrate by use of a series of chemicals and allows the DNA from lysed cells to be taken forward for DNA typing. To allow processing of the increased number of forensic samples submitted for DNA typing, automated systems have become more commonplace within forensic laboratories. The Qiagen BioSprint® 96 workstation utilizes magnetic particle technology (Qiagen, BioSprint® 96 DNA Handbook, 2012) to process a variety of samples, such as liquid blood, blood stain cards, and buccal (saliva) swabs. The following methods outlined within this chapter are based upon the automated DNA extraction of three commonly received types of reference samples (liquid blood, bloodstain cards, and buccal swabs) utilizing the Qiagen BioSprint® 96 DNA Blood Kit.

Establishing an integrated pipeline for automatic and efficient detection of trace DNA encountered in forensic applications

The analysis of trace DNA is a crucial component in forensic applications. Biological materials containing low-level DNA collected at crime scenes, such as fingerprints, can be valuable as evidence. Automatic detection of biological samples has been largely embraced in forensic applications to meet the increasing throughput requirements. However, the amount of DNA automatically retrieved from trace evidence often tends to be small and unstable, ultimately resulting in poor detection of DNA profiles. Thus, in this work, we introduced a robust DNA extraction and purification platform named Bionewtech® BN3200 (Bionewtech®, Shanghai, China) with the goal of constructing a rapid automatic detection system for trace DNA. The establishment of automatic detection system for trace DNA mainly encompassed two parts: assessing the sensitivity of automatic extraction platform and screening the optimal short tandem repeat (STR) typing kit. The sensitivity of Bionewtech® BN3200 platform based on Ultra-sensitive DNA Extraction kit was initially estimated, demonstrating that this extraction platform might contain large potential in the trace DNA extraction. For the amplification part, three sets of commercial multiplex STR typing kits were selected as candidates, and the amplified products were further genotyped on the Applied Biosystems 3500xl Genetic Analyzer. After comparation, SiFa™ 23 Plex Kit was determined as the most suitable amplification system for trace DNA. Eventually, the newly exploited trace DNA detection system was successfully implemented in the detection of fingerprints derived from glass surfaces with the five-seconds contact time. As a result, the DNA recovered from the fingerprints fluctuated approximately from 57.60 pg to 18.05 ng, in addition, over 70% of the total STR loci were detected in 75% of the fingerprint samples.

Drop-to-drop liquid-liquid extraction of DNA in an electrowetting-on-dielectric digital microfluidics

Recent advancements in microfluidics and lab-on-a-chip technologies enabled miniaturization and automation of many downstream nucleic acid analysis steps such as PCR. However, DNA extraction/isolation protocol remains a stand-alone sample preparation step. For a quick sample-to-result solution, downstream protocols and sample preparation protocols need to be seamlessly integrated into a single lab-on-a-chip platform. As a step toward such integration, this paper introduces microfluidic DNA isolation using the liquid-liquid extraction (LLE) method in the drop-to-drop (DTD) format. The electrowetting-on-dielectric digital microfluidic platform is capable of handling a two-phase liquid system easily, which enables DTD LLE. In this study, the extraction of plasmid DNA (pDNA) from an aqueous sample to an ionic liquid is demonstrated. Prior to pDNA extraction study, the DTD LLE protocol was developed and optimized using organic dyes as solutes. The selective extraction of pDNA in the presence of proteins as interfering molecules is also demonstrated. This work implies that DTD LLE can substitute for magnetic beads steps in standard DNA isolation protocols.

A portable nucleic acid extraction system based on gigahertz acoustic tweezers

In this study, a portable and compatible system for extraction of DNA based on gigahertz acoustic was proposed and verified. The system is based on tunable multiple acoustic tweezers which can switch between the mixing and separation mode to enable the efficient DNA extraction with a relatively small and portable setup. Using this system, we extracted DNA from the rat's whole blood and achieved about 80% recovery. By combining with real-time qPCR, this proposed detection method was able to detect adenovirus (ADV) DNA as low as 10² IU/mL.Clinical Relevance-The whole system is only in centimeter scale and can be applied for portable DNA extraction. There is great potential application in molecular diagnostics and point of care test (POCT).

Magnetic particles for integrated nucleic acid purification, amplification and detection without pipetting

Nucleic acid amplification based detection plays an important role in food safety, environmental monitoring and clinical diagnosis. However, traditional nucleic acid detection process involves transferring liquid from one tube to another by pipetting. It requires trained persons, equipped labs and consumes lots of time. The ideal nucleic acid detection is integrated, closed, simplified and automated. Magnetic particles actuated by magnetic fields can efficiently adsorb nucleic acids and promote integrated nucleic acid assays without pipetting driven by pumps and centrifuges. We will comprehensively review magnetic particles assisted integrated system for nucleic acid detection and hope it can inspire further related study.

Evaluation of commercial forensic DNA extraction kits for decontamination and extraction of DNA from biological samples contaminated with radionuclides

In preparing to respond to security incidents involving radioactive material, States should consider how they might address the unique challenge of analysing forensic evidence contaminated with these materials. In the case of DNA evidence, previous research has suggested that commercial forensic DNA extraction kits may be able to remove radioactive contamination from biological samples. If viable, this would allow the extraction and decontamination of biological samples to be undertaken in a laboratory equipped to handle radioactive material, with the subsequent quantification and profiling of extracted DNA performed in a conventional forensics laboratory. In order to inform the development of an operational capability, this study sought to expand upon previous work to provide a more comprehensive quantitative assessment of the efficacy of commercial DNA extraction kits for the removal of radionuclide contamination from biological samples and the quality of the resultant DNA profiles. Three commercial DNA extraction kits were tested for their ability to remove contaminating radionuclides. Two of these kits proved more effective at removing radionuclide contamination and produced DNA extracts of higher quality. Under all conditions tested in this study, decontamination efficiency was sufficient to allow the release of samples to a forensic laboratory. However, consistent with a prudent approach to radiation safety it is recommended that all samples be screened by gamma spectrometry prior to their release to a forensic laboratory in order to verify decontamination.

A novel fully automated system for quantification of Hepatitis B virus DNA using magnetic bead-based method combined with real-time PCR

BACKGROUND

Hepatitis B virus (HBV) infection is a major global health problem and causes liver damage as cirrhosis of the liver or liver cancer. Development of an accurate, sensitive and reproducible detection method for detecting and monitoring HBV DNA is very necessary and urgent.

OBJECTIVES

The aims were to evaluate the analytical performances of the fully automated Pre-NAT system comparing to domestic assay, and to explore the role of highly sensitive quantification of HBV DNA in the management of chronic HBV infection.

STUDY DESIGN

Pseudo-viral particles at high HBV DNA concentration were serially diluted to assess linear range. Accuracy and lower limit of detection were assessed by determining a panel of HBV standard substance. HBV DNA positive clinical specimen and internal quality control were measured 20 times to evaluate precision and reproducibility. 20 non HBV-infected specimens were used for the specificity assay. 96 chronic hepatitis B samples were quantified for HBV DNA to evaluating the correlation between the new test and Da-an assay. HBV serological markers were detected using ELISA method.

RESULTS

Pre-NAT quantitated HBV DNA levels covered a wide dynamic range (10 logs) with a close correlation between expected and observed values (r=0.999, P<0.05), satisfactory precision and higher specificity. The lower detection limit was 20IU/mL. Comparability assay showed Pre-NAT had a good agreement with but more sensitive than Da-an assay (t=0.149, P>0.05). HBV DNA level was partially correlated to but more reliable and sensitive than serological evidence in reflecting the viral level.

CONCLUSION

This novel fully-automated real-time PCR assay exhibits good analytical and clinical performances for highly sensitive detection of HBV DNA. It is well suited for monitoring antiviral responses and making treatment strategies according to current clinical practice guidelines for the management of chronic HBV infection.

Influence of genetic polymorphisms in cytochrome P450 oxidoreductase on the variability in stable warfarin maintenance dose in Han Chinese

PURPOSE

The aim of this study was to investigate whether any of the single-nucleotide polymorphisms (SNPs) in the POR gene were significantly associated with CYP activity and expression, and could contribute to the total variability in stable warfarin maintenance doses in Han Chinese.

METHODS

A total of 408 patients treated at the First Affiliated Hospital of Sun Yat-Sen University were eligible for the study and had attained a stable warfarin maintenance dose at the start of the investigation. Demographics, warfarin maintenance doses, and concomitant medications were documented. Genomic DNA was extracted from peripheral blood samples and genotyped for ten SNPs (CYP 2C9*2 and *3, CYP4F2 rs2108622, VKORC1 -1639C>T, and potential POR genes of rs10239977, rs3815455, rs41301394, rs56256515, rs1057868, and rs2286823) using the Sequenom MassARRAY genotyping system.

RESULTS

A predictive model of warfarin maintenance dose was established and indicated that age, gender, body surface area, aspirin use, CYP2C9*3, CYP4F2 rs2108622, VKORC1 -1639C>T, and POR*37 831-35C>T accounted for 42.4 % of dose variance in patients undergoing anticoagulant treatment. The contribution of POR*37 831-35C>T to warfarin dose variation was only 3.9 %.

CONCLUSIONS

For the first time, the SNP POR*37 831-35C>T was confirmed as a minor but statistically significant factor associated with interindividual variation in warfarin maintenance dose in Han Chinese. The POR*37 gene polymorphism should be considered in future algorithms for faster and more reliable achievement of stable warfarin maintenance doses.

Does Epoetin Beta Still Have a Place in Peginterferon Alpha-2a Plus Ribavirin Treatment Strategies for Chronic Hepatitis C?

To investigate the impact of epoetin beta (EPO) on sustained virological response (SVR) in hepatitis C virus (HCV)-infected patients treated with peginterferon-ribavirin (RBV). Controlled, randomized, pragmatic multicenter study to assess 2 strategies, ie, the use (EPO group) or nonuse (control group) of EPO in terms of achieving SVR in treatment-naive, genotype non-2/non-3 HCV-infected patients receiving a 48-week treatment regimen of pegylated interferon α-2a (peg-IFN) plus RBV (randomization 2:1). The single-nucleotide polymorphisms of interferon lambda 3 (IFNL3) (rs12979860 and rs8099917), interferon lambda 4 (IFNL4) (ss469415590), and inosine triphosphatase (ITPA) (rs1127354 and rs7270101) were determined retrospectively. Two hundred twenty-seven patients were included in the study. In the global population (n = 227), the overall SVR rate was 52% (118/227). Nonresponse and relapse occurred in respectively 46/227 (20.3%) and 42/227 (18.5%) patients. In the intention-to-treat analysis, 55.5% of patients with anemia (n = 164) had a SVR, specifically 57.4% in the EPO group versus 52.4% in the control group, but the difference was not statistically significant. In the anemic population, independent factors associated with SVR were IFNL3 and IFNL4 polymorphisms, pretreatment HCV RNA level, iron level, and aspartate aminotransferase/alanine aminotransferase (AST/ALT) ratio. EPO has little impact on SVR in patients treated with peg-IFN+RBV and should be recommended only for patients with severe anemia.

Developmental validation of a fully integrated sample-to-profile rapid human identification system for processing single-source reference buccal samples

Short tandem repeat (STR) DNA typing is a global standard for human identification. Current practice involves highly trained forensic analysts, operating in a laboratory setting, using multiple instruments to process samples and analyze the data. Here, we report the developmental validation of a fully integrated and automated DNA profiling system, the RapidHIT® System, capable of producing up to five high quality STR profiles with full controls in approximately 90min using PowerPlex®16 HS RapidHIT chemistry. The system integrates all sample handling steps: starting from lysis of cells on buccal swabs or other buccal sample types through DNA extraction, normalization, amplification,capillary array electrophoresis, detection, and integrated software analysis. The results describe the developmental validation of the RapidHIT™ System for buccal samples processed with the DNA IQ™ extraction chemistry using a guandinium chaotropic agent and paramagnetic beads followed by amplification using a modified version of PowerPlex 16 HS chemistry (PowerPlex 16 HS RapidHIT chemistry), and capillary electrophoresis with manual review of genotyping data following interpretation guidelines. All processing from the buccal swab to generation and processing of the profile occurs on the RapidHIT platform.

RESULT

are concordant with traditional methods, with 88% first pass success rates for both the CODIS and PowerPlex 16 loci. Average peak height ratios were 0.89 for buccal swabs. The system produces full profiles from swabs with at least 176 ng of saliva DNA. Rapid DNA identification systems will significantly enhance capabilities for forensic labs, intelligence, defense, law enforcement, refugee and immigration applications, and kinship analysis.

Superparamagnetic-bead Based Method: An Effective DNA Extraction from Dried Blood Spots (DBS) for Diagnostic PCR

INTRODUCTION

Storing blood as dried spots on filter paper is a trustworthy approach used in genetic screening issues which justifies the necessity for a reliable DNA extraction method. The present work aims to investigate the effectiveness of superparamagnetic-bead based method in extracting DNA from dried blood spots (DBS).

MATERIALS AND METHODS

Sixteen venous blood samples collected in K3-EDTA tubes (400μl of whole blood) were used for the spotting (4 circles each 100μl) on Ahlstrom 226 grad filter papers, for extraction and comparison. To ensure effectiveness, the extracted DNA was checked for quantity using the Quant-iT™ dsDNA Broad-Range Assay Kit and for quality by polymerase chain reaction (PCR) amplification of 344 bp segment of the HBB gene. Hybridization assays based on the dynamic allele specific hybridization (DASH) technique for two hemoglobin beta (HBB) mutations in genomic DNA extracted from DBS of ß-thalassemia patients were also performed to ensure the quality of extraction.

RESULTS

The results revealed a compatible effectiveness of the superparamagnetic-bead based method in extracting DNA from DBS particularly when incubating the DBS with lysis buffers BL+BLM overnight. A mean concentration of 21ng/ μl was obtained with lysis buffers BL+BLM overnight incubation compared to 5.2 ng/μl for 2 h incubation with lysis buffers BL+BLM and 4.7 ng/μl when extraction performed using the lysis buffer BLM alone. Moreover, PCR amplification of 344 bp segment of the HBB showed a good quality of the extracted DNA.

CONCLUSION

It was concluded that the superparamagnetic-bead based method is a reliable and effective method for DNA extraction from DBS and can be adopted for genetic diagnostic purposes.

Dual-force aggregation of magnetic particles enhances label-free quantification of DNA at the sub-single cell level

We recently reported the 'pinwheel effect' as the foundation for a DNA assay based on a DNA concentration-dependent aggregation of silica-coated magnetic beads in a rotating magnetic field (RMF). Using a rotating magnet that generated a 5 cm magnetic field that impinged on a circular array of 5mm microwells, aggregation was found to only be effective in a single well at the center of the field. As a result, when multiple samples needed to be analyzed, the single-plex (single well) analysis was tedious, time-consuming and labor-intensive, as each well needed to be exposed to the center of the RMF in a serial manner for consistent well-to-well aggregation. For more effective multiplexing (simultaneous aggregation in 12 wells), we used a circular array of microwells and incorporated 'agitation' as a second force that worked in concert with the RMF to provide effective multiplexed aggregation-based DNA quantitation. The dual-force aggregation (DFA) approach allows for effective simultaneous aggregation in multiple wells (12 demonstrated) of the multi-well microdevice, allowing for 12 samples to be interrogated for DNA content in 140 s, providing a ∼35-fold improvement in time compared to single-plex approach (80 min) and ∼4-fold improvement over conventional fluorospectrometric methods. Furthermore, the increased interaction between DNA and beads provided by DFA improved the limit of detection to 250 fg μL(-1). The correlation between the DFA results and those from a fluorospectrometer, demonstrate DFA as an inexpensive and rapid alternative to more conventional methods (fluorescent and spectrophotometric).

Role of oral fluids in DNA investigations

The assay of oral fluid (OF), a biofluid historically well-studied biochemically and physiologically, is a growing area of research with implications for basic and clinical purposes. In the last decade, it has gained considerable attention and lately, the use of OF has provided a substantial addition as an investigative tool in forensic and/or legal procedures. This article is an appraisal of various applications of OF sourced DNA in the field of forensic analysis. We have discussed the significance of different collection methods and their variations along with the application of specific analytical methods based on the condition of the sample. It is likely that the germaneness of OF assays will continue to expand thus providing a new instrument for investigation in criminal/legal proceedings.

Immunomagnetic nanoparticle-based assays for detection of biomarkers

The emergence of biomarkers as key players in the paradigm shift towards preventative medicine underscores the need for their detection and quantification. Advances made in the field of nanotechnology have played a crucial role in achieving these needs, and have contributed to recent advances in the field of medicine. Nanoparticle-based immunomagnetic assays, in particular, offer numerous advantages that utilize the unique physical properties of magnetic nanoparticles. In this review, we focus on recent developments and trends with regards to immunomagnetic assays used for detection of biomarkers. The various immunomagnetic assays are categorized into the following: particle-based multiplexing, signal control, microfluidics, microarray, and automation. Herein, we analyze each category and discuss their advantages and disadvantages.

An integratable microfluidic cartridge for forensic swab samples lysis

Fully automated rapid forensic DNA analysis requires integrating several multistep processes onto a single microfluidic platform, including substrate lysis, extraction of DNA from the released lysate solution, multiplexed PCR amplification of STR loci, separation of PCR products by capillary electrophoresis, and analysis for allelic peak calling. Over the past several years, most of the rapid DNA analysis systems developed started with the reference swab sample lysate and involved an off-chip lysis of collected substrates. As a result of advancement in technology and chemistry, addition of a microfluidic module for swab sample lysis has been achieved in a few of the rapid DNA analysis systems. However, recent reports on integrated rapid DNA analysis systems with swab-in and answer-out capability lack any quantitative and qualitative characterization of the swab-in sample lysis module, which is important for downstream forensic sample processing. Maximal collection and subsequent recovery of the biological material from the crime scene is one of the first and critical steps in forensic DNA technology. Herein we present the design, fabrication and characterization of an integratable swab lysis cartridge module and the test results obtained from different types of commonly used forensic swab samples, including buccal, saliva, and blood swab samples, demonstrating the compatibility with different downstream DNA extraction chemistries. This swab lysis cartridge module is easy to operate, compatible with both forensic and microfluidic requirements, and ready to be integrated with our existing automated rapid forensic DNA analysis system. Following the characterization of the swab lysis module, an integrated run from buccal swab sample-in to the microchip CE electropherogram-out was demonstrated on the integrated prototype instrument. Therefore, in this study, we demonstrate that this swab lysis cartridge module is: (1) functionally, comparable with routine benchtop lysis, (2) compatible with various types of swab samples and chemistries, and (3) integratable to achieve a micro total analysis system (μTAS) for rapid DNA analysis.