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Sakyi SA, Effah A, Naturinda E, Senu E, Opoku S, Amoani B, Agordzo SK, Mensah OSO, Grant J, Abban E, Buckman TA, Kwarteng A, Ephraim RKD, Danquah KO. Comparison of Modified Manual Acid-Phenol Chloroform Method and Commercial RNA Extraction Kits for Resource Limited Laboratories. Int J Clin Pract 2023; 2023:9593796. [PMID: 37333947 PMCID: PMC10275685 DOI: 10.1155/2023/9593796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/11/2023] [Accepted: 05/30/2023] [Indexed: 06/20/2023] Open
Abstract
Method In a comparative experimental cross-sectional study, RNA was extracted from oral swabs and blood samples from 25 healthy individuals at the Department of Molecular Medicine, KNUST. RNA was extracted by the manual AGPC extraction method and commercial RNA extraction kits. The quantity (ng/μl) and purities (260/280 nm) of the extracted RNA were measured spectrophotometrically using the IMPLEN NanoPhotometer® N60. The presence of RNA in the extracts was confirmed using 2% agarose gel electrophoresis. Statistical analyses were conducted using R language. Results The yield of RNA extracted from blood and oral swab samples using modified AGPC was significantly higher compared to the commercial methods (p < 0.0001). However, the purity of RNA extracted by the manual AGPC method from blood was significantly lower than the commercial methods (p < 0.0001). Moreover, the purity from oral swabs using the manual AGPC method was significantly lower compared to QIAamp (p < 0.0001) and the OxGEn kits method (p < 0.001). Conclusion The modified manual AGPC method has a very high yield of RNA extracts using blood samples, which could serve as an alternate cost-effective method for RNA extraction in resource-limited laboratories; however, its purity may not be suitable for downstream processes. Moreover, the manual AGPC method may not be suitable for extracting RNA from oral swab samples. Future investigation is needed to improve the purity of the manual AGPC RNA extraction method and also confirmation of the obtained results by PCR amplification and RNA purity verification by sequencing.
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Affiliation(s)
- Samuel Asamoah Sakyi
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alfred Effah
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Department of Medical Diagnostics, Faculty of Allied Health Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emmanuel Naturinda
- Department of Medical Diagnostics, Faculty of Allied Health Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ebenezer Senu
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Stephen Opoku
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, UK
| | - Benjamin Amoani
- Department of Biomedical Science, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Samuel Kekeli Agordzo
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Oscar Simon Olympio Mensah
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - James Grant
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Elizabeth Abban
- Department of Medical Diagnostics, Faculty of Allied Health Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Department of Medical Laboratory Technology, Garden City University College, Kumasi, Ghana
| | - Tonnies Abeku Buckman
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richard K. Dadzie Ephraim
- Department of Medical Laboratory Sciences, Faculty of Allied Health, University of Cape Coast, Cape Coast, Ghana
| | - Kwabena Owusu Danquah
- Department of Clinical Pathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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2
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A simplified viral RNA extraction method based on magnetic nanoparticles for fast and high-throughput detection of SARS-CoV-2. Talanta 2023; 258:124479. [PMID: 36966663 PMCID: PMC10035799 DOI: 10.1016/j.talanta.2023.124479] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/25/2023]
Abstract
The ongoing outbreak of the novel coronavirus disease 2019 (COVID-19) draws worldwide concerns due to its long incubation period and strong infectivity. Although RT-PCR-based methods are being widely applied for clinical diagnosis, timely and accurate diagnosis towards COVID-19 causing virus, the SARS-CoV-2, is still limited due to labor-intensive and time-consuming operations. Herein, we report a new viral RNA extraction method based on poly-(amino ester) with carboxyl group (PC)-coated magnetic nanoparticles (pcMNPs) for the sensitive detection of SARS-CoV-2. This method combines the lysis and binding steps into one step, and refines multiple washing steps into one step, giving a turnaround time of less than 9 min. Furthermore, the extracted pcMNP-RNA complexes can be directly introduced into subsequent RT-PCR reactions without elution. This simplified viral RNA method could be well adapted in fast manual and automated high-throughput nucleic acids extraction protocols suitable for different scenarios. A high sensitivity down to 100 copies/mL and a linear correlation between 100 and 106 copies/mL of SARS-CoV-2 pseudovirus particles are achieved in both protocols. Benefitting from the simplicity and excellent performances, this new method can dramatically improve the efficiency and reduce operational requirements for the early clinical diagnosis and large-scale SARS-CoV-2 nucleic acid screening.
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3
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Dawnay N, Sheppard K. From crime scene to courtroom: A review of the current bioanalytical evidence workflows used in rape and sexual assault investigations in the United Kingdom. Sci Justice 2023; 63:206-228. [PMID: 36870701 DOI: 10.1016/j.scijus.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Sexual assault casework requires the collaboration of multiple agency staff to formalise an investigative pipeline running from crime scene to court. While the same could be said of many other forensic investigations, few require the additional support of health care staff and the combined forensic involvement of body-fluid examiners, DNA experts and analytical chemists. The sheer amount of collaborative effort between agencies is laid out through a detailed examination of the investigative workflow from crime scene to courtroom with each step in the pipelines detailed and discussed. Beginning with a review of sexual assault legislation in the United Kingdom this article details how sexual assault investigations are initiated by police and supported by sexual assault referral centre (SARC) staff who are often the first responders providing primary healthcare and patient support to victims while simultaneously collecting and assessing forensic evidence. Detailing the myriad of evidential material that can be documented and collected at the SARC, the review identifies and categorises key forensic tests to first detect and identify body-fluids recovered from evidence through to the secondary analysis of DNA to help identify the suspect. This review also focusses on the collection and analysis of biological material used to support the allegation that the sexual activity was non-consensual and provides a breakdown of common marks and trauma as well as a review of common analytical methods used to infer Drug Facilitated Sexual Assault (DFSA). The culmination of the investigative pipeline is discussed by reviewing the Rape and Serious Sexual Assault (RASSO) workflow used by the Crown Prosecution Service before providing our thoughts on the future of forensic analysis and possible changes to the described workflows.
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Affiliation(s)
- Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom.
| | - Kayleigh Sheppard
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom
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4
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Szymczyk A, Drozd M, Kamińska A, Matczuk M, Trzaskowski M, Mazurkiewicz-Pawlicka M, Ziółkowski R, Malinowska E. Comparative Evaluation of Different Surface Coatings of Fe3O4-Based Magnetic Nano Sorbent for Applications in the Nucleic Acids Extraction. Int J Mol Sci 2022; 23:ijms23168860. [PMID: 36012139 PMCID: PMC9408759 DOI: 10.3390/ijms23168860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/01/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acid extraction and purification are crucial steps in sample preparation for multiple diagnostic procedures. Routine methodologies of DNA isolation require benchtop equipment (e.g., centrifuges) and labor-intensive steps. Magnetic nanoparticles (MNPs) as solid-phase sorbents could simplify this procedure. A wide range of surface coatings employs various molecular interactions between dsDNA and magnetic nano-sorbents. However, a reliable, comparative evaluation of their performance is complex. In this work, selected Fe3O4 modifications, i.e., polyethyleneimine, gold, silica, and graphene derivatives, were comprehensively evaluated for applications in dsDNA extraction. A family of single batch nanoparticles was compared in terms of morphology (STEM), composition (ICP-MS/MS and elemental analysis), surface coating (UV-Vis, TGA, FTIR), and MNP charge (ζ-potential). ICP-MS/MS was also used to unify MNPs concentration allowing a reliable assessment of individual coatings on DNA extraction. Moreover, studies on adsorption medium (monovalent vs. divalent ions) and extraction buffer composition were carried out. As a result, essential relationships between nanoparticle coatings and DNA adsorption efficiencies have been noticed. Fe3O4@PEI MNPs turned out to be the most efficient nano sorbents. The optimized composition of the extraction buffer (medium containing 0.1 mM EDTA) helped avoid problems with Fe3+ stripping, which improved the validity of the spectroscopic determination of DNA recovery.
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Affiliation(s)
- Anna Szymczyk
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
- Doctoral School No. 1, Warsaw University of Technology, Plac Politechniki 1, 00-661 Warsaw, Poland
| | - Marcin Drozd
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
- Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
| | - Agnieszka Kamińska
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
| | - Magdalena Matczuk
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
| | - Maciej Trzaskowski
- Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
| | - Marta Mazurkiewicz-Pawlicka
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Ludwika Waryńskiego 1, 00-645 Warsaw, Poland
| | - Robert Ziółkowski
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
- Correspondence:
| | - Elżbieta Malinowska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
- Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
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Khizar S, Al-Dossary AA, Zine N, Jaffrezic-Renault N, Errachid A, Elaissari A. Contribution of magnetic particles in molecular diagnosis of human viruses. Talanta 2022; 241:123243. [PMID: 35121538 PMCID: PMC8779935 DOI: 10.1016/j.talanta.2022.123243] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/16/2022]
Abstract
Viral diseases are the primary source of death, making a worldwide influence on healthcare, social, and economic development. Thus, diagnosis is the vital approach to the main aim of virus control and elimination. On the other hand, the prompt advancement of nanotechnology in the field of medicine possesses the probability of being beneficial to diagnose infections normally in labs as well as specifically. Nanoparticles are efficiently in use to make novel strategies because of permitting analysis at cellular in addition to the molecular scale. Henceforth, they assist towards pronounced progress concerning molecular analysis at the nanoscale. In recent times, magnetic nanoparticles conjugated through covalent bonds to bioanalytes for instance peptides, antibodies, nucleic acids, plus proteins are established like nanoprobes aimed at molecular recognition. These modified magnetic nanoparticles could offer a simple fast approach for extraction, purification, enrichment/concentration, besides viruses' recognition precisely also specifically. In consideration of the above, herein insight and outlook into the limitations of conventional methods and numerous roles played by magnetic nanoparticles to extract, purify, concentrate, and additionally in developing a diagnostic regime for viral outbreaks to combat viruses especially the ongoing novel coronavirus (COVID-19).
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Affiliation(s)
- Sumera Khizar
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, F-69622, Lyon, France
| | - Amal A Al-Dossary
- Department of Basic Sciences, Deanship of Preparatory Year and Supporting Studies, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 34212, Saudi Arabia
| | - Nadia Zine
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, F-69622, Lyon, France
| | | | - Abdelhamid Errachid
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, F-69622, Lyon, France
| | - Abdelhamid Elaissari
- Univ Lyon, Université Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, F-69622, Lyon, France.
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Leonel JAF, Vioti G, Alves ML, da Silva DT, Meneghesso PA, Benassi JC, Spada JCP, Galvis-Ovallos F, Soares RM, Oliveira TMFDS. DNA extraction from individual Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) specimens: Which is the method with better results? Exp Parasitol 2020; 218:107981. [PMID: 32871144 DOI: 10.1016/j.exppara.2020.107981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 07/03/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) are a group of small insects of great concern for Public Health. These dipterous are intensely studied worldwide due to their involvement in the transmission of several pathogens, mainly Leishmania spp. parasites. Nowadays, the molecular tools have been included in Phlebotomine sand flies studies and has shown to be powerful tools in bioecology studies of these dipterous. Thereby, when molecular approaches are employed, there is a great concern regarding the amount and quality of the DNA obtained for analysis. Here, seven methods of DNA extraction, between commercial kits and in house extraction protocols were evaluated. We considered measure of DNA concentration and purity ratios using a spectrophotometer to check the performance of each protocol. In addition, the quality evaluation of the DNA extracted was performed by endogenous gene PCR on samples. The results of the seven evaluated DNA extraction protocols and their implications are discussed.
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Affiliation(s)
- João Augusto Franco Leonel
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Geovanna Vioti
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Maria Luana Alves
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Diogo Tiago da Silva
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Pedro Armando Meneghesso
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Julia Cristina Benassi
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Julio Cesar Pereira Spada
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Fredy Galvis-Ovallos
- Laboratory of Entomology in Public Health, School of Public Health, University of São Paulo - USP, São Paulo, São Paulo state, Brazil
| | - Rodrigo Martins Soares
- Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Trícia Maria Ferreira de Sousa Oliveira
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil.
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Silgado A, Moure Z, de Oliveira MT, Serre-Delcor N, Salvador F, Oliveira I, Molina I, Pumarola T, Ramírez JC, Sulleiro E. Comparison of DNA extraction methods and real-time PCR assays for the molecular diagnostics of chronic Chagas disease. Future Microbiol 2020; 15:1139-1145. [PMID: 32954845 DOI: 10.2217/fmb-2020-0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Aim: This work aimed to compare the sensitivity of four protocols for the detection of Trypanosoma cruzi DNA in 98 blood samples from chronic Chagas disease patients. Materials & methods: Two DNA extraction (automated and manual) methods and two T. cruzi satellite DNA qPCRs (with a recent design and the usually used set of primers) were analyzed. Results: Both DNA extraction methods and qPCR assays tested in this work gave comparable qualitative results, although the lowest Ct values were obtained when samples were analyzed using the new set of primers for T. cruzi satellite DNA. Conclusion: Our results encourage the implementation of automated DNA extraction systems and the new T. cruzi qPCR for the molecular diagnostics and treatment response monitoring of chronic Chagas disease patients.
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Affiliation(s)
- Aroa Silgado
- Department of Microbiology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, PROSICS Barcelona, Spain
| | - Zaira Moure
- Department of Microbiology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, PROSICS Barcelona, Spain
| | - Maykon T de Oliveira
- Departamento de Clínica Médica, Unidade de Cardiologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (FMRP-USP), Brazil
| | - Núria Serre-Delcor
- Tropical Medicine Unit Vall d´Hebron-Drassanes, Universitat Autònoma de Barcelona, PROSICS Barcelona, Spain
| | - Fernando Salvador
- Department of Infectious Diseases, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, PROSICS Barcelona, Spain
| | - Inés Oliveira
- Tropical Medicine Unit Vall d´Hebron-Drassanes, Universitat Autònoma de Barcelona, PROSICS Barcelona, Spain
| | - Israel Molina
- Department of Infectious Diseases, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, PROSICS Barcelona, Spain
| | - Tomàs Pumarola
- Department of Microbiology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, PROSICS Barcelona, Spain
| | - Juan C Ramírez
- Instituto Nacional de Parasitología "Dr. Mario Fatala Chaben" (INP-ANLIS), Buenos Aires, Argentina
| | - Elena Sulleiro
- Department of Microbiology, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, PROSICS Barcelona, Spain
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TAS2R38 Haplotype Predicts 24-Hour Urinary Sodium Excretion in Patients With Heart Failure and Their Family Caregivers. J Cardiovasc Nurs 2020; 36:238-244. [PMID: 32453275 DOI: 10.1097/jcn.0000000000000692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Adherence to a low-sodium diet is essential to self-care of heart failure (HF). Genetic determinants of preference for high-sodium foods may impede adherence but have not been well-studied. OBJECTIVE Our purpose was to examine if TAS2R38 haplotype predicted salt taste sensitivity and dietary sodium intake among patients with HF. METHOD This pilot study used baseline data from a large interventional randomized control trial to support adherence to a low-sodium diet in patients with HF and their family caregivers. Participants were tested for salt taste sensitivity and provided a 24-hour urinary sodium sample and a blood sample for DNA analysis at baseline. Fungiform papillae were counted. χ2 Test and 1-way analysis of variance were used to compare haplotype groups. Linear regression was performed to examine predictors of salt taste sensitivity and 24-hour urinary sodium excretion, controlling for age, gender, ethnicity, smoking status, and fungiform papillae density. RESULTS There were 42 patients with HF and their family caregivers (age, 64.6 ± 13.4 years, 46.5% male, 97.7% white, and 90.7% nonsmoker). Pronine-alanine-valine homozygous haplotype predicted lower urinary sodium excretion (b = -1780.59, t41 = -2.18, P = .036), but genotype was not a significant predictor of salt taste sensitivity. CONCLUSIONS The results of our study partially supported our hypothesis that PAV homozygous haplotype predicts 24-hour urinary sodium excretion. With our small sample size, more research is needed. Understanding genetic influences on taste can lead to development of educational interventions tailored to patients with HF and their family caregivers to better support dietary adherence.
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Huggins LG, Koehler AV, Schunack B, Inpankaew T, Traub RJ. A Host-Specific Blocking Primer Combined with Optimal DNA Extraction Improves the Detection Capability of a Metabarcoding Protocol for Canine Vector-Borne Bacteria. Pathogens 2020; 9:E258. [PMID: 32244645 PMCID: PMC7238069 DOI: 10.3390/pathogens9040258] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Bacterial canine vector-borne diseases are responsible for some of the most life-threatening conditions of dogs in the tropics and are typically poorly researched with some presenting a zoonotic risk to cohabiting people. Next-generation sequencing based methodologies have been demonstrated to accurately characterise a diverse range of vector-borne bacteria in dogs, whilst also proving to be more sensitive than conventional PCR techniques. We report two improvements to a previously developed metabarcoding tool that increased the sensitivity and diversity of vector-borne bacteria detected from canine blood. Firstly, we developed and tested a canine-specific blocking primer that prevents cross-reactivity of bacterial primer amplification on abundant canine mitochondrial sequences. Use of our blocking primer increased the number of canine vector-borne infections detected (five more Ehrlichia canis and three more Anaplasma platys infections) and increased the diversity of bacterial sequences found. Secondly, the DNA extraction kit employed can have a significant effect on the bacterial community characterised. Therefore, we compared four different DNA extraction kits finding the Qiagen DNeasy Blood and Tissue Kit to be superior for detection of blood-borne bacteria, identifying nine more A. platys, two more E. canis, one more Mycoplasma haemocanis infection and more putative bacterial pathogens than the lowest performing kit.
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Affiliation(s)
- Lucas G. Huggins
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
| | - Anson V. Koehler
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
| | | | - Tawin Inpankaew
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
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10
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Oeser C, Pond M, Butcher P, Bedford Russell A, Henneke P, Laing K, Planche T, Heath PT, Harris K. PCR for the detection of pathogens in neonatal early onset sepsis. PLoS One 2020; 15:e0226817. [PMID: 31978082 PMCID: PMC6980546 DOI: 10.1371/journal.pone.0226817] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/05/2019] [Indexed: 11/21/2022] Open
Abstract
Background A large proportion of neonates are treated for presumed bacterial sepsis with broad spectrum antibiotics even though their blood cultures subsequently show no growth. This study aimed to investigate PCR-based methods to identify pathogens not detected by conventional culture. Methods Whole blood samples of 208 neonates with suspected early onset sepsis were tested using a panel of multiplexed bacterial PCRs targeting Streptococcus pneumoniae, Streptococcus agalactiae (GBS), Staphylococcus aureus, Streptococcus pyogenes (GAS), Enterobacteriaceae, Enterococcus faecalis, Enterococcus faecium, Ureaplasma parvum, Ureaplasma urealyticum, Mycoplasma hominis and Mycoplasma genitalium, a 16S rRNA gene broad-range PCR and a multiplexed PCR for Candida spp. Results Two-hundred and eight samples were processed. In five of those samples, organisms were detected by conventional culture; all of those were also identified by PCR. PCR detected bacteria in 91 (45%) of the 203 samples that did not show bacterial growth in culture. S. aureus, Enterobacteriaceae and S. pneumoniae were the most frequently detected pathogens. A higher bacterial load detected by PCR was correlated positively with the number of clinical signs at presentation. Conclusion Real-time PCR has the potential to be a valuable additional tool for the diagnosis of neonatal sepsis.
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Affiliation(s)
- Clarissa Oeser
- Paediatric Infectious Diseases, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
- * E-mail:
| | - Marcus Pond
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Philip Butcher
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | | | - Philipp Henneke
- Pediatric Infectious Disease and Rheumatology, University Medical Center Freiburg, Freiburg, Germany
| | - Ken Laing
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Timothy Planche
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Paul T. Heath
- Paediatric Infectious Diseases, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Kathryn Harris
- Microbiology, Virology and Infection Control, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
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11
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Domínguez-Vigil IG, Barajas-Olmos VH, Gallardo-Alvarado L, Pérez-Maya AA, Garza-Rodríguez ML, Magallanes-Garza GI, Cardona-Huerta S, Méndez-Lozano DH, Vidal-Gutiérrez O, Cantú De León DF, Barrera-Saldaña HA. Comparison of Automated and Manual DNA Isolation Methods of Liquid-Based Cytology Samples. Biopreserv Biobank 2019; 17:591-597. [PMID: 31556699 PMCID: PMC6921247 DOI: 10.1089/bio.2018.0148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Liquid-based cytology (LBC) has been used as a diagnostic tool for cervical cancer for years and is now being adopted for other gynecological cancers. LBC represents an important challenge to ensure that the process yields representative biospecimens for quality control (QC) of diagnostic procedures. In this study, we compare QC parameters (integrity, yield and purity, and polymerase chain reaction [PCR] amplification) of DNA isolated from LBC (N = 296) using two different nucleic acid isolation methods, manual (n = 233) or automated (n = 63). We also evaluated two different types of cytological brushes for sampling from the cervix. Our results suggest that manual isolation (yield 22.81 ± 1.92 μg) resulted in increased DNA recovery when compared with automated isolation (yield 9.96 ± 1.11 μg) from LBC samples, with a p-value of <0.0003. We estimated that 98% (53/54) of the samples preserved the integrity of DNA and were suitable for standard molecular biology analyses. The β-globin gene was amplified in 100% (296/296) of the DNA samples by endpoint PCR. We found no significant difference between the performance of the cytological brushes (p value of <0.6711) in a general overview. However, when looking at the results from using each brush individually, the manual isolation method was statistically superior to the automated method. Our work illustrates the impact of good QC of preanalytic conditions, which will be important for the application of LBC for developing early detection methods for gynecological cancers.
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Affiliation(s)
- Irma G Domínguez-Vigil
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, Mexico.,Laboratory for Translational Research, Rudy L. Ruggles Biomedical Research Institute, Western Connecticut Health Network, Danbury, Connecticut
| | - Víctor H Barajas-Olmos
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, Mexico
| | - Lenny Gallardo-Alvarado
- Subdireccion de Investigación Clínica, Instituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Antonio A Pérez-Maya
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, Mexico
| | - Maria L Garza-Rodríguez
- Servicio de Oncología, Hospital Universitario "Dr. José Eleuterio González," Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | | | | | | | - Oscar Vidal-Gutiérrez
- Servicio de Oncología, Hospital Universitario "Dr. José Eleuterio González," Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - David F Cantú De León
- Subdireccion de Investigación Clínica, Instituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Hugo A Barrera-Saldaña
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, NL, Mexico.,Mexican Biobanks Network at Vitagénesis, SA.,National Laboratory of Specialized Services of Research, Development, and Innovation for Chemical and Biotechnological Drugs at Innbiogem, SC, Monterrey, Mexico
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12
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Kovacs Z, Jung I, Csernak E, Szentirmay Z, Banias L, Rigmanyi G, Gurzu S. DNA extraction from paraffin embedded colorectal carcinoma samples: A comparison study of manual vs automated methods, using four commercially kits. World J Clin Oncol 2019; 10:307-317. [PMID: 31572667 PMCID: PMC6766462 DOI: 10.5306/wjco.v10.i9.307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 08/19/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Nucleic acid isolation from formalin-fixed, paraffin-embedded tissue (FFPET) samples is a daily routine in molecular pathology laboratories, but extraction from FFPET is not always easily achieved. Choosing the right extraction technique is key for further examinations.
AIM To compare the performance of four commercially available kits used for DNA extraction in routine practice.
METHODS DNA isolation was performed on 46 randomly selected formalin-fixed, paraffin-embedded (FFPE) colorectal adenocarcinoma (CRC) surgical specimens. Four commercially available extraction kits were used: two for manual DNA extraction (the PureLink Genomic DNA Mini Kit from Invitrogen and the High Pure FFPE DNA Isolation Kit from Roche) and two for automated DNA extraction (the iPrep Genomic DNA Kit from Invitrogen and the MagnaPure LC DNA Isolation Kit from Roche). The DNA concentration and quality (odds ratio) among the four systems were compared. The results were correlated with the clinicopathological aspects of CRC cases: age, gender, localization, macro- and microscopic features, lymph node metastases, and the lymph node ratio.
RESULTS The highest DNA concentration was obtained using the manual kits: 157.24 ± 62.99 ng/µL for the PureLink Genomic DNA Mini Kit and 86.64 ng/µL ± 43.84 for the High Pure FFPE DNA Isolation Kit (P < 0.0001). Lower concentrations were obtained with automated systems: 20.39 ± 21.19 ng/µL for the MagnaPure LC DNA Isolation Kit and 8.722 ± 6.408 ng/µL for the iPrep Genomic DNA Kit, with differences between the systems used (P < 0.0001). The comparison between age, gender, tumor localization, pT or pN stage and the lymph node ratio indicated no statistically significant difference in DNA concentration using any of the nucleic acid isolation kits. DNA concentration was influenced by the macroscopic features and grade of differentiation. A higher DNA concentration was obtained for well-differentiated polypoid colorectal adenocarcinomas (CRCs), compared with undifferentiated ulcero-infiltrative carcinomas, irrespective of the kit used.
CONCLUSION For research or diagnosis that needs high DNA concentrations, manual methods of DNA isolation should be used. A higher amount of DNA can be obtained from polypoid-type differentiated CRCs. Automated systems confer comfort and a lower amount of DNA that is, however, sufficient for classic polymerase chain reaction (PCR) and real-time quantitative PCR molecular examinations. All four commercially available kits can be successfully used in daily practice.
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Affiliation(s)
- Zsolt Kovacs
- Department of Pathology, University of Medicine, Pharmacy, Sciences and Technology, Targu-Mures 530149, Romania
| | - Ioan Jung
- Department of Pathology, University of Medicine, Pharmacy, Sciences and Technology, Targu-Mures 530149, Romania
| | | | | | - Laura Banias
- Department of Pathology, University of Medicine, Pharmacy, Sciences and Technology, Targu-Mures 530149, Romania
| | - Genoveva Rigmanyi
- Research Center (CCAMF), University of Medicine, Pharmacy, Sciences and Technology, Targu-Mures 540139, Romania
| | - Simona Gurzu
- Department of Pathology, University of Medicine, Pharmacy, Sciences and Technology, Targu-Mures 530149, Romania
- Research Center (CCAMF), University of Medicine, Pharmacy, Sciences and Technology, Targu-Mures 540139, Romania
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13
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Automated Platform for Rapid and Reproducible Sample Preparations in Point-of-Care(POC) Molecular Diagnostics. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3304-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Brassard D, Geissler M, Descarreaux M, Tremblay D, Daoud J, Clime L, Mounier M, Charlebois D, Veres T. Extraction of nucleic acids from blood: unveiling the potential of active pneumatic pumping in centrifugal microfluidics for integration and automation of sample preparation processes. LAB ON A CHIP 2019; 19:1941-1952. [PMID: 30997461 DOI: 10.1039/c9lc00276f] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This paper describes the development of an on-chip nucleic acid (NA) extraction assay from whole blood using a centrifugal microfluidic platform that allows for pneumatic actuation of liquids during rotation. The combination of pneumatic and centrifugal forces makes it possible to perform fluidic operations without the need for integrating active control elements on the microfluidic cartridge. The cartridge is fabricated from thermoplastic polymers (e.g., Zeonor 1060R) and features a simple design that is compatible with injection molding. In addition, the cartridge is interfaced with two external vials for off-chip storage of the blood sample and retrieval of the eluted NA solution, respectively. On-chip capture of NAs is performed using an embedded solid-phase extraction matrix composed of commercial glass microfiber filters (Whatman GF/D and GF/F). The yield of the automated, on-chip extraction protocol, determined by measuring absorbance at 260 nm, is comparable to some of the best manually operated kits (e.g., Qiagen QIAamp DNA Mini Kit) while providing low assay-to-assay variability due to the high level of control provided by the platform for each processing step. The A260/A280 and A260/A230 ratios of the absorbance spectra also reveal that protein contamination of the sample is negligible. The capability of the pneumatic platform to circulate air flux through the microfluidic conduit was used to dry leftover ethanol residues retained in the capture matrix during washing. This method, applied in combination with localized heating, proved effective for reducing ethanol contamination in eluted samples from ∼12% to 1% (v/v).
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Affiliation(s)
- Daniel Brassard
- National Research Council of Canada, Life Sciences Division, 75 de Mortagne Boulevard, Boucherville, QC J4B 6Y4, Canada.
| | - Matthias Geissler
- National Research Council of Canada, Life Sciences Division, 75 de Mortagne Boulevard, Boucherville, QC J4B 6Y4, Canada.
| | - Marianne Descarreaux
- National Research Council of Canada, Life Sciences Division, 75 de Mortagne Boulevard, Boucherville, QC J4B 6Y4, Canada. and Department of Biology, Université de Sherbrooke, 2500 de l'Université Boulevard, Sherbrooke, QC J1K 2R1, Canada and Canadian Space Agency, 6767 Route de l'Aéroport, Saint-Hubert, QC J3Y 8Y9, Canada
| | - Dominic Tremblay
- National Research Council of Canada, Life Sciences Division, 75 de Mortagne Boulevard, Boucherville, QC J4B 6Y4, Canada. and Canadian Space Agency, 6767 Route de l'Aéroport, Saint-Hubert, QC J3Y 8Y9, Canada and Centre hospitalier universitaire de Sherbrooke and Department of Medicine, Centre de recherche clinique, Université de Sherbrooke, 3001 12th Avenue North, Sherbrooke, QC J1H 5N4, Canada
| | - Jamal Daoud
- National Research Council of Canada, Life Sciences Division, 75 de Mortagne Boulevard, Boucherville, QC J4B 6Y4, Canada.
| | - Liviu Clime
- National Research Council of Canada, Life Sciences Division, 75 de Mortagne Boulevard, Boucherville, QC J4B 6Y4, Canada.
| | - Maxence Mounier
- National Research Council of Canada, Life Sciences Division, 75 de Mortagne Boulevard, Boucherville, QC J4B 6Y4, Canada.
| | - Denis Charlebois
- Canadian Space Agency, 6767 Route de l'Aéroport, Saint-Hubert, QC J3Y 8Y9, Canada
| | - Teodor Veres
- National Research Council of Canada, Life Sciences Division, 75 de Mortagne Boulevard, Boucherville, QC J4B 6Y4, Canada. and Department of Biomedical Engineering, McGill University, 3775 University Street, Montreal, QC H3A 2B4, Canada
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15
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Mardan-Nik M, Saffar Soflaei S, Biabangard-Zak A, Asghari M, Saljoughian S, Tajbakhsh A, Meshkat Z, Ferns GA, Pasdar A, Ghayour-Mobarhan M. A method for improving the efficiency of DNA extraction from clotted blood samples. J Clin Lab Anal 2019; 33:e22892. [PMID: 31074532 PMCID: PMC6642314 DOI: 10.1002/jcla.22892] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 02/16/2019] [Accepted: 03/12/2019] [Indexed: 01/18/2023] Open
Abstract
Background The efficient and rapid extraction of high‐quality genomic DNA from clotted blood samples, which normally have a low yield and poor quality, is an important factor in genomic research. The objective of this study was to develop a simple and safe technique for dispersing the blood clots by the ball bearing metal shots. Normally, such clot samples may not have an acceptable yield by conventional DNA extraction methods. Also, in the present study, we have further investigated to improve salting‐out DNA extraction methods. Methods Initially, 500 µL phosphate‐buffered saline (PBS) (1×) and two ball bearing metal shots were added to each tube of the clotted blood sample and then were gently rotated in an electric laboratory rotator for 1 hour at room temperature (18‐25°C). Genomic DNA was then extracted from samples using a modified salting‐out method and a modified QIAamp® DNA Blood Midi Kit and was compared with QIAamp® DNA Blood Midi Kit as a control. An assessment of the concentration and quality of the extracted DNA was performed using the UV‐visible spectrophotometer. The isolated DNA proved amenable to PCR amplification and gel electrophoresis. Results The yield and purity of DNA obtained by these three methods were significantly different (P < 0.001), with a higher yield in the modified salting‐out method. Conclusions Our proposed modified salting‐out method is simple and efficient for the isolation of DNA from old blood clot samples. It is both easy to use and is of low cost in routine laboratory tasks.
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Affiliation(s)
- Maryam Mardan-Nik
- Cardiovascular Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sara Saffar Soflaei
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Modern Sciences & Technology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atefeh Biabangard-Zak
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahla Asghari
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sania Saljoughian
- Department of Modern Sciences & Technology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Tajbakhsh
- Department of Modern Sciences & Technology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Meshkat
- Department of Microbiology and Virology, Antimicrobial Resistance Research Center, Bu Ali Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Division of Medical Education, Brighton & Sussex Medical School, Brighton, UK
| | - Alireza Pasdar
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK.,Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Ghayour-Mobarhan
- Biochemistry of Nutrition Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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16
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Zhang Y, Lee DYS, Farwin A, Ying JY. Sieve-through vertical flow platform for efficient liquid exchange in particle-based assays. Anal Chim Acta 2019; 1051:94-102. [DOI: 10.1016/j.aca.2018.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 12/28/2022]
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17
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Hulsen T, Jamuar SS, Moody AR, Karnes JH, Varga O, Hedensted S, Spreafico R, Hafler DA, McKinney EF. From Big Data to Precision Medicine. Front Med (Lausanne) 2019; 6:34. [PMID: 30881956 PMCID: PMC6405506 DOI: 10.3389/fmed.2019.00034] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 02/04/2019] [Indexed: 02/05/2023] Open
Abstract
For over a decade the term "Big data" has been used to describe the rapid increase in volume, variety and velocity of information available, not just in medical research but in almost every aspect of our lives. As scientists, we now have the capacity to rapidly generate, store and analyse data that, only a few years ago, would have taken many years to compile. However, "Big data" no longer means what it once did. The term has expanded and now refers not to just large data volume, but to our increasing ability to analyse and interpret those data. Tautologies such as "data analytics" and "data science" have emerged to describe approaches to the volume of available information as it grows ever larger. New methods dedicated to improving data collection, storage, cleaning, processing and interpretation continue to be developed, although not always by, or for, medical researchers. Exploiting new tools to extract meaning from large volume information has the potential to drive real change in clinical practice, from personalized therapy and intelligent drug design to population screening and electronic health record mining. As ever, where new technology promises "Big Advances," significant challenges remain. Here we discuss both the opportunities and challenges posed to biomedical research by our increasing ability to tackle large datasets. Important challenges include the need for standardization of data content, format, and clinical definitions, a heightened need for collaborative networks with sharing of both data and expertise and, perhaps most importantly, a need to reconsider how and when analytic methodology is taught to medical researchers. We also set "Big data" analytics in context: recent advances may appear to promise a revolution, sweeping away conventional approaches to medical science. However, their real promise lies in their synergy with, not replacement of, classical hypothesis-driven methods. The generation of novel, data-driven hypotheses based on interpretable models will always require stringent validation and experimental testing. Thus, hypothesis-generating research founded on large datasets adds to, rather than replaces, traditional hypothesis driven science. Each can benefit from the other and it is through using both that we can improve clinical practice.
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Affiliation(s)
- Tim Hulsen
- Department of Professional Health Solutions and Services, Philips Research, Eindhoven, Netherlands
- *Correspondence: Tim Hulsen
| | - Saumya S. Jamuar
- Department of Paediatrics, KK Women's and Children's Hospital, and Paediatric Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Alan R. Moody
- Department of Medical Imaging, University of Toronto, Toronto, ON, Canada
| | - Jason H. Karnes
- Pharmacy Practice and Science, College of Pharmacy, University of Arizona Health Sciences, Phoenix, AZ, United States
| | - Orsolya Varga
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Stine Hedensted
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - David A. Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, United States
| | - Eoin F. McKinney
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Eoin F. McKinney
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18
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Porter BW, Venkatappa TK. Uncloaking an ancient adversary: Can pathogen biomarker elicitors play a role in confirming extrapulmonary TB and latent TB infection? Tuberculosis (Edinb) 2018; 113:30-37. [PMID: 30514511 DOI: 10.1016/j.tube.2018.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/07/2018] [Accepted: 08/29/2018] [Indexed: 10/28/2022]
Abstract
Latent tuberculosis infection (LTBI) is diagnosed immunologically using the Mantoux tuberculin skin test (TST) or interferon-gamma release assays (IGRAs). While widely used, immunodiagnostics can produce false negative or false positive results. Pathogen biomarkers provide an alternative, but direct detection in LTBI and extrapulmonary TB cases is challenging. Mycobacterium tuberculosis grows slowly, has limited hematogenous movement, is protected by a lipid rich cell wall, and produces low levels of secreted factors. Here we discuss the potential of elicitors by first considering pathogen markers that may be released following the administration of isoniazid. Isoniazid targets the cell wall of mycobacteria found in extracellular compartments and within monocytes, macrophages, dendritic cells, and lymphatic endothelial cells. Isoniazid's dual-purpose potential as an antibiotic and elicitor is supported by knowledge of latent infection dynamics, time-kill kinetics, and new detection techniques. Within hours, the bactericidal action of isoniazid likely enriches plasma with M. tuberculosis DNA, RNA, proteins/peptides, and lipids. Undoubtedly a portion of these biomarkers are eliminated as some bacilli undergo phagocytosis and lysosomal destruction. However, advances in immunoprecipitation and nucleic acid amplification, combined with the use of larger blood volumes during assay development, may overcome these losses. Other anticipated challenges include determining optimal sample collection times and designing diagnostic workflows that minimize processing-associated marker loss and degradation. Conventional, commercial, and emerging technologies that address these variables are discussed. If realized, isoniazid associated markers could provide proof of concept for novel elicitor-based diagnostic approaches capable of confirming LTBI and empirically treated extrapulmonary TB.
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Affiliation(s)
- Brad W Porter
- Independent Researcher; P.O. Box 56224, Atlanta, GA 30343, USA.
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19
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A simple, rapid and economic manual method for human sperm DNA extraction in genetic and epigenetic studies. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2018. [DOI: 10.1016/j.mefs.2017.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Impact of Preanalytical Handling and Timing for Peripheral Blood Mononuclear Cells Isolation and RNA Studies: The Experience of the Interinstitutional Multidisciplinary BioBank (BioBIM). Int J Biol Markers 2018; 27:e90-8. [PMID: 22562396 DOI: 10.5301/jbm.2012.9235] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2012] [Indexed: 02/04/2023]
Abstract
Multicenter studies and biobanking projects require blood transportation from the participating center to a central collection or diagnostic laboratory. The impact of time delays between venous blood collection and peripheral blood mononuclear cells (PBMC) isolation prior to RNA extraction may affect the quality and quantity of isolated nucleic acids for genomic applications. Thus, standard operating procedure (SOP) optimization for the treatment of biological samples before RNA extraction is crucial in a biological repository. In order to define SOPs for whole blood preservation prior to RNA extraction, we sought to determine whether different blood storage times (0, 3, 6, 10, 24, and 30 hours) prior to PBMCs isolation and storage at –80°C, could affect the quality and quantity of extracted RNA. After spectrophotometric quantification, the quality and integrity of RNA were assessed by agarose gel electrophoresis, RNA integrity number and real time-PCR (RT-PCR). Across the different time points we did not observe significant differences within the first 24 hours of blood storage at room temperature, while a significant loss in RNA yield and integrity was detected between 24 and 30 hours. We conclude that time delays before PBMCs isolation prior to RNA extraction may have a significant impact on downstream molecular biological applications.
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Das S, Rundell MS, Mirza AH, Pingle MR, Shigyo K, Garrison AR, Paragas J, Smith SK, Olson VA, Larone DH, Spitzer ED, Barany F, Golightly LM. A Multiplex PCR/LDR Assay for the Simultaneous Identification of Category A Infectious Pathogens: Agents of Viral Hemorrhagic Fever and Variola Virus. PLoS One 2015; 10:e0138484. [PMID: 26381398 PMCID: PMC4575071 DOI: 10.1371/journal.pone.0138484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 08/30/2015] [Indexed: 02/04/2023] Open
Abstract
CDC designated category A infectious agents pose a major risk to national security and require special action for public health preparedness. They include viruses that cause viral hemorrhagic fever (VHF) syndrome as well as variola virus, the agent of smallpox. VHF is characterized by hemorrhage and fever with multi-organ failure leading to high morbidity and mortality. Smallpox, a prior scourge, has been eradicated for decades, making it a particularly serious threat if released nefariously in the essentially non-immune world population. Early detection of the causative agents, and the ability to distinguish them from other pathogens, is essential to contain outbreaks, implement proper control measures, and prevent morbidity and mortality. We have developed a multiplex detection assay that uses several species-specific PCR primers to generate amplicons from multiple pathogens; these are then targeted in a ligase detection reaction (LDR). The resultant fluorescently-labeled ligation products are detected on a universal array enabling simultaneous identification of the pathogens. The assay was evaluated on 32 different isolates associated with VHF (ebolavirus, marburgvirus, Crimean Congo hemorrhagic fever virus, Lassa fever virus, Rift Valley fever virus, Dengue virus, and Yellow fever virus) as well as variola virus and vaccinia virus (the agent of smallpox and its vaccine strain, respectively). The assay was able to detect all viruses tested, including 8 sequences representative of different variola virus strains from the CDC repository. It does not cross react with other emerging zoonoses such as monkeypox virus or cowpox virus, or six flaviviruses tested (St. Louis encephalitis virus, Murray Valley encephalitis virus, Powassan virus, Tick-borne encephalitis virus, West Nile virus and Japanese encephalitis virus).
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Affiliation(s)
- Sanchita Das
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Mark S. Rundell
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aashiq H. Mirza
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Maneesh R. Pingle
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Kristi Shigyo
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aura R. Garrison
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Jason Paragas
- Integrated Research Facility, Division of Clinical Research, NIAID, NIH, Fort Detrick, Maryland, United States of America
| | - Scott K. Smith
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Victoria A. Olson
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Davise H. Larone
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, United States of America
| | - Eric D. Spitzer
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, New York, United States of America
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Linnie M. Golightly
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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22
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Adams NM, Bordelon H, Wang KKA, Albert LE, Wright DW, Haselton FR. Comparison of three magnetic bead surface functionalities for RNA extraction and detection. ACS APPLIED MATERIALS & INTERFACES 2015; 7:6062-9. [PMID: 25710198 DOI: 10.1021/am506374t] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Magnetic beads are convenient for extracting nucleic acid biomarkers from biological samples prior to molecular detection. These beads are available with a variety of surface functionalities designed to capture particular subsets of RNA. We hypothesized that bead surface functionality affects binding kinetics, processing simplicity, and compatibility with molecular detection strategies. In this report, three magnetic bead surface chemistries designed to bind nucleic acids, silica, oligo (dT), and a specific oligonucleotide sequence were evaluated. Commercially available silica-coated and oligo (dT) beads, as well as beads functionalized with oligonucleotides complementary to respiratory syncytial virus (RSV) nucleocapsid gene, respectively recovered ∼75, ∼71, and ∼7% target RSV mRNA after a 1 min of incubation time in a surrogate patient sample spiked with the target. RSV-specific beads required much longer incubation times to recover amounts of the target comparable to the other beads (∼77% at 180 min). As expected, silica-coated beads extracted total RNA, oligo (dT) beads selectively extracted total mRNA, and RSV-specific beads selectively extracted RSV N gene mRNA. The choice of bead functionality is generally dependent on the target detection strategy. The silica-coated beads are most suitable for applications that require nucleic acids other than mRNA, especially with detection strategies that are tolerant of a high concentration of nontarget background nucleic acids, such as RT-PCR. On the other hand, oligo (dT) beads are best-suited for mRNA targets, as they bind biomarkers rapidly, have relatively high recovery, and enable detection strategies to be performed directly on the bead surface. Sequence-specific beads may be best for applications that are not tolerant of a high concentration of nontarget nucleic acids that require short RNA sequences without poly(A) tails, such as microRNAs, or that perform RNA detection directly on the bead surface.
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Affiliation(s)
- Nicholas M Adams
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Hali Bordelon
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Kwo-Kwang A Wang
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Laura E Albert
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - David W Wright
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Frederick R Haselton
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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Psifidi A, Dovas CI, Bramis G, Lazou T, Russel CL, Arsenos G, Banos G. Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples. PLoS One 2015; 10:e0115960. [PMID: 25635817 PMCID: PMC4312062 DOI: 10.1371/journal.pone.0115960] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/28/2014] [Indexed: 12/21/2022] Open
Abstract
Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.
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Affiliation(s)
- Androniki Psifidi
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Chrysostomos I. Dovas
- Microbiology and Infectious Diseases Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Bramis
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Thomai Lazou
- Food safety Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Claire L. Russel
- Department of Clinical Veterinary Sciences, University of Bristol, Langford House, Langford, Bristol, United Kingdom
| | - Georgios Arsenos
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Banos
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Scotland’s Rural College, Edinburgh, United Kingdom
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24
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Kalmár A, Péterfia B, Wichmann B, Patai ÁV, Barták BK, Nagy ZB, Furi I, Tulassay Z, Molnár B. Comparison of Automated and Manual DNA Isolation Methods for DNA Methylation Analysis of Biopsy, Fresh Frozen, and Formalin-Fixed, Paraffin-Embedded Colorectal Cancer Samples. ACTA ACUST UNITED AC 2015; 20:642-51. [PMID: 25576093 DOI: 10.1177/2211068214565903] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 12/18/2022]
Abstract
Automated DNA isolation can decrease hands-on time in routine pathology. Our aim was to apply automated DNA isolation and perform DNA methylation analyses. DNA isolation was performed manually from fresh frozen (CRC = 10, normal = 10) specimens and colonic biopsies (CRC = 10, healthy = 10) with QIAamp DNA Mini Kit and from FFPE blocks (CRC = 10, normal = 10) with QIAamp DNA FFPET Kit. Automated DNA isolation was performed with MagNA Pure DNA and Viral NA SV kit on MagNA Pure 96 system. DNA methylation of MAL, SFRP1, and SFRP2 were analyzed with methylation-specific high-resolution melting analysis. Yield of automatically isolated samples was equal in fresh frozens and significantly lower compared to manually isolated biopsy and FFPE samples. OD260/280 of fresh frozen and biopsy samples were similar after both isolations, automated isolation resulted in lower purity in FFPE samples. Both protocols resulted in similar OD260/230 from fresh frozens, automated isolation method was superior in biopsies and manual protocol in FFPE samples. DNA methylation of biopsies, fresh frozen samples were highly similar after both methods, results of automatically and manually isolated FFPE samples were different. Automated DNA isolation from fresh frozen samples can be suitable for high-throughput laboratories.
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Affiliation(s)
- Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Barbara K Barták
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Zsófia B Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - István Furi
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Zsolt Tulassay
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Béla Molnár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
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25
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Fisher KE, Smith GH, Neill SG, Rossi MR. Section I: integrating laboratory medicine with tissue specimens. Curr Probl Cancer 2014; 38:144-58. [PMID: 25239562 DOI: 10.1016/j.currproblcancer.2014.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Jeong TD, Cho YU, Lee W, Chun S, Min WK. An efficient genomic DNA extraction from whole blood using Nextractor. Clin Chim Acta 2014; 435:14-7. [DOI: 10.1016/j.cca.2014.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/15/2014] [Accepted: 04/15/2014] [Indexed: 11/26/2022]
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Palmirotta R, De Marchis ML, Ludovici G, Ferroni P, Abete P, Guadagni F, Della-Morte D. Diagnostic procedures for paraffin-embedded tissues analysis in pharmacogenomic studies. Methods Mol Biol 2014; 1175:45-65. [PMID: 25150866 DOI: 10.1007/978-1-4939-0956-8_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this book chapter we report our own experience of mutational analysis in selecting tailored anticancer treatments for solid tumors. Our Department of Advanced Biotechnologies and Bioimaging, IRCCS San Raffaele Pisana, Rome, Italy, routinely performs pharmacogenetic screenings for different genes such as K-ras, BRAF, KIT, PDGFRα, and EGFR on paraffin-embedded cancer sections. Therefore, the chapter describes the mutational analysis procedures on paraffin-embedded tumors aimed to predict individual response to anticancer therapy. These molecular diagnostic methodologies may help us in improving the translational impact of genetic information on clinical practice.
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Affiliation(s)
- Raffaele Palmirotta
- Department of Advanced Biotechnologies and Bioimaging, IRCCS San Raffaele Pisana, Rome, Italy
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Holmberg RC, Gindlesperger A, Stokes T, Brady D, Thakore N, Belgrader P, Cooney CG, Chandler DP. High-throughput, automated extraction of DNA and RNA from clinical samples using TruTip technology on common liquid handling robots. J Vis Exp 2013:e50356. [PMID: 23793016 DOI: 10.3791/50356] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
TruTip is a simple nucleic acid extraction technology whereby a porous, monolithic binding matrix is inserted into a pipette tip. The geometry of the monolith can be adapted for specific pipette tips ranging in volume from 1.0 to 5.0 ml. The large porosity of the monolith enables viscous or complex samples to readily pass through it with minimal fluidic backpressure. Bi-directional flow maximizes residence time between the monolith and sample, and enables large sample volumes to be processed within a single TruTip. The fundamental steps, irrespective of sample volume or TruTip geometry, include cell lysis, nucleic acid binding to the inner pores of the TruTip monolith, washing away unbound sample components and lysis buffers, and eluting purified and concentrated nucleic acids into an appropriate buffer. The attributes and adaptability of TruTip are demonstrated in three automated clinical sample processing protocols using an Eppendorf epMotion 5070, Hamilton STAR and STARplus liquid handling robots, including RNA isolation from nasopharyngeal aspirate, genomic DNA isolation from whole blood, and fetal DNA extraction and enrichment from large volumes of maternal plasma (respectively).
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29
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Lang PO, Govind S, Dramé M, Aspinall R. Comparison of manual and automated DNA purification for measuring TREC in dried blood spot (DBS) samples with qPCR. J Immunol Methods 2012; 384:118-27. [DOI: 10.1016/j.jim.2012.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 07/24/2012] [Accepted: 07/24/2012] [Indexed: 12/16/2022]
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30
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Ndlovu BG, Danaviah S, Moodley E, Ghebremichael M, Bland R, Viljoen J, Newell ML, Ndung'u T, Carr WH. Use of dried blood spots for the determination of genetic variation of interleukin-10, killer immunoglobulin-like receptor and HLA class I genes. TISSUE ANTIGENS 2012; 79:114-22. [PMID: 22107032 PMCID: PMC3253194 DOI: 10.1111/j.1399-0039.2011.01807.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Optimal methods for using dried blood spots (DBSs) for population genetics-based studies have not been well established. Using DBS stored for 8 years from 21 pregnant South African women, we evaluated three methods of gDNA extraction with and without whole-genome amplification (WGA) to characterize immune-related genes: interleukin-10 (IL-10), killer immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) class I. We found that the QIAamp DNA mini kit yielded the highest gDNA quality (P< 0.05; Wilcoxon signed rank test) with sufficient yield for subsequent analyses. In contrast, we found that WGA was not reliable for sequence-specific primer polymerase chain reaction (SSP-PCR) analysis of KIR2DL1, KIR2DS1, KIR2DL5 and KIR2DL3 or high-resolution HLA genotyping using a sequence-based approach. We speculate that unequal template amplification by WGA underrepresents gene repertoires determined by sequence-based approaches.
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Affiliation(s)
- B G Ndlovu
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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Frégeau CJ, De Moors A. Competition for DNA binding sites using Promega DNA IQ™ paramagnetic beads. Forensic Sci Int Genet 2012; 6:511-22. [PMID: 22264505 DOI: 10.1016/j.fsigen.2011.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 10/21/2011] [Accepted: 12/14/2011] [Indexed: 11/25/2022]
Abstract
The Promega DNA IQ™ system is easily amenable to automation and has been an integral part of standard operating procedures for many forensic laboratories including those of the Royal Canadian Mounted Police (RCMP) since 2004. Due to some failure to extract DNA from samples that should have produced DNA using our validated automated DNA IQ™-based protocol, the competition for binding sites on the DNA IQ™ magnetic beads was more closely examined. Heme from heavily blooded samples interfered slightly with DNA binding. Increasing the concentration of Proteinase K during lysis of these samples did not enhance DNA recovery. However, diluting the sample lysate following lysis prior to DNA extraction overcame the reduction in DNA yield and preserved portions of the lysates for subsequent manual or automated extraction. Dye/chemicals from black denim lysates competed for binding sites on the DNA IQ™ beads and significantly reduced DNA recovery. Increasing the size or number of black denim cuttings during lysis had a direct adverse effect on DNA yield from various blood volumes. The dilution approach was successful on these samples and permitted the extraction of high DNA yields. Alternatively, shortening the incubation time for cell lysis to 30 min instead of the usual overnight at 56 °C prevented competition from black denim dye/chemicals and increased DNA yields.
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Affiliation(s)
- Chantal J Frégeau
- Royal Canadian Mounted Police, National Services and Research, 1200 Vanier Parkway, Ottawa, Ontario K1G 3M8, Canada.
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Boesenberg-Smith KA, Pessarakli MM, Wolk DM. Assessment of DNA Yield and Purity: an Overlooked Detail of PCR Troubleshooting. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.clinmicnews.2011.12.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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33
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Khokhar SK, Mitui M, Leos NK, Rogers BB, Park JY. Evaluation of Maxwell® 16 for automated DNA extraction from whole blood and formalin-fixed paraffin embedded (FFPE) tissue. Clin Chem Lab Med 2011; 50:267-72. [PMID: 22022984 DOI: 10.1515/cclm.2011.763] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 10/05/2011] [Indexed: 11/15/2022]
Abstract
BACKGROUND The aim of the study was to assess the performance of Promega, Maxwell® 16 for the extraction of genomic DNA from whole blood and FFPE tissue. METHODS DNA was extracted from 10 whole blood and 10 FFPE specimens using six different commercial kits. RESULTS For whole blood, the mean DNA concentration obtained by Maxwell® 16 was significantly greater than either easyMAG® (p<0.0001) or QIAamp® Blood DNA kit (p<0.001). For FFPE, the mean DNA concentration obtained by the AllPrep® FFPE specific DNA/RNA kit was significantly greater than either the Maxwell® 16 (p<0.0001) or the general AllPrep® DNA/RNA kit (p<0.0001). CONCLUSIONS Comparative evaluation of the six DNA extraction kits indicated that the semi-automated Maxwell® 16 was superior for whole blood extraction while the manual AllPrep® FFPE DNA/RNA kit (Qiagen) performed better for FFPE DNA extraction in terms of quantity of DNA obtained. All six extraction methods (blood and FFPE) performed well in terms of purity. Although there were variances in the quantity of DNA obtained, there were no significant differences in the efficiency of these methods in yielding amplifiable DNA extracts, as demonstrated by β-actin for whole blood specimens. In evaluation of FFPE DNA extraction methods, the Qiagen AllPrep® FFPE DNA/RNA Mini Kit was the best for applications requiring larger amplicons, but for smaller amplicons the Maxwell was most consistent.
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34
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Update on the Detection and Characterization of Bacterial Pathogens by Nucleic Acid Amplification. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Real time-PCR assay estimating the naive T-cell pool in whole blood and dried blood spot samples: Pilot study in young adults. J Immunol Methods 2011; 369:133-40. [DOI: 10.1016/j.jim.2011.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 05/10/2011] [Indexed: 11/21/2022]
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Stangegaard M, Frøslev TG, Frank-Hansen R, Hansen AJ, Morling N. Automated Extraction of DNA from Blood and PCR Setup using a Tecan Freedom EVO Liquid Handler for Forensic Genetic STR Typing of Reference Samples. ACTA ACUST UNITED AC 2011; 16:134-40. [DOI: 10.1016/j.jala.2010.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Indexed: 10/18/2022]
Abstract
We have implemented and validated automated protocols for DNA extraction and PCR setup using a Tecan Freedom EVO liquid handler mounted with the Te-MagS magnetic separation device (Tecan, Mannedorf, Switzerland). The protocols were validated for accredited forensic genetic work according to ISO 17025 using the Qiagen MagAttract DNA Mini M48 kit (Qiagen GmbH, Hilden, Germany) from fresh whole blood and blood from deceased individuals. The workflow was simplified by returning the DNA extracts to the original tubes minimizing the risk of misplacing samples. The tubes that originally contained the samples were washed with MilliQ water before the return of the DNA extracts. The PCR was setup in 96-well microtiter plates. The methods were validated for the kits: AmpFSTR Identifier, SGM Plus and Yfiler (Applied Biosystems, Foster City, CA), GenePrint FFFL and PowerPlex Y (Promega, Madison, Wl). The automated protocols allowed for extraction and addition of PCR master mix of 96 samples within 3.5 h. In conclusion, we demonstrated that (1) DNA extraction with magnetic beads and (2) PCR setup for accredited, forensic genetic short tandem repeat typing can be implemented on a simple automated liquid handler leading to the reduction of manual work, and increased quality and throughput.
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Affiliation(s)
- Michael Stangegaard
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tobias G. Frøslev
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rune Frank-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders J. Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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Venkatesh M, Flores A, Luna RA, Versalovic J. Molecular microbiological methods in the diagnosis of neonatal sepsis. Expert Rev Anti Infect Ther 2011; 8:1037-48. [PMID: 20818947 DOI: 10.1586/eri.10.89] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Neonatal sepsis is a major cause of neonatal mortality and morbidity. The current gold standard for diagnosis of sepsis, namely blood culture, suffers from low sensitivity and a reporting delay of approximately 48-72 h. Rapid detection of sepsis and institution of antimicrobial therapy may improve patient outcomes. Rapid and sensitive tests that can inform clinicians regarding the institution or optimization of antimicrobial therapy are urgently needed. The ideal diagnostic test should have adequate specificity and negative predictive value to reliably exclude sepsis and avoid unnecessary antibiotic therapy. We comprehensively searched for neonatal studies that evaluated molecular methods for diagnosis of sepsis. We identified 19 studies that were assessed with respect to assay methodology and diagnostic characteristics. In addition, we also reviewed newer molecular microbiological assays of relevance that have not been fully evaluated in neonates. Molecular methods offer distinct advantages over blood cultures, including increased sensitivity and rapid diagnosis. However, diagnostic accuracy and cost-effectiveness should be established before implementation in clinical practice.
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Affiliation(s)
- Mohan Venkatesh
- Section of Neonatology, Department of Pediatrics, Texas Children's Hospital & Baylor College of Medicine, 6621 Fannin St, Houston, TX 77030, USA.
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Palmirotta R, Ludovici G, De Marchis ML, Savonarola A, Leone B, Spila A, De Angelis F, Morte DD, Ferroni P, Guadagni F. Preanalytical Procedures for DNA Studies: The Experience of the Interinstitutional Multidisciplinary BioBank (BioBIM). Biopreserv Biobank 2011; 9:35-45. [DOI: 10.1089/bio.2010.0027] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Raffaele Palmirotta
- Laboratory of Molecular Diagnostics, Department of Laboratory Medicine & Advanced Biotechnologies, Institute of Care and Scientific Research San Raffaele Pisana, Rome, Italy
| | - Giorgia Ludovici
- Laboratory of Molecular Diagnostics, Department of Laboratory Medicine & Advanced Biotechnologies, Institute of Care and Scientific Research San Raffaele Pisana, Rome, Italy
| | - Maria Laura De Marchis
- Laboratory of Molecular Diagnostics, Department of Laboratory Medicine & Advanced Biotechnologies, Institute of Care and Scientific Research San Raffaele Pisana, Rome, Italy
| | - Annalisa Savonarola
- Laboratory of Molecular Diagnostics, Department of Laboratory Medicine & Advanced Biotechnologies, Institute of Care and Scientific Research San Raffaele Pisana, Rome, Italy
| | - Barbara Leone
- Laboratory of Molecular Diagnostics, Department of Laboratory Medicine & Advanced Biotechnologies, Institute of Care and Scientific Research San Raffaele Pisana, Rome, Italy
| | - Antonella Spila
- Interinstitutional Multidisciplinary BioBank (BioBIM), Department of Laboratory Medicine & Advanced Biotechnologies, Institute of Care and Scientific Research San Raffaele Pisana, Rome, Italy
| | - Francesco De Angelis
- Interinstitutional Multidisciplinary BioBank (BioBIM), Department of Laboratory Medicine & Advanced Biotechnologies, Institute of Care and Scientific Research San Raffaele Pisana, Rome, Italy
| | - David Della Morte
- Interinstitutional Multidisciplinary BioBank (BioBIM), Department of Laboratory Medicine & Advanced Biotechnologies, Institute of Care and Scientific Research San Raffaele Pisana, Rome, Italy
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Patrizia Ferroni
- Laboratory of Thrombosis and Hemostasis, Department of Laboratory Medicine & Advanced Biotechnologies, Institute of Care and Scientific Research San Raffaele Pisana, Rome, Italy
| | - Fiorella Guadagni
- Interinstitutional Multidisciplinary BioBank (BioBIM), Department of Laboratory Medicine & Advanced Biotechnologies, Institute of Care and Scientific Research San Raffaele Pisana, Rome, Italy
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Broutian TR, He X, Gillison ML. Automated high throughput DNA isolation for detection of human papillomavirus in oral rinse samples. J Clin Virol 2011; 50:270-5. [PMID: 21273118 DOI: 10.1016/j.jcv.2010.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 12/08/2010] [Accepted: 12/14/2010] [Indexed: 12/18/2022]
Abstract
BACKGROUND Oral HPV infection elevates risk of oropharyngeal cancer, but its natural history is unknown. Natural history studies necessitate validation of an automated, high-throughput method for HPV genomic DNA detection in oral rinse samples (ORS). OBJECTIVES To compare agreement of oral HPV detection in ORS processed by a magnetic-bead based automated platform to a previous gold-standard, manual protein-precipitation method. Agreement was compared to that of repeat sampling and repeat HPV testing. STUDY DESIGN HIV-infected individuals (n=100) provided two ORS collected 15 min apart. DNA was isolated from equal aliquots by either a protein-precipitation based (Puregene, Qiagen) or magnetic bead-based (QIAsymphony™ SP, Qiagen) method. HPV DNA was detected and type-specified by consensus primer PCR and reverse line blot hybridization. The kappa statistic was used to assess overall agreement (OA) and agreement on a positive test (Ps+). RESULTS The DNA purification methods had very high agreement for categorizing an individual as HPV infected (OA=0.95; Ps+=0.94) as well as for detection of HPV type-specific infection (OA=0.99; Ps+=0.88) in ORS. Agreement for detection of HPV type-specific infection was greater than that observed with repeat oral rinse sampling (OA=0.99, Ps+=0.76) but comparable to inter-assay agreement (OA=1.00, Ps+=0.90). CONCLUSIONS HPV detection in ORS processed with a magnetic-bead based automated platform will facilitate large natural history studies of oral HPV infection necessary to evaluate the potential use of oral HPV detection in oral cancer screening.
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Affiliation(s)
- Tatevik R Broutian
- Viral Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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Park BG, Ja Park A, Choi JH, Park J, Kim SS, Wang JS, Kee MK, Choi JY. Development of candidate reference reagent for HIV-1 RNA and comparison analysis for different HIV-1 RNA quantitative assay. Clin Chem Lab Med 2011; 49:1519-24. [DOI: 10.1515/cclm.2011.231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Lay MLJ, Lucas RM, Ratnamohan M, Taylor J, Ponsonby AL, Dwyer DE. Measurement of Epstein-Barr virus DNA load using a novel quantification standard containing two EBV DNA targets and SYBR Green I dye. Virol J 2010; 7:252. [PMID: 20860842 PMCID: PMC2958162 DOI: 10.1186/1743-422x-7-252] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 09/22/2010] [Indexed: 12/15/2022] Open
Abstract
Background Reactivation of Epstein-Barr virus (EBV) infection may cause serious, life-threatening complications in immunocompromised individuals. EBV DNA is often detected in EBV-associated disease states, with viral load believed to be a reflection of virus activity. Two separate real-time quantitative polymerase chain reaction (QPCR) assays using SYBR Green I dye and a single quantification standard containing two EBV genes, Epstein-Barr nuclear antigen-1 (EBNA-1) and BamHI fragment H rightward open reading frame-1 (BHRF-1), were developed to detect and measure absolute EBV DNA load in patients with various EBV-associated diseases. EBV DNA loads and viral capsid antigen (VCA) IgG antibody titres were also quantified on a population sample. Results EBV DNA was measurable in ethylenediaminetetraacetic acid (EDTA) whole blood, peripheral blood mononuclear cells (PBMCs), plasma and cerebrospinal fluid (CSF) samples. EBV DNA loads were detectable from 8.0 × 102 to 1.3 × 108 copies/ml in post-transplant lymphoproliferative disease (n = 5), 1.5 × 103 to 2.0 × 105 copies/ml in infectious mononucleosis (n = 7), 7.5 × 104 to 1.1 × 105 copies/ml in EBV-associated haemophagocytic syndrome (n = 1), 2.0 × 102 to 5.6 × 103 copies/ml in HIV-infected patients (n = 12), and 2.0 × 102 to 9.1 × 104 copies/ml in the population sample (n = 218). EBNA-1 and BHRF-1 DNA were detected in 11.0% and 21.6% of the population sample respectively. There was a modest correlation between VCA IgG antibody titre and BHRF-1 DNA load (rho = 0.13, p = 0.05) but not EBNA-1 DNA load (rho = 0.11, p = 0.11). Conclusion Two sensitive and specific real-time PCR assays using SYBR Green I dye and a single quantification standard containing two EBV DNA targets, were developed for the detection and measurement of EBV DNA load in a variety of clinical samples. These assays have application in the investigation of EBV-related illnesses in immunocompromised individuals.
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Affiliation(s)
- Meav-Lang J Lay
- Virology Department, Centre For Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Institute Road, Westmead Hospital, Westmead 2145, New South Wales, Australia.
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A comparison of six methods for genomic DNA extraction suitable for PCR-based genotyping applications using ovine milk samples. Mol Cell Probes 2010; 24:93-8. [DOI: 10.1016/j.mcp.2009.11.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 10/01/2009] [Accepted: 11/02/2009] [Indexed: 11/19/2022]
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Lee JH, Park Y, Choi JR, Lee EK, Kim HS. Comparisons of three automated systems for genomic DNA extraction in a clinical diagnostic laboratory. Yonsei Med J 2010; 51:104-10. [PMID: 20046522 PMCID: PMC2799962 DOI: 10.3349/ymj.2010.51.1.104] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 07/14/2009] [Accepted: 07/14/2009] [Indexed: 01/12/2023] Open
Abstract
PURPOSE The extraction of nucleic acid is initially a limiting step for successful molecular-based diagnostic workup. This study aims to compare the effectiveness of three automated DNA extraction systems for clinical laboratory use. MATERIALS AND METHODS Venous blood samples from 22 healthy volunteers were analyzed using QIAamp Blood Mini Kit (Qiagen), MagNA Pure LC Nucleic Acid Isolation Kit I (Roche), and Magtration-Magnazorb DNA common kit-200N (PSS). The concentration of extracted DNAs was measured by NanoDrop ND-1000 (PeqLab). Also, extracted DNAs were confirmed by applying in direct agarose gel electrophoresis and were amplified by polymerase chain reaction (PCR) for human beta-globin gene. RESULTS The corrected concentrations of extracted DNAs were 25.42 +/- 8.82 ng/microL (13.49-52.85 ng/microL) by QIAamp Blood Mini Kit (Qiagen), and 22.65 +/- 14.49 ng/microL (19.18-93.39 ng/microL) by MagNA Pure LC Nucleic Acid Isolation Kit I, and 22.35 +/- 6.47 ng/microL (12.57-35.08 ng/microL) by Magtration-Magnazorb DNA common kit-200N (PSS). No statistically significant difference was noticed among the three commercial kits (p > 0.05). Only the mean value of DNA purity through PSS was slightly lower than others. All the extracted DNAs were successfully identified in direct agarose gel electrophoresis. And all the product of beta-globin gene PCR showed a reproducible pattern of bands. CONCLUSION The effectiveness of the three automated extraction systems is of an equivalent level and good enough to produce reasonable results. Each laboratory could select the automated system according to its clinical and laboratory conditions.
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Affiliation(s)
- Jong-Han Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Yongjung Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Kyung Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Hyon-Suk Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
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Bechlian D, Honstettre A, Terrier M, Brest C, Malenfant C, Mozziconacci MJ, Chabannon C. RNA extracted from blood samples with a rapid automated procedure is fit for molecular diagnosis or minimal residual disease monitoring in patients with a variety of malignant blood disorders. Biopreserv Biobank 2009; 7:123-8. [PMID: 24835684 DOI: 10.1089/bio.2009.0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Scientific studies in oncology, cancer diagnosis, and monitoring tumor response to therapeutics currently rely on a growing number of clinico-pathological information. These often include molecular analyses. The quality of these analyses depends on both pre-analytical and analytical information and often includes the extraction of DNA and/or RNA from human tissues and cells. The quality and quantity of obtained nucleic acids are of utmost importance. The use of automated techniques presents several advantages over manual techniques, such as reducing technical time and thus cost, and facilitating standardization. The purpose of this study was to validate an automated technique for RNA extraction from cells of patients treated for various malignant blood diseases. A well-established manual technique was compared to an automated technique, in order to extract RNA from blood samples drawn for the molecular diagnosis of a variety of leukemic diseases or monitoring of minimal residual disease. The quality of the RNA was evaluated by real-time quantitative RT-PCR (RQ-PCR) analyses of the Abelson gene transcript. The results show that both techniques produce RNA with comparable quality and quantity, thus suggesting that an automated technique can be substituted for the reference and manual technique used in the daily routine of a molecular pathology laboratory involved in minimal residual disease monitoring. Increased costs of reagents and disposables used for automated techniques can be compensated by a decrease in human resource.
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Affiliation(s)
- Didier Bechlian
- Institut Paoli-Calmettes, Biothèque, Tumorothèque, Centre de Ressources Biologiques en Oncologie, Marseille, France. , Réseau des Centres de Ressources Biologiques et Tumorothèques de l'Agglomération Marseillaise, Marseille, France
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He J, Kraft AJ, Fan J, Van Dyke M, Wang L, Bose ME, Khanna M, Metallo JA, Henrickson KJ. Simultaneous Detection of CDC Category "A" DNA and RNA Bioterrorism Agents by Use of Multiplex PCR & RT-PCR Enzyme Hybridization Assays. Viruses 2009; 1:441-459. [PMID: 20224751 PMCID: PMC2836126 DOI: 10.3390/v1030441] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 09/22/2009] [Accepted: 10/20/2009] [Indexed: 11/16/2022] Open
Abstract
Assays to simultaneously detect multiple potential agents of bioterrorism are limited. Two multiplex PCR and RT-PCR enzyme hybridization assays (mPCR-EHA, mRT-PCR-EHA) were developed to simultaneously detect many of the CDC category "A" bioterrorism agents. The "Bio T" DNA assay was developed to detect: Variola major (VM), Bacillus anthracis (BA), Yersinia pestis (YP), Francisella tularensis (FT) and Varicella zoster virus (VZV). The "Bio T" RNA assay (mRT-PCR-EHA) was developed to detect: Ebola virus (Ebola), Lassa fever virus (Lassa), Rift Valley fever (RVF), Hantavirus Sin Nombre species (HSN) and dengue virus (serotypes 1-4). Sensitivity and specificity of the 2 assays were tested by using genomic DNA, recombinant plasmid positive controls, RNA transcripts controls, surrogate (spiked) clinical samples and common respiratory pathogens. The analytical sensitivity (limit of detection (LOD)) of the DNA asssay for genomic DNA was 1x10(0)~1x10(2) copies/mL for BA, FT and YP. The LOD for VZV whole organism was 1x10(-2) TCID(50)/mL. The LOD for recombinant controls ranged from 1x10(2)~1x10(3)copies/mL for BA, FT, YP and VM. The RNA assay demonstrated LOD for RNA transcript controls of 1x10(4)~1x10(6) copies/mL without extraction and 1x10(5)~1x10(6) copies/mL with extraction for Ebola, RVF, Lassa and HSN. The LOD for dengue whole organisms was ~1x10(-4) dilution for dengue 1 and 2, 1x10(4) LD(50)/mL and 1x10(2) LD(50)/mL for dengue 3 and 4. The LOD without extraction for recombinant plasmid DNA controls was ~1x10(3) copies/mL (1.5 input copies/reaction) for Ebola, RVF, Lassa and HSN. No cross-reactivity of primers and probes used in both assays was detected with common respiratory pathogens or between targeted analytes. Clinical sensitivity was estimated using 264 surrogate clinical samples tested with the BioT DNA assay and 549 samples tested with the BioT RNA assay. The clinical specificity is 99.6% and 99.8% for BioT DNA assay and BioT RNA assay, respectively. The surrogate sensitivities of these two assays were 100% (95%CI 83-100) for FT, BA (pX02), YP, VM, VZV, dengue 2,3,4 and 95% (95%CI 75-100) for BA (pX01) and dengue 1 using spiked clinical specimens. The specificity of both BioT multiplex assays on spiked specimens was 100% (95% CI 99-100). Compared to other available assays (culture, serology, PCR, etc.) both the BioT DNA mPCR-EHA and BioT RNA mRT-PCR-EHA are rapid, sensitive and specific assays for detecting many category "A" Bioterrorism agents using a standard thermocycler.
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Affiliation(s)
- Jie He
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Andrea J. Kraft
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Jiang Fan
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Meredith Van Dyke
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Lihua Wang
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Michael E. Bose
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Marilyn Khanna
- National Institutes of Health, Bethesda, MD 20892-7616, USA; E-Mail: (M.K.)
| | - Jacob A. Metallo
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
| | - Kelly J. Henrickson
- Department of Pediatric, Medical College of Wisconsin, Milwaukee, WI 53226, USA; E-Mails: (J.H.); (A.J.K.); (J.F.); (M.V.D.); (L.W.); (M.E.B.); (J.A.M.)
- Children’s Research Institute, Children’s Hospital of Wisconsin, P.O. Box 1997, Milwaukee, WI 53201-1997, USA
- Children’s Hospital of Wisconsin, P.O. Box 1997, Milwaukee, WI 53201-1997, USA
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Evaluation of automated nucleic acid extraction methods for virus detection in a multicenter comparative trial. J Virol Methods 2009; 155:87-90. [DOI: 10.1016/j.jviromet.2008.09.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 09/15/2008] [Accepted: 09/25/2008] [Indexed: 11/19/2022]
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Abstract
The polymerase chain reaction (PCR) technique has become an indispensable method in molecular research. However, PCR-amplification of GC-rich templates is often hampered by the formation of secondary structures like hairpins and higher melting temperatures. We present a novel method termed 'Slowdown PCR', which allows the successful PCR-amplification of extremely GC-rich (>83%) DNA targets. The protocol relies on the addition of 7-deaza-2'-deoxyguanosine, a dGTP analog to the PCR mixture and a novel standardized cycling protocol with varying temperatures. The latter consists of a generally lowered ramp rate of 2.5 degrees C s(-1) and a low cooling rate of 1.5 degrees C s(-1) for reaching an annealing temperature and is run for 48 cycles. We established this protocol as a versatile method not only for amplification of extremely GC-rich regions, but also for routine DNA diagnostics and pharmacogenetics for templates with different annealing temperatures. The protocol takes 5 h to complete.
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Dundas N, Leos NK, Mitui M, Revell P, Rogers BB. Comparison of automated nucleic acid extraction methods with manual extraction. J Mol Diagn 2008; 10:311-6. [PMID: 18556770 DOI: 10.2353/jmoldx.2008.070149] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Automated nucleic acid extractors can improve workflow and decrease variability in the clinical laboratory. We evaluated Qiagen EZ1 (Valencia, CA) and bioMérieux (Durham, NC) easyMAG extractors compared with Qiagen manual extraction using targets and matrices commonly available in the clinical laboratory. Pooled samples were spiked with various organisms, serially diluted, and extracted in duplicate. The organisms/matrices were Bordetella pertussis/bronchoalveolar lavage, herpes simplex virus II/cerebrospinal fluid, coxsackievirus A9/cerebrospinal fluid, BK virus/plasma, and Mycoplasma pneumoniae/endotracheal tube samples. Extracts were amplified in duplicate using real-time PCR assays, and amplification of the target at a cycle threshold of 35 using the manual method was used for comparison. Amplification efficiency of nucleic acids extracted by automated methods was similar to that by the manual method except for a loss of efficiency for M. pneumoniae in endotracheal tube samples. The EZ1 viral kit 2.0 gave better results for coxsackievirus A9 than the EZ1 viral kit version 1.0. At the lowest limit of detection (past a cycle threshold of 35), the easyMAG was more likely to produce amplifiable nucleic acid than were either the EZ1 or manual extraction. Operational complexity, defined as the number of manipulations required to obtain an extracted sample, was the lowest for the easyMAG. The easyMAG was the most expensive of the methods, followed by the EZ1 kit and manual extraction.
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Affiliation(s)
- Nicola Dundas
- Department of Pathology, Children's Medical Center, 1935 Motor Street, Dallas, TX 75235, USA
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