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Yilmaz E, Baghban N, Soylak M. Solid-Phase Extraction (SPE) of Salmon Sperm DNA Using a Polyaniline@Molybdenum(IV) Sulfide@Multiwalled Carbon Nanotubes (MWCNTs) Nanocomposite with Spectrophotometric Detection. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2139835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Erkan Yilmaz
- Faculty of Pharmacy, Department of Analytical Chemistry, Erciyes University, Kayseri, Turkey
- Technology Research & Application Center (ERU-TAUM), Erciyes University, Kayseri, Turkey
- ERNAM-Nanotechnology Application and Research Center, Erciyes University, Kayseri, Turkey
| | - Neda Baghban
- Faculty of Sciences, Department of Chemistry, Erciyes University, Kayseri, Turkey
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mustafa Soylak
- Technology Research & Application Center (ERU-TAUM), Erciyes University, Kayseri, Turkey
- Faculty of Sciences, Department of Chemistry, Erciyes University, Kayseri, Turkey
- Turkish Academy of Sciences (TUBA), Ankara, Turkey
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Improved DNA extraction on bamboo paper and cotton is tightly correlated with their crystallinity and hygroscopicity. PLoS One 2022; 17:e0277138. [PMID: 36342943 PMCID: PMC9639815 DOI: 10.1371/journal.pone.0277138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
DNA extraction, a vital pre-requisite for most biological studies, continues to be studied extensively. According to some studies, DNA shows a certain degree of absorbability on filter paper made of plant fiber-based adsorbent material. However, the principle underlying such specific adsorption as well as plant species associated with plant fiber-based adsorbents and optimized extraction conditions have not yet been studied. This study demonstrates the tight correlation between crystallinity and hygroscopicity in plant fiber-based adsorbents used for DNA extraction and proposes the concept of DNA adsorption on plant fiber-based adsorbents, for the first time. We also explored optimal extracting and eluting conditions and developed a novel plant fiber-based DNA extraction method that was quadruple times more powerful than current approaches. Starting with the screening of various types of earthed plant fiber-based adsorbents, we went on to mine new plant fiber-based adsorbents, bamboo paper and degreased cotton, and succeeded in increasing their efficiency of DNA extraction to 4.2 times than that of current approaches. We found a very strong correlation between the crystallinity and hygroscopicity of plant fiber-based adsorbents which showed efficiency for DNA extraction, and thus propose a principle that potentially governs such specific adsorption processes, in the hope that this information may guide related multidisciplinary research studies in the future. Nanodrop, electrophoresis and PCR were selected to demonstrate the quantity, quality, integrity and utility of the extracted DNA. Furthermore, crystallinity, hygroscopicity, pore size distribution and composition of plant fiber-based adsorbents were studied to explore their correlation in an attempt to understand the principle underlying this particular type of adsorption. The findings of this study may be further extended to the extraction of other types of nucleic acids with similar biochemical properties.
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Nauwelaerts SJD, Van Geel D, Delvoye M, De Cremer K, Bernard A, Roosens NHC, De Keersmaecker SCJ. Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva? J Biomol Tech 2021; 31:27-35. [PMID: 32042275 DOI: 10.7171/jbt.20-3101-004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic epidemiology requires an appropriate approach to measure genetic variation within the population. The aim of this study was to evaluate the characteristics and genotyping results of DNA extracted from 2 human DNA sources, selected for their rapid and noninvasive sampling, and the use of simple and standardized protocols that are essential for large-scale epidemiologic studies. Saliva and urine samples were collected at the same day from 20 subjects aged 9-10 yr. Genomic DNA was extracted using commercial kits. Quantitative and qualitative evaluation was done by assessing the yield, the purity, and integrity of the extracted DNA. As a proof-of-concept, genotyping was performed targeting CC16 A38G and uteroglobin-related protein 1 (UGRP1)-112G/A. Saliva was found to provide the highest yield and concentration of total DNA extracted. Salivary DNA showed higher purity and a significantly less degraded state compared to urinary DNA. Consequently, the salivary DNA gave better genotyping results than urinary DNA. Therefore, if the choice exists, saliva is the preferred noninvasive matrix for genotyping purposes in large-scale genetic epidemiologic studies. Only in particular cases using urine could nevertheless be considered useful, although specific limitations need to be taken into account.
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Affiliation(s)
- Sarah J D Nauwelaerts
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium.,Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Dirk Van Geel
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Maud Delvoye
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Koen De Cremer
- Platform Chromatography and Mass Spectrometry, Sciensano, 1050 Brussels, Belgium; and
| | - Alfred Bernard
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
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Kim SE, Tieu MV, Hwang SY, Lee MH. Magnetic Particles: Their Applications from Sample Preparations to Biosensing Platforms. MICROMACHINES 2020; 11:mi11030302. [PMID: 32183074 PMCID: PMC7142445 DOI: 10.3390/mi11030302] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/28/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023]
Abstract
The growing interest in magnetic materials as a universal tool has been shown by an increasing number of scientific publications regarding magnetic materials and its various applications. Substantial progress has been recently made on the synthesis of magnetic iron oxide particles in terms of size, chemical composition, and surface chemistry. In addition, surface layers of polymers, silica, biomolecules, etc., on magnetic particles, can be modified to obtain affinity to target molecules. The developed magnetic iron oxide particles have been significantly utilized for diagnostic applications, such as sample preparations and biosensing platforms, leading to the selectivity and sensitivity against target molecules and the ease of use in the sensing systems. For the process of sample preparations, the magnetic particles do assist in target isolation from biological environments, having non-specific molecules and undesired molecules. Moreover, the magnetic particles can be easily applied for various methods of biosensing devices, such as optical, electrochemical, and magnetic phenomena-based methods, and also any methods combined with microfluidic systems. Here we review the utilization of magnetic materials in the isolation/preconcentration of various molecules and cells, and their use in various techniques for diagnostic biosensors that may greatly contribute to future innovation in point-of-care and high-throughput automation systems.
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Affiliation(s)
- Seong-Eun Kim
- Human IT Convergence Research Center, Korea Electronics Technology Institute, Gyeonggi-do 13509, Korea;
| | - My Van Tieu
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Seoul 06974, Korea; (M.V.T.); (S.Y.H.)
| | - Sei Young Hwang
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Seoul 06974, Korea; (M.V.T.); (S.Y.H.)
| | - Min-Ho Lee
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Seoul 06974, Korea; (M.V.T.); (S.Y.H.)
- Correspondence: ; Tel.: +82-2-820-5503; Fax: +82-2-814-2651
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Rosenbohm JM, Robson JM, Singh R, Lee R, Zhang JY, Klapperich CM, Pollock NR, Cabodi M. Rapid electrostatic DNA enrichment for sensitive detection of Trichomonas vaginalis in clinical urinary samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:1085-1093. [PMID: 35154421 PMCID: PMC8837197 DOI: 10.1039/c9ay02478f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Estimated to be the most common non-viral sexually transmitted infection globally, Trichomonas vaginalis (TV) can lead to pelvic inflammatory disease, pregnancy complications, and increased risk of acquiring and transmitting HIV. Once diagnosed, TV infection can be treated with oral antibiotics; however, infected individuals are often asymptomatic and do not seek treatment. The WHO and others have identified a need for point-of-care tests to expand access to TV testing and screening; ideal test characteristics include high sensitivity and specificity and the ability to use urine as a sample type, rather than invasively collected swab samples. Here, we report on a proof-of-concept prototype for rapid, electrostatic enrichment of DNA from urine samples and demonstrate the use of large volumes of urine to increase sensitivity of downstream nucleic acid amplification testing. We developed an internally controlled thermophilic helicase-dependent amplification (tHDA) assay with lateral flow immunoassay readout and demonstrate that this tHDA assay can be performed directly on our DNA capture filter. We validated our method using clinical urine samples with qPCR-quantified TV loads. Using 62 clinical urine samples and a simple sample processing device, our tHDA assay displayed 96.6% sensitivity and 100% specificity. Our analytical limit of detection was found to be approximately 7 genomic equivalents of TV DNA per mL of sample when 1 mL of sample was tested, comparable to existing isothermal tests for TV. Using large-volume simulated samples (40 mL of buffered urine with spiked-in TV DNA), we also demonstrated that sensitivity could be improved 28-fold to 0.25 genomic equivalents of TV DNA per mL, with a sample processing time of only 2 minutes.
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Affiliation(s)
| | - James M. Robson
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Rishabh Singh
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Rose Lee
- Department of Laboratory Medicine (NRP) and Division of Infectious Diseases (RL), Boston Children’s Hospital, Boston, MA, USA
| | - Jane Y. Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | | | - Nira R. Pollock
- Department of Laboratory Medicine (NRP) and Division of Infectious Diseases (RL), Boston Children’s Hospital, Boston, MA, USA
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
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Identification phenotypic and genotypic characterization of biofilm formation in Escherichia coli isolated from urinary tract infections and their antibiotics resistance. BMC Res Notes 2019; 12:796. [PMID: 31805997 PMCID: PMC6896667 DOI: 10.1186/s13104-019-4825-8] [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: 08/09/2019] [Accepted: 11/26/2019] [Indexed: 01/06/2023] Open
Abstract
Objective Urinary tract infections (UTIs) are the most common infectious diseases, and Escherichia coli is the most common pathogen isolated from patients with UTIs. The products of sfa, afa and foc genes are important for binding of the bacterium to urinary tract epithelium. Our aim was to investigate these genes in E. colis isolated from patients with UTIS. The frequencies of the genes were determined using PCR. Biofilm formation and antibiotic resistance rates were determined using microtiter plate and disk diffusion methods, respectively. The P < 0.05 was considered statistically significant. Results The frequencies of sfa, afa and foc were 75.3%, 17.5% and 22.5%, respectively showing a significantly higher prevalence of the sfa gene. The most effective antibiotics against the E. colis were nitrofurantoin and amikacin. The highest microbial resistance rates were also observed against amoxicillin and ampicillin. Furthermore, 12.7%, 6.3%, 74.7% and 6.3% of the isolates showed strong, moderate, weak capacities and no connections to form biofilms, respectively. The expression of the sfa gene was significantly associated with forming strong biofilms. Regarding the variabilities in the characteristics of E. coli strains associated with UTIs, it seems reasonable to adjust diagnostic and therapeutic methods according to the regional microbial characteristics.
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Lee S, Khoo VSL, Medriano CAD, Lee T, Park SY, Bae S. Rapid and in-situ detection of fecal indicator bacteria in water using simple DNA extraction and portable loop-mediated isothermal amplification (LAMP) PCR methods. WATER RESEARCH 2019; 160:371-379. [PMID: 31163314 DOI: 10.1016/j.watres.2019.05.049] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/19/2019] [Accepted: 05/17/2019] [Indexed: 05/02/2023]
Abstract
Contamination of water by fecal matter and potential human enteric pathogens is a serious health concern. Microbiological water quality has been assessed by conventional culture-based methods of fecal indicator bacteria (FIB). Recently, molecular techniques for FIB have been introduced as alternative tools for rapid detection. However, such molecular techniques require a modern laboratory setting, expensive equipment, and skilled personnel. In this study, we developed a simple and rapid DNA extraction method based on a syringe filter without any specialized equipment. Furthermore, loop-mediated isothermal amplification (LAMP) PCR for fecal indicator bacteria (FIB) (i.e. E. coli and E. faecalis) was carried out using the DNA extracts from the syringe-filter based DNA extraction method. The efficiency of the extracted DNA from the syringe-filter based method was comparable to the results of the commercial kit method. We also tested fresh and marine-water collected directly from different locations in Singapore that were spiked with E. coli or E. faecalis. The LAMP assays combined with our DNA extraction method showed higher sensitivity and more tolerance to PCR inhibitors than that of conventional PCR methods. We further developed a portable LAMP device to conduct isothermal PCR reactions for rapid on-site measurement of FIB. As the color changes in the end point of the LAMP reaction can be observed with the naked eye, the portable LAMP device was easily operated and quick, obtaining results in 30 min. The simple, portable and user-friendly platform can be used as an initial screening for the rapid detection of the presence FIB in lower-resource settings. In conclusion, the portable LAMP device coupled with a syringe-filter based DNA extraction method enables us to detect the presence of FIB for assessing microbial water quality within 1 h without any sophisticated laboratory equipment or highly trained personnel.
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Affiliation(s)
- Seunguk Lee
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Valerie Si Ling Khoo
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | | | - Taewoo Lee
- Department of Mechanical Engineering, National University of Singapore, Singapore
| | - Sung-Yong Park
- Department of Mechanical Engineering, National University of Singapore, Singapore
| | - Sungwoo Bae
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore.
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Li P, Ning J, Luo X, Du H, Zhang Q, Zhou G, Du Q, Ou Z, Wang L, Wang Y. New method to preserve the original proportion and integrity of urinary cell-free DNA. J Clin Lab Anal 2019; 33:e22668. [PMID: 30175467 PMCID: PMC6818579 DOI: 10.1002/jcla.22668] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/01/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Due to high nuclease activity and complex contents in urine, urinary cell-free DNA (ucfDNA) was prone to degrade. So, we developed standardized urine collection tube (UCT) to prevent ucfDNA degradation and simultaneously maintain urinary cells in their original form during the sample collection process, ensuring stabilization of the original proportion and integrity of ucfDNA. METHODS Urine samples were collected from bladder cancer patients and divided into 10-mL normal tubes and 10-mL UCTs, respectively, and kept at ambient temperature. Urine supernatant was separated by centrifuging, and ucfDNA was extracted. Then ucfDNA was quantified by quantitative real-time polymerase chain reaction. UcfDNA fragments distribution was analyzed by Agilent 2200, and the frequency of specific mutations of urinary system disease was detected by next-generation sequencing method. RESULTS Urine collected into UCTs showed no statistically significant changes in their original proportion and integrity of ucfDNA up to 7 days at ambient temperature and also ucfDNA fragments were maintained well. Conversely, urine collected into normal tubes was observed an obviously decline in their original proportion of ucfDNA and ucfDNA fragments changed greatly. The △% of allele fraction (AF) for specific genes of ucfDNA from UCTs was lower than from normal tubes by 3.7-fold. CONCLUSION Using UCTs, they can maximally keep the original proportion and integrity of ucfDNA and stabilize urinary cells and minimize the background noise caused by urinary cellular DNA releasing, it will be help to open the door of next-generation noninvasive liquid biopsy applications utilizing urine.
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Affiliation(s)
- Pei Li
- XiangYa Hospital of Central South UniversityChangshaHunanChina
- Hunan UPSBio, Inc.Hunan University National Science ParkChangshaHunanChina
| | - Jun Ning
- XiangYa Hospital of Central South UniversityChangshaHunanChina
| | - Xipeng Luo
- Hunan UPSBio, Inc.Hunan University National Science ParkChangshaHunanChina
| | - Hongli Du
- School of Bioscience and BioengineeringSouth China University of TechnologyGuangzhouGuangdongChina
| | - Qing Zhang
- Hunan UPSBio, Inc.Hunan University National Science ParkChangshaHunanChina
| | - Ganlin Zhou
- Hunan UPSBio, Inc.Hunan University National Science ParkChangshaHunanChina
| | - Qiu Du
- XiangYa Hospital of Central South UniversityChangshaHunanChina
| | - Zhenyu Ou
- XiangYa Hospital of Central South UniversityChangshaHunanChina
| | - Long Wang
- XiangYa Hospital of Central South UniversityChangshaHunanChina
| | - Yu Wang
- Hunan UPSBio, Inc.Hunan University National Science ParkChangshaHunanChina
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Ghahari S, Ghahari S, Nematzadeh GA. Magnetic nano fluids for isolation of genomic DNA and total RNA from various prokaryote and eukaryote cells. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:125-134. [PMID: 30388702 DOI: 10.1016/j.jchromb.2018.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 09/24/2018] [Accepted: 10/06/2018] [Indexed: 10/28/2022]
Abstract
The correct isolation of nucleic acid from various cells is an important preliminary step before many biochemical and diagnostic processes such as cloning, sequencing, replication, hybridization, and complementary DNA (cDNA) synthesis. In this study, the coated magnetic nanoparticles (MNFs) with Tween 20 and oleic acid because of paramagnetic and bio-compatibility properties used in the extractions of genomic DNA (gDNA) and total RNA from prokaryote and eukaryote cells. The amount and accuracy of gDNA and total RNA extracted were proved via agarose gel electrophoresis, digestion and polymerase chain reaction (PCR) techniques. According to UV-Vis spectrophotometry data and gDNA and ribosomal RNA (rRNA) bands observed on the agarose gel, the results showed that extraction of this nano-kit can be comparable with the existing methods used to purifying nucleic acids such as purification based on the use of Cetyltrimethylammonium bromide (CTAB) and phenol-chloroform methods. Characterization of the particles defines them to be ~34.85 nm in diameter and exhibiting high saturation magnetization (28 emu/g). Elimination of hazardous reagents such as phenol and chloroform from extraction solutions, the replacement for inorganic coating such as silica with organic oil, and reduction of reaction time are some advantages of this method. Therefore, according to the challenges in the nucleic acid purification pathway, the use of these kits can be remarkable.
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Affiliation(s)
- Sajjad Ghahari
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Iran
| | - Somayeh Ghahari
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Iran
| | - Ghorban Ali Nematzadeh
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Iran.
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Centrifugation-free extraction of circulating nucleic acids using immiscible liquid under vacuum pressure. Sci Rep 2018; 8:5467. [PMID: 29615736 PMCID: PMC5883035 DOI: 10.1038/s41598-018-23766-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/20/2018] [Indexed: 12/11/2022] Open
Abstract
Extraction of cell-free DNA (cfDNA), which exists at an extremely low concentration in plasma, is a critical process for either targeted-sensing or massive sequencing of DNAs. However, such small amount of DNA cannot be fully obtained without high-speed centrifugation (<20,000 g). Here, we developed a centrifugation-free cfDNA extraction method and system that utilizes an immiscible solvent under single low vacuum pressure throughout the entire process. It has been named Pressure and Immiscibility-Based EXtraction (PIBEX). The amounts of extracted cfDNA by PIBEX were compared with those extracted by the conventional gold standards such as QIAGEN using quantitative PCR (qPCR). The PIBEX system showed equal performance regarding extraction amount and efficiency compared to the existing method. Because the PIBEX eliminates the troublous and repetitive centrifugation processes in DNA extraction, it can be further utilized in microfluidic-sample preparation systems for circulating nucleic acids, which would lead to an integrated sample-to-answer system in liquid biopsies.
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Nejdl L, Zelnickova J, Vaneckova T, Hynek D, Adam V, Vaculovicova M. Rapid preparation of self-assembled CdTe quantum dots used for sensing of DNA in urine. NEW J CHEM 2018. [DOI: 10.1039/c7nj05167k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this article, the authors report a systematic study of the self-assembly of CdTe quantum dots (QDs) stabilized by mercaptosuccinic acid (MSA) at laboratory temperature (25 °C) or after thermal treatment (90 °C).
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Affiliation(s)
- Lukas Nejdl
- Department of Chemistry and Biochemistry
- Mendel University in Brno
- CZ 613 00 Brno
- Czech Republic
- Central European Institute of Technology
| | - Jaroslava Zelnickova
- Department of Chemistry and Biochemistry
- Mendel University in Brno
- CZ 613 00 Brno
- Czech Republic
| | - Tereza Vaneckova
- Department of Chemistry and Biochemistry
- Mendel University in Brno
- CZ 613 00 Brno
- Czech Republic
| | - David Hynek
- Department of Chemistry and Biochemistry
- Mendel University in Brno
- CZ 613 00 Brno
- Czech Republic
- Central European Institute of Technology
| | - Vojtech Adam
- Department of Chemistry and Biochemistry
- Mendel University in Brno
- CZ 613 00 Brno
- Czech Republic
- Central European Institute of Technology
| | - Marketa Vaculovicova
- Department of Chemistry and Biochemistry
- Mendel University in Brno
- CZ 613 00 Brno
- Czech Republic
- Central European Institute of Technology
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Lee H, Choi M, Hwang SH, Cho Y. A Versatile Nanowire Platform for Highly Efficient Isolation and Direct PCR-free Colorimetric Detection of Human Papillomavirus DNA from Unprocessed Urine. Am J Cancer Res 2018; 8:399-409. [PMID: 29290816 PMCID: PMC5743556 DOI: 10.7150/thno.21696] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 08/09/2017] [Indexed: 11/05/2022] Open
Abstract
Purpose: As human papillomavirus (HPV) is primarily responsible for the development of cervical cancer, significant efforts have been devoted to develop novel strategies for detecting and identifying HPV DNA in urine. The analysis of target DNA sequences in urine offers a potential alternative to conventional methods as a non-invasive clinical screening and diagnostic assessment tool for the detection of HPV. However, the lack of efficient approaches to isolate and directly detect HPV DNA in urine has restricted its potential clinical use. In this study, we demonstrated a novel approach of using polyethylenimine-conjugated magnetic polypyrrole nanowires (PEI-mPpy NWs) for the extraction, identification, and PCR-free colorimetric detection of high-risk strains of HPV DNA sequences, particularly HPV-16 and HPV-18, in urine specimens of cervical cancer patients. Materials and Methods: We fabricated and characterized polyethylenimine-conjugated magnetic nanowires (PEI/mPpy NWs). PEI/mPpy NWs-based HPV DNA isolation and detection strategy appears to be a cost-effective and practical technology with greater sensitivity and accuracy than other urine-based methods. Results: The analytical and clinical performance of PEI-mPpy NWs was evaluated and compared with those of cervical swabs, demonstrating a superior type-specific concordance rate of 100% between urine and cervical swabs, even when using a small volume of urine (300 µL). Conclusion: We envision that PEI-mPpy NWs provide substantive evidence for clinical diagnosis and management of HPV-associated disease with their excellent performance in the recovery and detection of HPV DNA from minimal amounts of urine samples.
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Tangchaikeeree T, Polpanich D, Bentaher A, Baraket A, Errachid A, Agusti G, Elaissari A, Jangpatarapongsa K. Combination of PCR and dual nanoparticles for detection of Plasmodium falciparum. Colloids Surf B Biointerfaces 2017; 159:888-897. [DOI: 10.1016/j.colsurfb.2017.08.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/17/2017] [Accepted: 08/31/2017] [Indexed: 01/10/2023]
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Pham XH, Baek A, Kim TH, Lee SH, Rho WY, Chung WJ, Kim DE, Jun BH. Graphene Oxide Conjugated Magnetic Beads for RNA Extraction. Chem Asian J 2017; 12:1883-1888. [PMID: 28508435 DOI: 10.1002/asia.201700554] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/08/2017] [Indexed: 02/01/2023]
Abstract
A magnetic material that consists of silica-coated magnetic beads conjugated with graphene oxide (GO) was successfully prepared for facile ribonucleic acid (RNA) extraction. When the GO-modified magnetic beads were applied to separate the RNA from the lysed cell, the cellular RNAs were readily adsorbed to and readily desorbed from the surface of the GO-modified magnetic beads by urea. The amount of RNA extracted by the GO-modified magnetic beads was ≈170 % as much as those of the control extracted by a conventional phenol-based chaotropic solution. These results demonstrate that the facile method of RNA separation by using GO-modified magnetic beads as an adsorbent is an efficient and simple way to purify intact cellular RNAs and/or microRNA from cell lysates.
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Affiliation(s)
- Xuan-Hung Pham
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Ahruem Baek
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Tae Han Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Sang Hun Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 151-744, Republic of Korea
| | - Won-Yeop Rho
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Woo-Jae Chung
- Department of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 440-746, Republic of Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 143-701, Republic of Korea
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15
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He H, Li R, Chen Y, Pan P, Tong W, Dong X, Chen Y, Yu D. Integrated DNA and RNA extraction using magnetic beads from viral pathogens causing acute respiratory infections. Sci Rep 2017; 7:45199. [PMID: 28332631 PMCID: PMC5362898 DOI: 10.1038/srep45199] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/22/2017] [Indexed: 12/20/2022] Open
Abstract
Current extraction methods often extract DNA and RNA separately, and few methods are capable of co-extracting DNA and RNA from sputum. We established a nucleic acid co-extraction method from sputum based on magnetic beads and optimized the method by evaluating influencing factors, such as the guanidinium thiocyanate (GTC) and dithiothreitol (DTT) concentrations, magnetic bead amount, incubation temperature, lysis buffer pH and RNA carrier type. The feasibility of the simultaneous nucleic acid co-extraction method was evaluated by amplifying DNA and RNA viruses from a single clinical specimen with a multiplex RT-qPCR method. Both DNA and RNA were most efficiently extracted when the GTC and DTT concentrations were 2.0 M and 80 mM, respectively, 20 μl magnetic beads were added, the incubation temperature was 80 °C, the pH was 8 or 9, and RNA carrier A was used. Therefore, we established a simple method to extract nucleic acids from two important respiratory viruses compared with other commercial kits. This magnetic beads-based co-extraction method for sputum followed by a multiplex RT-qPCR can rapidly and precisely detect DNA and RNA viruses from a single clinical specimen and has many advantages, such as decreased time, low cost, and a lack of harmful chemicals.
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Affiliation(s)
- Hui He
- The Affiliated First Hospital of Hangzhou, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Pathology, Zhoushan Hospital, Zhoushan, Zhejiang Province, China
| | - Rongqun Li
- College of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yi Chen
- The Affiliated First Hospital of Hangzhou, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Clinical Laboratory, Hangzhou First People's Hospital, Hangzhou, China
| | - Ping Pan
- The Affiliated First Hospital of Hangzhou, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Clinical Laboratory, Hangzhou First People's Hospital, Hangzhou, China
| | - Wenjuan Tong
- Department of Clinical Laboratory, Hangzhou First People's Hospital, Hangzhou, China
| | - Xueyan Dong
- Department of Clinical Laboratory, Hangzhou First People's Hospital, Hangzhou, China
| | - Yueming Chen
- Department of Clinical Laboratory, Hangzhou First People's Hospital, Hangzhou, China
| | - Daojun Yu
- The Affiliated First Hospital of Hangzhou, Zhejiang Chinese Medical University, Hangzhou, China.,Department of Clinical Laboratory, Hangzhou First People's Hospital, Hangzhou, China
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16
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Lodha A, Ansari N, Shah S, Rao M, Menon SK. Isolation of PCR ready-human DNA using copper nanoparticles from skeletal remains. Forensic Sci Int 2017; 270:146-152. [DOI: 10.1016/j.forsciint.2016.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 10/24/2016] [Accepted: 12/03/2016] [Indexed: 01/28/2023]
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17
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Yan M, Liang Q, Wan W, Han Q, Tan S, Ding M. Amino acid-modified graphene oxide magnetic nanocomposite for the magnetic separation of proteins. RSC Adv 2017. [DOI: 10.1039/c7ra05114j] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A novel amino acid-modified graphene oxide magnetic nanocomposite was synthesized and successfully applied to the magnetic separation of proteins.
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Affiliation(s)
- Min Yan
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Ministry of Education
- Department of Chemistry
- Tsinghua University
- Beijing 100084
| | - Qionglin Liang
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Ministry of Education
- Department of Chemistry
- Tsinghua University
- Beijing 100084
| | - Wei Wan
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Ministry of Education
- Department of Chemistry
- Tsinghua University
- Beijing 100084
| | - Qiang Han
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Ministry of Education
- Department of Chemistry
- Tsinghua University
- Beijing 100084
| | - Siyuan Tan
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Ministry of Education
- Department of Chemistry
- Tsinghua University
- Beijing 100084
| | - Mingyu Ding
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Ministry of Education
- Department of Chemistry
- Tsinghua University
- Beijing 100084
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18
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Zhou Z, Irudayaraj J. A native chromatin extraction method based on salicylic acid coated magnetic nanoparticles and characterization of chromatin. Analyst 2015; 140:938-44. [PMID: 25475154 DOI: 10.1039/c4an01897d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Native chromatin contains valuable genetic, epigenetic and structural information. Though DNA and nucleosome structures are well defined, less is known about the higher-order chromatin structure. Traditional chromatin extraction methods involve fixation, fragmentation and centrifugation, which might distort the higher-order structural information of native chromatin. We present a simple approach to isolate native chromatin from cultured mammalian cells using salicylic acid coated magnetic nanoparticles (SAMNPs). Chromatin is magnetically separated from cell lysates without any filtration or high-speed centrifugation. The purified chromatin is suitable for the examination of histone modifications and other chromatin associated proteins as confirmed by western blotting analysis. The structure of chromatin was determined by confocal fluorescence microscopy, transmission electron microscopy (TEM) and atomic force microscopy (AFM). High-resolution AFM and TEM images clearly show a classical bead-on-a-string structure. The higher-order chromatin structure is also determined via electron microscopy. Our method provides a simple, inexpensive and an environmentally friendly means to extract native chromatin not possible before, suitable for both biochemical and structural analysis.
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Affiliation(s)
- Zhongwu Zhou
- Bindley Bioscience Center and Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA.
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19
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Zhou Z, Cho IIH, Shan Z, Irudayaraj J. Cross-platform detection of epigenetic modifications from extracted chromatin in leucocytes from blood. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.ancr.2015.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Hashemi E, Akhavan O, Shamsara M, Valimehr S, Rahighi R. DNA and RNA extractions from eukaryotic and prokaryotic cells by graphene nanoplatelets. RSC Adv 2014. [DOI: 10.1039/c4ra11458b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Gong R, Li S. Extraction of human genomic DNA from whole blood using a magnetic microsphere method. Int J Nanomedicine 2014; 9:3781-9. [PMID: 25143727 PMCID: PMC4134021 DOI: 10.2147/ijn.s59545] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
With the rapid development of molecular biology and the life sciences, magnetic extraction is a simple, automatic, and highly efficient method for separating biological molecules, performing immunoassays, and other applications. Human blood is an ideal source of human genomic DNA. Extracting genomic DNA by traditional methods is time‐consuming, and phenol and chloroform are toxic reagents that endanger health. Therefore, it is necessary to find a more convenient and efficient method for obtaining human genomic DNA. In this study, we developed urea–formaldehyde resin magnetic microspheres and magnetic silica microspheres for extraction of human genomic DNA. First, a magnetic microsphere suspension was prepared and used to extract genomic DNA from fresh whole blood, frozen blood, dried blood, and trace blood. Second, DNA content and purity were measured by agarose electrophoresis and ultraviolet spectrophotometry. The human genomic DNA extracted from whole blood was then subjected to polymerase chain reaction analysis to further confirm its quality. The results of this study lay a good foundation for future research and development of a high‐throughput and rapid extraction method for extracting genomic DNA from various types of blood samples.
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Affiliation(s)
- Rui Gong
- Pharmaceutical Department, The Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Shengying Li
- Clinical Laboratory, Tianjin Children's Hospital, Tianjin, People's Republic of China
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22
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Wierucka M, Biziuk M. Application of magnetic nanoparticles for magnetic solid-phase extraction in preparing biological, environmental and food samples. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.04.007] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Pershina AG, Sazonov AE, Filimonov VD. Magnetic nanoparticles–DNA interactions: design and applications of nanobiohybrid systems. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n04abeh004412] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Sun N, Deng C, Zhao X, Zhou Q, Ge G, Liu Y, Yan W, Xia Q. Extraction of total nucleic acid based on silica-coated magnetic particles for RT-qPCR detection of plant RNA virus/viroid. J Virol Methods 2014; 196:204-11. [DOI: 10.1016/j.jviromet.2013.11.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/16/2013] [Accepted: 11/20/2013] [Indexed: 10/26/2022]
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25
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Zhou Z, Kadam U, Irudayaraj J. One-stop genomic DNA extraction by salicylic acid-coated magnetic nanoparticles. Anal Biochem 2013; 442:249-52. [PMID: 23911528 PMCID: PMC4281273 DOI: 10.1016/j.ab.2013.07.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/18/2013] [Accepted: 07/19/2013] [Indexed: 11/29/2022]
Abstract
Salicylic acid-coated magnetic nanoparticles were prepared via a modified one-step synthesis and used for a one-stop extraction of genomic DNA from mammalian cells. The synthesized magnetic particles were used for magnetic separation of cells from the media by nonspecific binding of the particles as well as extraction of genomic DNA from the lysate. The quantity and quality were confirmed by agarose gel electrophoresis and polymerase chain reaction. The entire process of extraction and isolation can be completed within 30 min. Compared with traditional methods based on centrifugation and filtration, the established method is fast, simple, reliable, and environmentally friendly.
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Affiliation(s)
- Zhongwu Zhou
- Bindley Bioscience Center, Purdue University, West Lafayette, IN47906, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47906, USA
| | - Ulhas Kadam
- Bindley Bioscience Center, Purdue University, West Lafayette, IN47906, USA
| | - Joseph Irudayaraj
- Bindley Bioscience Center, Purdue University, West Lafayette, IN47906, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47906, USA
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26
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Abstract
The use of genetic information to guide medication decisions holds great promise to improve therapeutic outcomes through increased efficacy and reduced adverse events. As in many areas of medicine, pediatric research and clinical implementation in pharmacogenetics lag behind corresponding adult discovery and clinical applications. In adults, genotype-guided clinical decision support for medications such as clopidogrel, warfarin and simvastatin are in use in some medical centers. However, research conducted in pediatric populations demonstrates that the models and practices developed in adults may be inaccurate in children, and some applications lack any pediatric research to guide clinical decisions. To account for additional factors introduced by developmental considerations in pediatric populations and provide pediatric patients with maximal benefit from genotype-guided therapy, the field will need to develop and employ creative solutions. In this article, we detail some concerns about research and clinical implementation of pharmacogenetics in pediatrics, and present potential mechanisms for addressing them.
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Affiliation(s)
- Sara L Van Driest
- Department of Pediatrics, Vanderbilt University, 2200 Children's Way, Nashville, TN 37232, USA ; The Monroe Carell Jr Children's Hospital at Vanderbilt, 8232 DOT, 2200 Children's Way, Nashville, TN 37232, USA
| | - Tracy L McGregor
- Department of Pediatrics, Vanderbilt University, 2200 Children's Way, Nashville, TN 37232, USA ; The Monroe Carell Jr Children's Hospital at Vanderbilt, 8232 DOT, 2200 Children's Way, Nashville, TN 37232, USA ; The Center for Human Genetics Research, 519 Light Hall, 2215 Garland Avenue, Nashville, TN 37232-0700, USA
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27
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Abstract
The use of genetic information to guide medication decisions holds great promise to improve therapeutic outcomes through increased efficacy and reduced adverse events. As in many areas of medicine, pediatric research and clinical implementation in pharmacogenetics lag behind corresponding adult discovery and clinical applications. In adults, genotype-guided clinical decision support for medications such as clopidogrel, warfarin and simvastatin are in use in some medical centers. However, research conducted in pediatric populations demonstrates that the models and practices developed in adults may be inaccurate in children, and some applications lack any pediatric research to guide clinical decisions. To account for additional factors introduced by developmental considerations in pediatric populations and provide pediatric patients with maximal benefit from genotype-guided therapy, the field will need to develop and employ creative solutions. In this article, we detail some concerns about research and clinical implementation of pharmacogenetics in pediatrics, and present potential mechanisms for addressing them.
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Affiliation(s)
- Sara L Van Driest
- Department of Pediatrics, Vanderbilt University, 2200 Children’s Way, Nashville, TN 37232, USA
- The Monroe Carell Jr Children’s Hospital at Vanderbilt, 8232 DOT, 2200 Children’s Way, Nashville, TN 37232, USA
| | - Tracy L McGregor
- Department of Pediatrics, Vanderbilt University, 2200 Children’s Way, Nashville, TN 37232, USA
- The Monroe Carell Jr Children’s Hospital at Vanderbilt, 8232 DOT, 2200 Children’s Way, Nashville, TN 37232, USA
- The Center for Human Genetics Research, 519 Light Hall, 2215 Garland Avenue, Nashville, TN 37232-0700, USA
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28
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Rittich B, Španová A. SPE and purification of DNA using magnetic particles. J Sep Sci 2013; 36:2472-85. [DOI: 10.1002/jssc.201300331] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Bohuslav Rittich
- Faculty of Chemistry; Brno University of Technology; Brno Czech Republic
| | - Alena Španová
- Faculty of Chemistry; Brno University of Technology; Brno Czech Republic
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