1
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Okamura H, Yamano H, Tsuda T, Morihiro J, Hirayama K, Nagano H. Development of a clinical microarray system for genetic analysis screening. Pract Lab Med 2022; 33:e00306. [PMID: 36593945 PMCID: PMC9803787 DOI: 10.1016/j.plabm.2022.e00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Objectives Research on the relationship between diseases and genes and the advancement of genetic analysis technologies have made genetic testing in medical care possible. There are various methods for genetic testing, including PCR-based methods and next-generation sequencing; however, screening tests in clinical laboratories are becoming more diverse; therefore, novel measurement systems and equipment are required to meet the needs of each situation. In this study, we aimed to develop a novel microarray-based genetic analysis system that uses a Peltier element to overcome the issues of conventional microarrays, such as the long measurement time and high cost. Methods We constructed a microarray system to detect the UDP-glucuronosyltransferase gene polymorphisms UGT1A1*6 and UGT1A1*28 in patients eligible for irinotecan hydrochloride treatment for use in clinical laboratories. To evaluate the performance of the system, the hybridization temperature and reaction time were determined, and the results were compared with those obtained using a conventional hybridization oven. Results The hybridization temperature reached its target in 1/27th of the time required by the conventional system. We assessed 111 human clinical samples and found that our results agreed with those obtained using existing methods. The total time for the newly developed device was reduced by 85 min compared to that for existing methods, as the automated DNA microarray eliminates the time that existing methods spend on manual operation. Conclusions The surface treatment technology used in our system enables high-density and strong DNA fixation, allowing the construction of a measurement system suitable for clinical applications.
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Affiliation(s)
- Hiroshi Okamura
- Toyo Kohan Co., Ltd., Shinagawa, Tokyo, Japan,Corresponding author. Toyo Kohan Co., Ltd., Japan.
| | | | | | | | | | - Hiroaki Nagano
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
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2
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Herrmann A, Haag R, Schedler U. Hydrogels and Their Role in Biosensing Applications. Adv Healthc Mater 2021; 10:e2100062. [PMID: 33939333 DOI: 10.1002/adhm.202100062] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/12/2021] [Indexed: 12/16/2022]
Abstract
Hydrogels play an important role in the field of biomedical research and diagnostic medicine. They are emerging as a powerful tool in the context of bioanalytical assays and biosensing. In this context, this review gives an overview of different hydrogels and the role they adopt in a range of applications. Not only are hydrogels beneficial for the immobilization and embedding of biomolecules, but they are also used as responsive material, as wearable devices, or as functional material. In particular, the scientific and technical progress during the last decade is discussed. The newest hydrogel types, their synthesis, and many applications are presented. Advantages and performance improvements are described, along with their limitations.
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Affiliation(s)
- Anna Herrmann
- Department of Biology, Chemistry, Pharmacy Freie Universität Berlin Takustr. 3 Berlin 14195 Germany
| | - Rainer Haag
- Department of Biology, Chemistry, Pharmacy Freie Universität Berlin Takustr. 3 Berlin 14195 Germany
| | - Uwe Schedler
- PolyAn GmbH Rudolf‐Baschant‐Straße 2 Berlin 13086 Germany
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3
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Abstract
The regulation of brain cytochrome P450 enzymes (CYPs) is different compared with respective hepatic enzymes. This may result from anatomical bases and physiological functions of the two organs. The brain is composed of a variety of functional structures built of different interconnected cell types endowed with specific receptors that receive various neuronal signals from other brain regions. Those signals activate transcription factors or alter functioning of enzyme proteins. Moreover, the blood-brain barrier (BBB) does not allow free penetration of all substances from the periphery into the brain. Differences in neurotransmitter signaling, availability to endogenous and exogenous active substances, and levels of transcription factors between neuronal and hepatic cells lead to differentiated expression and susceptibility to the regulation of CYP genes in the brain and liver. Herein, we briefly describe the CYP enzymes of CYP1-3 families, their distribution in the brain, and discuss brain-specific regulation of CYP genes. In parallel, a comparison to liver CYP regulation is presented. CYP enzymes play an essential role in maintaining the levels of bioactive molecules within normal ranges. These enzymes modulate the metabolism of endogenous neurochemicals, such as neurosteroids, dopamine, serotonin, melatonin, anandamide, and exogenous substances, including psychotropics, drugs of abuse, neurotoxins, and carcinogens. The role of these enzymes is not restricted to xenobiotic-induced neurotoxicity, but they are also involved in brain physiology. Therefore, it is crucial to recognize the function and regulation of CYP enzymes in the brain to build a foundation for future medicine and neuroprotection and for personalized treatment of brain diseases.
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Affiliation(s)
- Wojciech Kuban
- Department of Pharmacokinetics and Drug Metabolism, Maj Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland
| | - Władysława Anna Daniel
- Department of Pharmacokinetics and Drug Metabolism, Maj Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland
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4
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Herrmann A, Rödiger S, Schmidt C, Schierack P, Schedler U. Spatial Separation of Microbeads into Detection Levels by a Bioorthogonal Porous Hydrogel for Size-Selective Analysis and Increased Multiplexity. Anal Chem 2019; 91:8484-8491. [PMID: 31247713 DOI: 10.1021/acs.analchem.9b01586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiplex detection techniques are emerging within the fields of life science research and medical diagnostics where it is mandatory to analyze a great number of molecules. The detection techniques need to be highly efficient but often involve complicated and expensive fabrication procedures. Here, we present the immobilization and geometric separation of fluorescence-labeled microbeads for a multiplex detection in k levels. A compound of differently sized target molecules (DNA, proteins) is channeled into the respective detection levels by making use of a hydrogel as a size selective filter. The immobilized microbeads (10-20 μm) are considerably larger than the pores of the hydrogel network and therefore stay fixed at the well bottom and in higher elevations, respectively. Small biomolecules can diffuse through the pores of the network, whereas medium-sized biomolecules pass slower and large molecules will be excluded. Besides filtering, this method discriminates the used microbeads into k levels and thereby introduces a geometric multiplexity. Additionally, the exclusion of large entities enables the simultaneous detection of two target molecules, which exhibit the same affinity interaction. The hydrogel is formed through the combination of two macromonomers. One component is a homobifunctional polyethylene glycol linker, carrying a strained alkyne (PEG-BCN) and the second component is the azide-functionalized dendritic polyglycerol (dPG-N3). They react via the bioorthogonal strain-promoted azide alkyne cycloaddition (SPAAC). The hydrogel creates a solution-like environment for the diffusion of the investigated biomolecules all the while providing a stable, bioinert, and surface bound network.
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Affiliation(s)
- Anna Herrmann
- Institut für Chemie und Biochemie , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Stefan Rödiger
- Brandenburgische Technische Universität Cottbus-Senftenberg , Universitätsplatz 1 , 01968 Senftenberg , Germany
| | - Carsten Schmidt
- Brandenburgische Technische Universität Cottbus-Senftenberg , Universitätsplatz 1 , 01968 Senftenberg , Germany
| | - Peter Schierack
- Brandenburgische Technische Universität Cottbus-Senftenberg , Universitätsplatz 1 , 01968 Senftenberg , Germany
| | - Uwe Schedler
- Institut für Chemie und Biochemie , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany.,PolyAn GmbH , Rudolf-Baschant-Straße 2 , 13086 Berlin , Germany
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5
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Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV. Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor. ACS Chem Biol 2018; 13:1235-1242. [PMID: 29562136 DOI: 10.1021/acschembio.8b00029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective base pairing is the foundation of DNA recognition. Here, we elucidate the molecular and structural details of a FRET-based two-component molecular beacon relying on steady-state fluorescence spectroscopy, small-angle X-ray scattering (SAXS), microscale thermophoresis (MST), and differential electrophoretic mobility. This molecular beacon was designed to detect the most common fusion sequences causing chronic myeloid leukemia, e14a2 and e13a2. The emission spectra indicate that the self-assembly of the different components of the biosensor occurs sequentially, triggered by the fully complementary target. We further assessed the structural alterations leading to the specific fluorescence FRET signature by SAXS, MST, and the differential electrophoretic mobility, where the size range observed is consistent with hybridization and formation of a 1:1:1 complex for the probe in the presence of the complementary target and revelator. These results highlight the importance of different techniques to explore conformational DNA changes in solution and its potential to design and characterize molecular biosensors for genetic disease diagnosis.
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Affiliation(s)
- Mílton Cordeiro
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
- LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Ana Rita Otrelo-Cardoso
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Hamburg, Germany, 22067
| | - Petr V. Konarev
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Hamburg, Germany, 22067
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Leninsky prospect 59, 119333 Moscow, Russia
- National Research Centre “Kurchatov Institute”, pl. Kurchatova 1, 123182 Moscow, Russia
| | - João Carlos Lima
- LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Teresa Santos-Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
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6
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Logun M, Zhao W, Mao L, Karumbaiah L. Microfluidics in Malignant Glioma Research and Precision Medicine. ADVANCED BIOSYSTEMS 2018; 2:1700221. [PMID: 29780878 PMCID: PMC5959050 DOI: 10.1002/adbi.201700221] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Indexed: 01/09/2023]
Abstract
Glioblastoma multiforme (GBM) is an aggressive form of brain cancer that has no effective treatments and a prognosis of only 12-15 months. Microfluidic technologies deliver microscale control of fluids and cells, and have aided cancer therapy as point-of-care devices for the diagnosis of breast and prostate cancers. However, a few microfluidic devices are developed to study malignant glioma. The ability of these platforms to accurately replicate the complex microenvironmental and extracellular conditions prevailing in the brain and facilitate the measurement of biological phenomena with high resolution and in a high-throughput manner could prove useful for studying glioma progression. These attributes, coupled with their relatively simple fabrication process, make them attractive for use as point-of-care diagnostic devices for detection and treatment of GBM. Here, the current issues that plague GBM research and treatment, as well as the current state of the art in glioma detection and therapy, are reviewed. Finally, opportunities are identified for implementing microfluidic technologies into research and diagnostics to facilitate the rapid detection and better therapeutic targeting of GBM.
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Affiliation(s)
- Meghan Logun
- Regenerative Bioscience Center, ADS Complex, University of Georgia, 425 River Road, Athens, GA 30602-2771, USA
| | - Wujun Zhao
- Department of Chemistry, University of Georgia, Athens, GA 30602-2771, USA
| | - Leidong Mao
- School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, GA 30602-2771, USA
| | - Lohitash Karumbaiah
- Regenerative Bioscience Center, ADS Complex, University of Georgia, 425 River Road, Athens, GA 30602-2771, USA
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7
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Wendt FR, Sajantila A, Budowle B. Predicted activity of UGT2B7, ABCB1, OPRM1, and COMT using full-gene haplotypes and their association with the CYP2D6-inferred metabolizer phenotype. Forensic Sci Int Genet 2018; 33:48-58. [DOI: 10.1016/j.fsigen.2017.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/01/2017] [Accepted: 11/22/2017] [Indexed: 12/20/2022]
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8
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Tang JH, Chia D. Liquid Biopsies in the Screening of Oncogenic Mutations in NSCLC and its Application in Targeted Therapy. Crit Rev Oncog 2018; 20:357-71. [PMID: 27279235 DOI: 10.1615/critrevoncog.v20.i5-6.90] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Non-small cell lung cancer (NSCLC) still dominates cancer-related deaths in America. Despite this, new discoveries and advancements in technology are helping with the detection and treatment of NSCLC. The discovery of circulating tumor DNA in blood and other biofluids is essential for the creation of a DNA biomarker. Limitations in technology and sequencing have stunted assay development, but with recent advancements in the next-generation sequencing, droplet digital PCR, and EFIRM, the detection of mutations in biofluids has become possible with reasonable sensitivity and specificity. These methods have been applied to the detection of mutations in NSCLC by measuring the levels of circulating tumor DNA. ALK fusion genes along with mutations in EGFR and KRAS have been shown to correlate to tumor size and metastasis. These methods allow for noninvasive, affordable, and efficient diagnoses of oncogenic mutations that overcome the issues of traditional biopsies. These issues include tumor heterogeneity and early detection of cancers with asymptomatic early stages. Early detection and treatment remain the best way to ensure survival. This review aims to describe these new technologies along with their application in mutation detection in NSCLC in order to proactively utilize targeted anticancer therapy.
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Affiliation(s)
- Jason H Tang
- Department of Pathology, UCLA David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - David Chia
- Department of Pathology, UCLA David Geffen School of Medicine at UCLA, Los Angeles, CA
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9
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Wendt FR, Sajantila A, Moura-Neto RS, Woerner AE, Budowle B. Full-gene haplotypes refine CYP2D6 metabolizer phenotype inferences. Int J Legal Med 2017; 132:1007-1024. [DOI: 10.1007/s00414-017-1709-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/11/2017] [Indexed: 01/08/2023]
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10
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Wendt FR, Pathak G, Sajantila A, Chakraborty R, Budowle B. Global genetic variation of select opiate metabolism genes in self-reported healthy individuals. THE PHARMACOGENOMICS JOURNAL 2017; 18:281-294. [PMID: 28398354 DOI: 10.1038/tpj.2017.13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/16/2017] [Accepted: 02/21/2017] [Indexed: 12/26/2022]
Abstract
CYP2D6 is a key pharmacogene encoding an enzyme impacting poor, intermediate, extensive and ultrarapid phase I metabolism of many marketed drugs. The pharmacogenetics of opiate drug metabolism is particularly interesting due to the relatively high incidence of addiction and overdose. Recently, trans-acting opiate metabolism and analgesic response enzymes (UGT2B7, ABCB1, OPRM1 and COMT) have been incorporated into pharmacogenetic studies to generate more comprehensive metabolic profiles of patients. With use of massively parallel sequencing, it is possible to identify additional polymorphisms that fine tune, or redefine, previous pharmacogenetic findings, which typically rely on targeted approaches. The 1000 Genomes Project data were analyzed to describe population genetic variation and statistics for these five genes in self-reported healthy individuals in five global super- and 26 sub-populations. Findings on the variation of these genes in various populations expand baseline understanding of pharmacogenetically relevant polymorphisms for future studies of affected cohorts.
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Affiliation(s)
- F R Wendt
- Institute for Molecular Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - G Pathak
- Institute for Molecular Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - A Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - R Chakraborty
- Institute for Molecular Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - B Budowle
- Institute for Molecular Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA.,Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX USA.,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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11
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Iravani M, Lee LK, Cannesson M. Standardized Care Versus Precision Medicine in the Perioperative Setting. Anesth Analg 2017; 124:1347-1353. [DOI: 10.1213/ane.0000000000001663] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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Su Q, Nöll G. A sandwich-like strategy for the label-free detection of oligonucleotides by surface plasmon fluorescence spectroscopy (SPFS). Analyst 2016; 141:5784-5791. [PMID: 27484040 PMCID: PMC5166564 DOI: 10.1039/c6an01129b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cutting surface-bound optical molecular beacons results in a sandwich-like detection strategy with lower background fluorescence.
For the detection of oligonucleotides a sandwich-like detection strategy has been developed by which the background fluorescence is significantly lowered in comparison with surface-bound molecular beacons. Surface bound optical molecular beacons are DNA hairpin structures comprising a stem and a loop. The end of the stem is modified with a fluorophore and a thiol anchor for chemisorption on gold surfaces. In the closed state the fluorophore is in close proximity to the gold surface, and most of the fluorescence is quenched. After hybridization with a target the hairpin opens, the fluorophore and surface become separated, and the fluorescence drastically increases. Using this detection method the sensitivity is limited by the difference in the fluorescence intensity in the closed and open state. As the background fluorescence is mainly caused by non-quenched fluorophores, a strategy to reduce the background fluorescence is to cut the beacon in two halves. First a thiolated ssDNA capture probe strand (first half) is chemisorbed to a gold surface together with relatively short thiol spacers. Next the target is hybridized by one end to the surface-anchored capture probe and by the other to a fluorophore-labeled reporter probe DNA (second half). The signal readout is done by surface plasmon fluorescence spectroscopy (SPFS). Using this detection strategy the background fluorescence can be significantly lowered, and the detection limit is lowered by more than one order of magnitude. The detection of a target takes only a few minutes and the sensor chips can be used for multiple detection steps without a significant decrease in performance.
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Affiliation(s)
- Qiang Su
- Nöll Junior Research Group, Organic Chemistry, Chem. Biol. Dept., Faculty IV, Siegen University, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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Haselmann V, Geilenkeuser WJ, Helfert S, Eichner R, Hetjens S, Neumaier M, Ahmad-Nejad P. Thirteen Years of an International External Quality Assessment Scheme for Genotyping: Results and Recommendations. Clin Chem 2016; 62:1084-95. [DOI: 10.1373/clinchem.2016.254482] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/03/2016] [Indexed: 12/19/2022]
Abstract
Abstract
BACKGROUND
Suboptimal laboratory procedures resulting in genotyping errors, misdiagnosis, or incorrect reporting bear greatly on a patient's health management, therapeutic decisions made on their behalf, and ultimate outcome. Participation in external quality assessment (EQA) is a key element of quality assurance in molecular genetic diagnostics. Therefore, the Reference Institute for Bioanalytics has tried for 13 years to improve the quality of genetic testing by offering an EQA for different clinically relevant sequence variations.
METHODS
Within each of the biannual EQA schemes offered, up to 18 samples of lyophilized human genomic DNA were provided for up to 50 different molecular genetic tests. Laboratories were asked to use their routine procedures for genotyping. At least 2 expert peer assessors reviewed the final returns. Data from 2002 to 2014 were evaluated.
RESULTS
In total, 82 462 reported results from 812 characterized samples were evaluated. Globally, the number of participants increased each year along with the number of sequence variations offered. The error rate decreased significantly over the years with an overall error rate of 1.44%. Additionally, a decreased error rate for samples repeated over time was noted. Interestingly, the error rate showed a high difference depending on the locus analyzed and the method used.
CONCLUSIONS
Based on the evaluation of this long-term EQA scheme, various recommendations can be given to improve the quality of molecular genetic testing, such as the use of 2 different methods for genotyping. Furthermore, some methods are inappropriate for analysis of certain sequence variations.
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Affiliation(s)
- Verena Haselmann
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
| | - Wolf J Geilenkeuser
- Reference-Institute for Bioanalytics, German Society for Clinical Chemistry and Laboratory Medicine (DGKL), Bonn, Germany
| | - Simona Helfert
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
| | - Romy Eichner
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
| | - Svetlana Hetjens
- Department for Statistical Analysis, University Hospital Mannheim of the University of Heidelberg, Mannheim, Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
| | - Parviz Ahmad-Nejad
- Institute for Medical Laboratory Diagnostics, Centre for Clinical and Translational Research (CCTR), HELIOS Hospital, Witten/Herdecke University, Wuppertal, Germany
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Cha EY, Jeong HE, Kim WY, Shin HJ, Kim HS, Shin JG. Brief introduction to current pharmacogenomics research tools. Transl Clin Pharmacol 2016. [DOI: 10.12793/tcp.2016.24.1.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Eun-Young Cha
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
| | - Hye-Eun Jeong
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
| | - Woo-Young Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
| | - Ho Jung Shin
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
| | - Ho-Sook Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
- Department of Clinical Pharmacology, Inje University Busan Paik Hospital, Busan 47392, Korea
| | - Jae-Gook Shin
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea
- Department of Clinical Pharmacology, Inje University Busan Paik Hospital, Busan 47392, Korea
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15
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Hodne K, Weltzien FA. Single-Cell Isolation and Gene Analysis: Pitfalls and Possibilities. Int J Mol Sci 2015; 16:26832-49. [PMID: 26569222 PMCID: PMC4661855 DOI: 10.3390/ijms161125996] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/14/2015] [Accepted: 11/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the last two decades single-cell analysis (SCA) has revealed extensive phenotypic differences within homogenous cell populations. These phenotypic differences are reflected in the stochastic nature of gene regulation, which is often masked by qualitatively and quantitatively averaging in whole tissue analyses. The ability to isolate transcripts and investigate how genes are regulated at the single cell level requires highly sensitive and refined methods. This paper reviews different strategies currently used for SCA, including harvesting, reverse transcription, and amplification of the RNA, followed by methods for transcript quantification. The review provides the historical background to SCA, discusses limitations, and current and future possibilities in this exciting field of research.
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Affiliation(s)
- Kjetil Hodne
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences-Campus Adamstuen, 0033 Oslo, Norway.
| | - Finn-Arne Weltzien
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences-Campus Adamstuen, 0033 Oslo, Norway.
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16
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Varela N, Quiñones LA, Stojanova J, Garay J, Cáceres D, Cespedes S, Sasso J, Miranda C. Characterization of the CYP2D6 drug metabolizing phenotypes of the Chilean mestizo population through polymorphism analyses. Pharmacol Res 2015. [PMID: 26211952 DOI: 10.1016/j.phrs.2015.07.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We tested the influence of four polymorphisms and gene duplication in CYP2D6 on in vivo enzyme activity in a Chilean mestizo population in order to identify the most relevant genetic profiles that account for observed phenotypes in this ethnic group. CYP2D6*2 (2850C>T), *3 (2549A>del), *4 (1846G>A), *17 (1023C>T) and gene duplication were determined by PCR-RFLP or PCRL in a group of 321 healthy volunteers. Individuals with different variant alleles were phenotyped by determining debrisoquine 4-hydroxylase activity as a metabolic ratio (MR) using a validated HPLC assay. Minor allele frequencies were 0.41, 0.01, 0.12 and 0.00 for CYP2D6*2, *3, *4 and *17 variants, respectively, and the duplication frequency was 0.003. Genotype analysis correlated with phenotypes in 18 of 23 subjects (78.3%). 11 subjects were extensive metabolizers (EM), 8 were intermediate metabolizers (IM), 2 were poor metabolizers (PM) and 2 were ultra-rapid metabolizers (UM) which is fairly coincident with expected phenotypes metabolic ratios ranged from 0.11 to 126.41. The influence of CYP2D6*3 was particularly notable, although only heterozygote carriers were present in our population. Individuals homozygous for *4 were always PM. As expected, the only subject with gene duplication was UM. In conclusion, there was a clear effect of genotype on observed CYP2D6 activity. Classification of EM, PM and UM through genotyping was useful to characterize CYP2D6 phenotype in the Chilean mestizo population.
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Affiliation(s)
- Nelson Varela
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, ICBM, Program of Molecular and Clinical Pharmacology, Faculty of Medicine, University of Chile, Chile; Department of Medical Technology, Faculty of Medicine, University of Chile, Chile
| | - Luis A Quiñones
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, ICBM, Program of Molecular and Clinical Pharmacology, Faculty of Medicine, University of Chile, Chile.
| | - Jana Stojanova
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, ICBM, Program of Molecular and Clinical Pharmacology, Faculty of Medicine, University of Chile, Chile
| | - Joselyn Garay
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, ICBM, Program of Molecular and Clinical Pharmacology, Faculty of Medicine, University of Chile, Chile
| | - Dante Cáceres
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, ICBM, Program of Molecular and Clinical Pharmacology, Faculty of Medicine, University of Chile, Chile; Environmental Health Program, School of Public Health, Faculty of Medicine, University of Chile, Chile
| | - Silvia Cespedes
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, ICBM, Program of Molecular and Clinical Pharmacology, Faculty of Medicine, University of Chile, Chile
| | - Jaime Sasso
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, ICBM, Program of Molecular and Clinical Pharmacology, Faculty of Medicine, University of Chile, Chile
| | - Carla Miranda
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, ICBM, Program of Molecular and Clinical Pharmacology, Faculty of Medicine, University of Chile, Chile
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Shen W, Tian Y, Ran T, Gao Z. Genotyping and quantification techniques for single-nucleotide polymorphisms. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Abul-Husn NS, Owusu Obeng A, Sanderson SC, Gottesman O, Scott SA. Implementation and utilization of genetic testing in personalized medicine. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2014; 7:227-40. [PMID: 25206309 PMCID: PMC4157398 DOI: 10.2147/pgpm.s48887] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Clinical genetic testing began over 30 years ago with the availability of mutation detection for sickle cell disease diagnosis. Since then, the field has dramatically transformed to include gene sequencing, high-throughput targeted genotyping, prenatal mutation detection, preimplantation genetic diagnosis, population-based carrier screening, and now genome-wide analyses using microarrays and next-generation sequencing. Despite these significant advances in molecular technologies and testing capabilities, clinical genetics laboratories historically have been centered on mutation detection for Mendelian disorders. However, the ongoing identification of deoxyribonucleic acid (DNA) sequence variants associated with common diseases prompted the availability of testing for personal disease risk estimation, and created commercial opportunities for direct-to-consumer genetic testing companies that assay these variants. This germline genetic risk, in conjunction with other clinical, family, and demographic variables, are the key components of the personalized medicine paradigm, which aims to apply personal genomic and other relevant data into a patient’s clinical assessment to more precisely guide medical management. However, genetic testing for disease risk estimation is an ongoing topic of debate, largely due to inconsistencies in the results, concerns over clinical validity and utility, and the variable mode of delivery when returning genetic results to patients in the absence of traditional counseling. A related class of genetic testing with analogous issues of clinical utility and acceptance is pharmacogenetic testing, which interrogates sequence variants implicated in interindividual drug response variability. Although clinical pharmacogenetic testing has not previously been widely adopted, advances in rapid turnaround time genetic testing technology and the recent implementation of preemptive genotyping programs at selected medical centers suggest that personalized medicine through pharmacogenetics is now a reality. This review aims to summarize the current state of implementing genetic testing for personalized medicine, with an emphasis on clinical pharmacogenetic testing.
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Affiliation(s)
- Noura S Abul-Husn
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aniwaa Owusu Obeng
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA ; Department of Pharmacy, Mount Sinai Hospital, New York, NY, USA
| | - Saskia C Sanderson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics. Int J Mol Sci 2014; 15:9670-717. [PMID: 24886813 PMCID: PMC4100115 DOI: 10.3390/ijms15069670] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 12/25/2022] Open
Abstract
DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is disease-causing or harmless is of great importance for the early detection of patients with a high risk of developing a particular disease and would pave the way for personalized medicine and diagnostics. Here we review existing methods and techniques to study and predict the effects of DNA mutations from three different perspectives: in silico, in vitro and in vivo. It is emphasized that the problem is complicated and successful detection of a pathogenic mutation frequently requires a combination of several methods and a knowledge of the biological phenomena associated with the corresponding macromolecules.
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Abstract
The US FDA has granted market approval for the first pharmacogenetic test using a DNA microarray, the AmpliChip CYP450, which genotypes cytochrome P450 (CYP)2D6 and CYP2C19. The test uses software to predict phenotypes and tests for 27 CYP2D6 alleles, including the deletions and duplications, and three CYP2C19 alleles. Other DNA microarray platforms are being developed for CYP testing, but none have been completely developed or approved by the FDA to date. The differences between an implementation of pharmacogenetic tests centered on the individual and implementation using a public health approach are discussed. In this review, the major obstacles to the wide implementation of pharmacogenetic testing in the clinical environment are summarized.
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Affiliation(s)
- Jose de Leon
- University of Kentucky, Mental Health Research Center at Eastern State Hospital, 627 West Fourth St., Lexington, KY 40508, USA.
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Chen T, Hansen G, Beske O, Yates K, Zhu Y, Anthony M, Agler M, Banks M. Analysis of cellular events using CellCard™ System in cell-based high-content multiplexed assays. Expert Rev Mol Diagn 2014; 5:817-29. [PMID: 16149883 DOI: 10.1586/14737159.5.5.817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
High-content screening technologies utilize assays that monitor and quantify multiple cellular events. These assays are typically performed on a single cell type with automated microscopy and image analysis. However, in order to better understand the selectivity of a compound across multiple cell lines, these types of assay must be run serially, which is time consuming. The CellCard System developed by Vitra Bioscience enables multiple cell types to be assayed within a single microtiter well, thereby enabling the simultaneous determination of cellular responses across ten cell types. This multiplexed approach could address the demand for assay capacity, increase the quality of the biologic data, reduce timelines, and improve cost-effectiveness in hit identification and lead evaluation. The authors have carried out an in-depth evaluation of this technology platform using ten cancer cell lines and a library of compounds that affect cellular growth through different mechanisms. Multiple assays were used to investigate the compound effects on membrane integrity, cell cycle progression and apoptosis. In this technology review, the authors discuss personal experience with assay validation, data analysis, results such as cell type-specific compound effects, and the potential application of the CellCard System in drug discovery.
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Affiliation(s)
- Taosheng Chen
- Bristol-Myers Squibb Company, Lead Discovery & Profiling, 5 Research Parkway, Wallingford, CT 06492, USA.
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22
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An Investigation of CYP2D6 Genotype and Response to Metoprolol CR/XL During Dose Titration in Patients With Heart Failure: A MERIT-HF Substudy. Clin Pharmacol Ther 2013; 95:321-30. [DOI: 10.1038/clpt.2013.193] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/16/2013] [Indexed: 12/18/2022]
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23
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Daher M, Costa FMM, Neves FAR. Genotyping the Mu-Opioid Receptor A118G Polymorphism Using the Real-time Amplification Refractory Mutation System: Allele Frequency Distribution Among Brazilians. Pain Pract 2013; 13:614-20. [DOI: 10.1111/papr.12042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/22/2013] [Indexed: 02/06/2023]
Affiliation(s)
- Mauricio Daher
- Department of Anesthesiology, University Hospital of Brasilia, University of Brasilia, Brasilia, Brazil
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Bollag G, Tsai J, Zhang J, Zhang C, Ibrahim P, Nolop K, Hirth P. Vemurafenib: the first drug approved for BRAF-mutant cancer. Nat Rev Drug Discov 2012; 11:873-86. [PMID: 23060265 DOI: 10.1038/nrd3847] [Citation(s) in RCA: 543] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The identification of driver oncogenes has provided important targets for drugs that can change the landscape of cancer therapies. One such example is the BRAF oncogene, which is found in about half of all melanomas as well as several other cancers. As a druggable kinase, oncogenic BRAF has become a crucial target of small-molecule drug discovery efforts. Following a rapid clinical development path, vemurafenib (Zelboraf; Plexxikon/Roche) was approved for the treatment of BRAF-mutated metastatic melanoma in the United States in August 2011 and the European Union in February 2012. This Review describes the underlying biology of BRAF, the technology used to identify vemurafenib and its clinical development milestones, along with future prospects based on lessons learned during its development.
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Affiliation(s)
- Gideon Bollag
- Plexxikon, 91 Bolivar Drive, Berkeley, California 94710, USA.
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Minarik M, Kopeckova M, Gassman M, Osmancik P, Benesova L. Rapid testing of clopidogrel resistance by genotyping of CYP2C19 and CYP2C9 polymorphisms using denaturing on-chip capillary electrophoresis. Electrophoresis 2012; 33:1306-10. [PMID: 22589111 DOI: 10.1002/elps.201100457] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Antiplatelet therapy is a cornerstone of cardiovascular treatment in patients with coronary artery disease and after myocardial infarction. Clopidogrel has become a popular antiplatelet agent due to its fast action and low frequency of adverse effects. Kinetics of clopidogrel metabolism is driven by enzymatic activity of the Cytochrome P450 system. Genotyping of CYP2C19 and CYP2C9 polymorphisms allows to identify slow metabolizers showing resistance to clopidogrel therapy. Today, a number of PCR-based techniques for single nucleotide polymorphism genotyping directed at clopidogrel resistance polymorphisms are in use. Here, we describe a new alternative genotyping approach combining the separation power of denaturing capillary electrophoresis with the analysis speed and ease of use of Bioanalyzer chipCE platform. Using an upgraded heater control, we present an optimization for allele separation of CYP2C19 I331V, CYP2C9 R144C, and CYP2C9 I359L polymorphisms employing run temperatures of up to 55°C. We demonstrate rapid and accessible approach to reproducible clopidogrel resistance with feasibility and low cost.
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Affiliation(s)
- Marek Minarik
- Center for Applied Genomics of Solid Tumors, Genomac Research Institute, Prague, Czech Republic.
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Multi-Beam Interference Advances and Applications: Nano-Electronics, Photonic Crystals, Metamaterials, Subwavelength Structures, Optical Trapping, and Biomedical Structures. MICROMACHINES 2011. [DOI: 10.3390/mi2020221] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Park S, Lee MR, Shin I. Chemical microarrays constructed by selective attachment of hydrazide-conjugated substances to epoxide surfaces and their applications. Methods Mol Biol 2011; 669:195-208. [PMID: 20857368 DOI: 10.1007/978-1-60761-845-4_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Microarray technology has received considerable attention for rapid analysis of biomolecular interactions and high-throughput screening to identify binding partners. An efficient and selective immobilization technique of substances on the surface is essential for successful construction of microarrays. Although a variety of immobilization methods have been exploited to prepare microarrays over the past decade, a superior technique needs to be developed for diverse applications. Recently, an efficient and simple method that relies on selective reactions between the hydrazide conjugated to substances and the epoxide derivatized on the solid surface was developed to fabricate chemical microarrays. Reactions between hydrazides with epoxides are highly selective in that they take place even in the presence of other potent nucleophiles such as amines and thiols. This technique is utilized to immobilize various substances such as small molecules, carbohydrates, and peptides to glass surfaces. The microarrays constructed by this immobilization method are used to evaluate protein binding to carbohydrates, peptides, and small molecules. In addition, the microarrays are also employed to determine binding affinities between proteins and binding partners as well as profiling of enzyme activities.
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Affiliation(s)
- Sungjin Park
- Department of Chemistry, Yonsei University, Seoul, Korea
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Park S, Pai J, Han EH, Jun CH, Shin I. One-step, aid-mediated method for modification of glass surfaces with N-hydroxysuccinimide esters and its application to the construction of microarrays for studies of biomolecular interactions. Bioconjug Chem 2010; 21:1246-53. [PMID: 20568727 DOI: 10.1021/bc100042j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microarray technologies have received considerable attention owing to the fact that they serve as powerful tools for the high-throughput analysis of biomolecular interactions and the identification of bioactive substances that bind to biomolecules. Most of the current methods used to construct microarrays rely on the immobilization of substances on properly derivatized surfaces. Among various functional groups used for this purpose, the N-hydroxysuccinimide (NHS) ester group has been largely employed because it can be readily reacted with amine or hydrazide functionalities in substances of interest. However, the NHS ester group is usually introduced onto the surface of a glass slide by employing inconvenient and time-consuming multistep processes. In recent studies, we have developed an efficient, single step method for derivatization of glass surfaces with NHS ester groups that takes advantage of an acid-mediated reaction of NHS ester functionalized dimethallylsilanes with silanols on the glass surface. Conditions for the surface modification procedure that utilize TfOH rather than Sc(OTf)(3) were found to be superior. Protein and RNA-binding experiments show that glass surfaces modified by employing this method are suitable for efficient immobilization of various substances that are appended by amine, hydrazide, and alcohol functionalities. The microarrays, generated in this way, are applicable to procedures for rapid analysis of protein-protein, protein-glycan, protein-small molecule, and peptide-RNA interactions, as well as for profiling enzyme activities. The newly developed acid-mediated, glass surface modification method should be generally applicable to the preparation of various functional group-modified surfaces.
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Affiliation(s)
- Sungjin Park
- Center for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature 2010; 467:596-9. [PMID: 20823850 PMCID: PMC2948082 DOI: 10.1038/nature09454] [Citation(s) in RCA: 1391] [Impact Index Per Article: 99.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 08/31/2010] [Indexed: 12/18/2022]
Abstract
B-RAF is the most frequently mutated protein kinase in human cancers.1 The finding that oncogenic mutations in BRAF are common in melanoma2 followed by the demonstration that these tumors are dependent on the RAF/MEK/ERK pathway3 offered hope that inhibition of B-RAF kinase activity could benefit melanoma patients. Herein, we describe the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic B-RAF kinase activity. Preclinical experiments demonstrated that PLX4032 selectively blocked the RAF/MEK/ERK pathway in BRAF mutant cells and caused regression of BRAF mutant xenografts.4 Toxicology studies confirmed a wide safety margin consistent with the high degree of selectivity, enabling Phase 1 clinical trials using a crystalline formulation of PLX4032.5 In a subset of melanoma patients, pathway inhibition was monitored in paired biopsy specimens collected before treatment initiation and following two weeks of treatment. This analysis revealed substantial inhibition of ERK phosphorylation, yet clinical evaluation did not show tumor regressions. At higher drug exposures afforded by a new amorphous drug formulation,4,5 greater than 80% inhibition of ERK phosphorylation in the tumors of patients correlated with clinical response. Indeed, the Phase 1 clinical data revealed a remarkably high 81% response rate in metastatic melanoma patients treated at an oral dose of 960 mg twice daily.5 These data demonstrate that BRAF-mutant melanomas are highly dependent on B-RAF kinase activity.
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Flaherty KT, Puzanov I, Kim KB, Ribas A, McArthur GA, Sosman JA, O'Dwyer PJ, Lee RJ, Grippo JF, Nolop K, Chapman PB. Inhibition of mutated, activated BRAF in metastatic melanoma. N Engl J Med 2010; 363:809-19. [PMID: 20818844 PMCID: PMC3724529 DOI: 10.1056/nejmoa1002011] [Citation(s) in RCA: 2748] [Impact Index Per Article: 196.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The identification of somatic mutations in the gene encoding the serine-threonine protein kinase B-RAF (BRAF) in the majority of melanomas offers an opportunity to test oncogene-targeted therapy for this disease. METHODS We conducted a multicenter, phase 1, dose-escalation trial of PLX4032 (also known as RG7204), an orally available inhibitor of mutated BRAF, followed by an extension phase involving the maximum dose that could be administered without adverse effects (the recommended phase 2 dose). Patients received PLX4032 twice daily until they had disease progression. Pharmacokinetic analysis and tumor-response assessments were conducted in all patients. In selected patients, tumor biopsy was performed before and during treatment to validate BRAF inhibition. RESULTS A total of 55 patients (49 of whom had melanoma) were enrolled in the dose-escalation phase, and 32 additional patients with metastatic melanoma who had BRAF with the V600E mutation were enrolled in the extension phase. The recommended phase 2 dose was 960 mg twice daily, with increases in the dose limited by grade 2 or 3 rash, fatigue, and arthralgia. In the dose-escalation cohort, among the 16 patients with melanoma whose tumors carried the V600E BRAF mutation and who were receiving 240 mg or more of PLX4032 twice daily, 10 had a partial response and 1 had a complete response. Among the 32 patients in the extension cohort, 24 had a partial response and 2 had a complete response. The estimated median progression-free survival among all patients was more than 7 months. CONCLUSIONS Treatment of metastatic melanoma with PLX4032 in patients with tumors that carry the V600E BRAF mutation resulted in complete or partial tumor regression in the majority of patients. (Funded by Plexxikon and Roche Pharmaceuticals.)
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Affiliation(s)
- Keith T Flaherty
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, USA.
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Characterization of DNA chips by nanogold staining. Anal Biochem 2009; 389:118-23. [DOI: 10.1016/j.ab.2009.03.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 03/23/2009] [Accepted: 03/23/2009] [Indexed: 11/16/2022]
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Fogli S, Caraglia M. Genotype-based therapeutic approach for colorectal cancer: state of the art and future perspectives. Expert Opin Pharmacother 2009; 10:1095-108. [DOI: 10.1517/14656560902889775] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Tedford NC, Hall AB, Graham JR, Murphy CE, Gordon NF, Radding JA. Quantitative analysis of cell signaling and drug action via mass spectrometry-based systems level phosphoproteomics. Proteomics 2009; 9:1469-87. [PMID: 19294625 DOI: 10.1002/pmic.200800468] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein phosphorylation is a primary form of information transfer in cell signaling pathways and plays a crucial role in regulating biological responses. Aberrant phosphorylation has been implicated in a number of diseases, and kinases and phosphatases, the cellular enzymes that control dynamic phosphorylation events, present attractive therapeutic targets. However, the innate complexity of signaling networks has presented many challenges to therapeutic target selection and successful drug development. Approaches in phosphoproteomics can contribute functional, systems-level datasets across signaling networks that can provide insight into suitable drug targets, more broadly profile compound activities, and identify key biomarkers to assess clinical outcomes. Advances in MS-based phosphoproteomics efforts now provide the ability to quantitate phosphorylation with throughput and sensitivity to sample a significant portion of the phosphoproteome in clinically relevant systems. This review will discuss recent work and examples of application data that demonstrate the utility of MS, with a particular focus on the use of quantitative phosphoproteomics and phosphotyrosine-directed signaling analyses to provide robust measurement for functional biological interpretation of drug action on signaling and phenotypic outcomes.
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de Leon J. The future (or lack of future) of personalized prescription in psychiatry. Pharmacol Res 2009; 59:81-9. [DOI: 10.1016/j.phrs.2008.10.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 10/09/2008] [Indexed: 12/24/2022]
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37
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Gu Z, Huang S, Chen Y. Biomolecular Nanopatterning by Magnetic Electric Lithography. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200803456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gu Z, Huang S, Chen Y. Biomolecular Nanopatterning by Magnetic Electric Lithography. Angew Chem Int Ed Engl 2009; 48:952-5. [DOI: 10.1002/anie.200803456] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
This review focuses first on the concept of pharmacogenomics and its related concepts (biomarkers and personalized prescription). Next, the first generation of five DNA pharmacogenomic tests used in the clinical practice of psychiatry is briefly reviewed. Then the possible involvement of these pharmacogenomic tests in the exploration of early clinical proof of mechanism is described by using two of the tests and one example from the pharmaceutical industry (iloperidone clinical trials). The initial attempts to use other microarray tests (measuring RNA expression) as peripheral biomarkers for CNS disorders are briefly described. Then the challenge of taking pharmacogenomic tests (compared to drugs) into clinical practice is explained by focusing on regulatory oversight, the methodological/scientific issues concerning diagnostic tests, and cost-effectiveness issues. Current information on medicine-based evidence and cost-effectiveness usually focuses on average patients and not the outliers who are most likely to benefit from personalized prescription. Finally, future research directions are suggested. The future of 'personalized prescription' in psychiatry requires consideration of pharmacogenomic testing and environmental and personal variables that influence pharmacokinetic and pharmacodynamic drug response for each individual drug used by each patient.
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Scott SA, Edelmann L, Kornreich R, Erazo M, Desnick RJ. CYP2C9, CYP2C19 and CYP2D6 allele frequencies in the Ashkenazi Jewish population. Pharmacogenomics 2008; 8:721-30. [PMID: 18240905 DOI: 10.2217/14622416.8.7.721] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE To determine and compare the cytochrome P450 (CYP)2C9, CYP2C19 and CYP2D6 allele and genotype frequencies in the Ashkenazi Jewish (AJ) population with other populations. METHODS CYP2C9, CYP2C19 and CYP2D6 genotypes were determined in 250 anonymous, unrelated, healthy AJ individuals from the greater New York (USA) metropolitan area. Genotyping was performed using the Tag-Ittrade mark Mutation Detection system and the recently redefined CYP2D6*41A allele was identified by a restriction fragment length polymorphism assay. RESULTS Among the 250 AJ individuals, the CYP2C9*1, *2, *3 and *5 allele frequencies were 0.772, 0.140, 0.086 and 0.002, respectively, and the genotypes were distributed into extensive- (60.8%), intermediate- (32.8%) and poor- (6.4%) metabolizer phenotypes. The CYP2C19*1, *2 and *4 allele frequencies were 0.830, 0.152 and 0.018, respectively, and the genotypes were distributed into extensive (69.2%), intermediate (27.6%) and poor (3.2%) metabolizers. The most common CYP2D6 alleles identified were *1, *2A, *4 and *41A, and their frequencies were 0.286 0.152 0.226 and 0.140, respectively. The CYP2D6 genotypes were distributed into ultrarapid- (8.8%), extensive- (70.0%), intermediate- (16.0%) and poor- (5.2%) metabolizer phenotypes. CONCLUSION Although the CYP2C9 allele and genotype frequencies in the AJ subjects were similar to those in other North American Caucasian populations, genotyping the CYP2C19*4 and CYP2D6*41A alleles in the AJ population resulted in the clinically relevant reclassification of the predicted metabolizer phenotypes. Inclusion of CYP2C19*4 reclassified individuals from either extensive- or intermediate- to the intermediate- or poor-metabolizer phenotypes, respectively. Inclusion of the redefined CYP2D6*41A allele increased the ultrarapid-, intermediate- and poor-metabolizer phenotype combined frequencies to 30%, indicating that approximately one in three AJ individuals may benefit from genotype-based drug selection and dosage. In addition, the ultrarapid CYP2D6 genotype frequency in the AJ population (8.8%) was approximately twofold higher than that in other North American Caucasians.
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Affiliation(s)
- Stuart A Scott
- Mount Sinai School of Medicine of New York University, Department of Genetics and Genomic Sciences, Box 1498, Fifth Avenue at 100th Street, New York, NY 10029, USA
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A multidisciplinary approach for molecular diagnostics based on biosensors and microarrays. Ing Rech Biomed 2008. [DOI: 10.1016/j.rbmret.2007.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bhatnagar P, Nixon AJ, Kim I, Kameoka J. Protein functionalized micro hydrogel features for cell–surface interaction. Biomed Microdevices 2008; 10:567-71. [DOI: 10.1007/s10544-008-9167-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Beeton-Kempen N, Shoko A, Blackburn J. Personalizing protein-drug interactions. PURE APPL CHEM 2008. [DOI: 10.1351/pac200880081811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The development of new drugs today is a hugely expensive process, with estimated costs of up to $1 billion to take a drug through to market. However, despite this seemingly massive expenditure, statistics show that the great majority of prescription drugs on the market today are only effective for around 40 % of the patients to whom they are administered. Worse still, recently there have been a series of high-profile instances where potentially block-busting FDA-approved drugs have subsequently been withdrawn due to unanticipated side effects that were only revealed when the drug entered use in the general population. A variety of factors are at play in underpinning such statistics, but at the heart of the problem is the fact that, despite the extensive knowledge being generated in the postgenomic era about the genetic differences between individuals, Western medicine still today largely ignores such differences. The hope therefore is that by gaining a greater understanding of the individual nature of disease progression and of drug response, we might move toward a new era of personalized medicine in which the right drug is prescribed at the right dose to treat the precise disease afflicting the specific patient. As a step along this road, this review will discuss new approaches in the pharmacogenomics field to understanding in a quantitative manner the molecular consequence of polymorphic variation and mutation, both on encoded protein function and on protein-drug interactions.
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Affiliation(s)
- Natasha Beeton-Kempen
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
| | - Aubrey Shoko
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
| | - Jonathan Blackburn
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, Cape Town, South Africa
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Govindaraju T, Jonkheijm P, Gogolin L, Schroeder H, Becker CFW, Niemeyer CM, Waldmann H. Surface immobilization of biomolecules by click sulfonamide reaction. Chem Commun (Camb) 2008:3723-5. [DOI: 10.1039/b806764c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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45
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Coyer S, García A, Delamarche E. Facile Preparation of Complex Protein Architectures with Sub-100-nm Resolution on Surfaces. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700989] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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46
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Coyer SR, García AJ, Delamarche E. Facile Preparation of Complex Protein Architectures with Sub-100-nm Resolution on Surfaces. Angew Chem Int Ed Engl 2007; 46:6837-40. [PMID: 17577910 DOI: 10.1002/anie.200700989] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sean R Coyer
- IBM Research GmbH, Zurich Research Laboratory, 8803 Rüschlikon, Switzerland
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47
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Vajda FJE. Pharmacotherapy of epilepsy: new armamentarium, new issues. J Clin Neurosci 2007; 14:813-23. [PMID: 17618119 DOI: 10.1016/j.jocn.2007.02.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Revised: 01/29/2007] [Accepted: 02/04/2007] [Indexed: 10/23/2022]
Abstract
Since 1990 there have been over ten antiepileptic drugs (AEDs) approved for the therapy of epilepsy. These agents have a new spectrum of efficacy and novel adverse effects, some totally unexpected. They also represent an enormous escalation of costs. Few have been subjected to head-to-head comparisons in monotherapy against established AEDs. The aim of therapy is to eliminate rather than to reduce seizure manifestations. Many traditional agents have been phased out due to poor tolerability. New epilepsy syndromes and genetic contributions to epilepsy have been refined. Special considerations apply to various classes of sufferers such as the elderly, women of childbearing age, and sufferers with concomitant disorders, treated with medications capable of drug interactions. There is a recognition of the value of slow introduction, a preference for monotherapy, recognition of the effects of AEDs on hormones and reproductive function and effects on the fetus exposed to AEDs in utero, comprising physical malformations and effects on cognitive development. A balance between efficacy and safety is pivotal, as every preference about the initial pharmacotherapy of epilepsy and subsequent polytherapy has its protagonists. With improvement in diagnostic techniques and new therapeutic modalities it is likely that in the future, pharmacogenomics and an understanding of pharmacoresistance may influence drug selection for individual patients with epilepsy.
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Affiliation(s)
- Frank J E Vajda
- Department of Medicine, Monash University and Medical Centre, 246 Clayton Road, Clayton 3168, Victoria, and Department of Medicine, St Vincents Hospital, Melbourne, Australia.
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48
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Carter DJ, Cary RB. Lateral flow microarrays: a novel platform for rapid nucleic acid detection based on miniaturized lateral flow chromatography. Nucleic Acids Res 2007; 35:e74. [PMID: 17478499 PMCID: PMC1904290 DOI: 10.1093/nar/gkm269] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Widely used nucleic acid assays are poorly suited for field deployment where access to laboratory instrumentation is limited or unavailable. The need for field deployable nucleic acid detection demands inexpensive, facile systems without sacrificing information capacity or sensitivity. Here we describe a novel microarray platform capable of rapid, sensitive nucleic acid detection without specialized instrumentation. The approach is based on a miniaturized lateral flow device that makes use of hybridization-mediated target capture. The miniaturization of lateral flow nucleic acid detection provides multiple advantages over traditional lateral flow devices. Ten-microliter sample volumes reduce reagent consumption and yield analyte detection times, excluding sample preparation and amplification, of <120 s while providing sub-femtomole sensitivity. Moreover, the use of microarray technology increases the potential information capacity of lateral flow. Coupled with a hybridization-based detection scheme, the lateral flow microarray (LFM) enables sequence-specific detection, opening the door to highly multiplexed implementations for broad-range assays well suited for point-of-care and other field applications. The LFM system is demonstrated using an isothermal amplification strategy for detection of Bacillus anthracis, the etiologic agent of anthrax. RNA from as few as two B. anthracis cells was detected without thermocycling hardware or fluorescence detection systems.
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Affiliation(s)
| | - R. Bruce Cary
- *To whom correspondence should be addressed. Tel: 505 665 6874; Fax: 505 665 3024;
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49
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Godfraind T. La médecine traditionnelle et la médecine translationnelle. BULLETIN DE L'ACADÉMIE NATIONALE DE MÉDECINE 2007. [DOI: 10.1016/s0001-4079(19)33005-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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50
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Cheng JC, Horwitz EM, Karsten SL, Shoemaker L, Kornblum HI, Malik P, Sakamoto KM. Report on the Workshop “New Technologies in Stem Cell Research,” Society for Pediatric Research, San Francisco, California, April 29, 2006. Stem Cells 2007; 25:1070-88. [PMID: 17255523 DOI: 10.1634/stemcells.2006-0397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jerry C Cheng
- Division of Hematology/Oncology, Department of Pediatrics, Gwynne Hazen Cherry Memorial Laboratories and Mattel Children's Hospital, Jonsson Comprehensive Cancer Center, Los Angeles, California, USA
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