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Hephzibah Cathryn R, Udhaya Kumar S, Younes S, Zayed H, George Priya Doss C. A review of bioinformatics tools and web servers in different microarray platforms used in cancer research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:85-164. [PMID: 35871897 DOI: 10.1016/bs.apcsb.2022.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Over the past decade, conventional lab work strategies have gradually shifted from being limited to a laboratory setting towards a bioinformatics era to help manage and process the vast amounts of data generated by omics technologies. The present work outlines the latest contributions of bioinformatics in analyzing microarray data and their application to cancer. We dissect different microarray platforms and their use in gene expression in cancer models. We highlight how computational advances empowered the microarray technology in gene expression analysis. The study on protein-protein interaction databases classified into primary, derived, meta-database, and prediction databases describes the strategies to curate and predict novel interaction networks in silico. In addition, we summarize the areas of bioinformatics where neural graph networks are currently being used, such as protein functions, protein interaction prediction, and in silico drug discovery and development. We also discuss the role of deep learning as a potential tool in the prognosis, diagnosis, and treatment of cancer. Integrating these resources efficiently, practically, and ethically is likely to be the most challenging task for the healthcare industry over the next decade; however, we believe that it is achievable in the long term.
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Affiliation(s)
- R Hephzibah Cathryn
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Salma Younes
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.
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Rajagopalan RM, Fujimura JH. Variations on a Chip: Technologies of Difference in Human Genetics Research. JOURNAL OF THE HISTORY OF BIOLOGY 2018; 51:841-873. [PMID: 30338423 DOI: 10.1007/s10739-018-9543-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this article we examine the history of the production of microarray technologies and their role in constructing and operationalizing views of human genetic difference in contemporary genomics. Rather than the "turn to difference" emerging as a post-Human Genome Project (HGP) phenomenon, interest in individual and group differences was a central, motivating concept in human genetics throughout the twentieth century. This interest was entwined with efforts to develop polymorphic "genetic markers" for studying human traits and diseases. We trace the technological, methodological and conceptual strategies in the late twentieth century that established single nucleotide polymorphisms (SNPs) as key focal points for locating difference in the genome. By embedding SNPs in microarrays, researchers created a technology that they used to catalog and assess human genetic variation. In the process of making genetic markers and array-based technologies to track variation, scientists also made commitments to ways of describing, cataloging and "knowing" human genetic differences that refracted difference through a continental geographic lens. We show how difference came to matter in both senses of the term: difference was made salient to, and inscribed on, genetic matter(s), as a result of the decisions, assessments and choices of collaborative and hybrid research collectives in medical genomics research.
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Affiliation(s)
- Ramya M Rajagopalan
- Institute for Practical Ethics, University of California, San Diego, 9500 Gilman Drive, MC 0406, San Diego, CA, 92093, USA.
| | - Joan H Fujimura
- Department of Sociology and Holtz Center for Science and Technology Studies, University of Wisconsin-Madison, 8128 Sewell Social Sciences Building 1180 Observatory Drive, Madison, WI, 53706, USA
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Kretova OV, Chechetkin VR, Fedoseeva DM, Kravatsky YV, Sosin DV, Alembekov IR, Gorbacheva MA, Gashnikova NM, Tchurikov NA. Analysis of Variability in HIV-1 Subtype A Strains in Russia Suggests a Combination of Deep Sequencing and Multitarget RNA Interference for Silencing of the Virus. AIDS Res Hum Retroviruses 2017; 33:194-201. [PMID: 27476852 DOI: 10.1089/aid.2016.0088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Any method for silencing the activity of the HIV-1 retrovirus should tackle the extremely high variability of HIV-1 sequences and mutational escape. We studied sequence variability in the vicinity of selected RNA interference (RNAi) targets from isolates of HIV-1 subtype A in Russia, and we propose that using artificial RNAi is a potential alternative to traditional antiretroviral therapy. We prove that using multiple RNAi targets overcomes the variability in HIV-1 isolates. The optimal number of targets critically depends on the conservation of the target sequences. The total number of targets that are conserved with a probability of 0.7-0.8 should exceed at least 2. Combining deep sequencing and multitarget RNAi may provide an efficient approach to cure HIV/AIDS.
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Affiliation(s)
- Olga V. Kretova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Daria M. Fedoseeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri V. Kravatsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitri V. Sosin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ildar R. Alembekov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria A. Gorbacheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Natalya M. Gashnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nickolai A. Tchurikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Parween S, Nahar P. Ultraminiaturized assay for rapid, low cost detection and quantification of clinical and biochemical samples. Biomed Microdevices 2016; 18:33. [PMID: 26973054 DOI: 10.1007/s10544-016-0059-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Herein, we report a simple, sensitive, rapid and low-cost ultraminiaturized assay technique for quantitative detection of 1 μl of clinical or biochemical sample on a novel ultraminiaturized assay plate (UAP). UAP is prepared by making tiny cavities on a polypropylene sheet. As UAP cannot immobilize a biomolecule through absorption, we have activated the tiny cavities of UAP by 1-fluoro-2-nitro-4-azidobenzene in a photochemical reaction. Activated UAP (AUAP) can covalently immobilize any biomolecule having an active nucleophilic group such as amino group. Efficacy of AUAP is demonstrated by detecting human IgE, antibody of hepatitis C virus core antigen and oligonucleotides. Quantification is performed by capturing the image of the colored assay solution and digitally quantifying the image by color saturation without using costly NanoDrop spectrophotometer. Image - based detection of human IgE and an oligonucleotide shows an excellent correlation with absorbance - based assay (recorded in a NanoDrop spectrophotometer); it is validated by Pearson's product-moment correlation with correlation coefficient of r = 0.9545088 and r = 0.9947444 respectively. AUAP is further checked by detecting hepatitis C virus Ab where strong correlation of color saturation with absorbance with respect to concentration is observed. Ultraminiaturized assay successfully detects target oligonucleotides by perfectly hybridizing with their respective complementary oligonucleotide probes but not with a random oligonucleotide. Ultraminiaturized assay technique has substantially reduced the requirement of reagents by 100 times and assay timing by 50 times making it a potential alternative to conventional method.
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Affiliation(s)
- Shahila Parween
- Innovative Diagnostic Lab, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110 007, India.,Academy of Scientific and Innovative Research, CRRI Campus, Mathura Road, Delhi, 110020, India
| | - Pradip Nahar
- Innovative Diagnostic Lab, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110 007, India. .,Academy of Scientific and Innovative Research, CRRI Campus, Mathura Road, Delhi, 110020, India.
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LI Y. Establishment and Application of a Visual DNA Microarray for the Detection of Food-borne Pathogens. ANAL SCI 2016; 32:215-8. [DOI: 10.2116/analsci.32.215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yongjin LI
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, Huzhou University
- College of Life Science, Yangtze University
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Lewis MA, Paquin RS, Roche MI, Furberg RD, Rini C, Berg JS, Powell CM, Bailey DB. Supporting Parental Decisions About Genomic Sequencing for Newborn Screening: The NC NEXUS Decision Aid. Pediatrics 2016; 137 Suppl 1:S16-23. [PMID: 26729698 PMCID: PMC4922487 DOI: 10.1542/peds.2015-3731e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Advances in genomic sequencing technology have raised fundamental challenges to the traditional ways genomic information is communicated. These challenges will become increasingly complex and will affect a much larger population in the future if genomics is incorporated into standard newborn screening practice. Clinicians, public health officials, and other stakeholders will need to agree on the types of information that they should seek and communicate to parents. Currently, few evidence-based and validated tools are available to support parental informed decision-making. These tools will be necessary as genomics is integrated into clinical practice and public health systems. In this article we describe how the North Carolina Newborn Exome Sequencing for Universal Screening study is addressing the need to support parents in making informed decisions about the use of genomic testing in newborn screening. We outline the context for newborn screening and justify the need for parental decision support. We also describe the process of decision aid development and the data sources, processes, and best practices being used in development. By the end of the study, we will have an evidenced-based process and validated tools to support parental informed decision-making about the use of genomic sequencing in newborn screening. Data from the study will help answer important questions about which genomic information ought to be sought and communicated when testing newborns.
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Affiliation(s)
- Megan A. Lewis
- Center for Communication Science, and,Address correspondence to Megan A. Lewis, PhD, 3040 Cornwallis Rd, PO Box 12194, Research Triangle Park, NC 27709-2194. E-mail:
| | | | - Myra I. Roche
- Department of Pediatrics, and,Department of Genetics, and
| | | | - Christine Rini
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Poirel L, Bonnin RA, Nordmann P. Rapid identification of antibiotic-resistant bacteria: how could new diagnostic tests halt potential endemics? Expert Rev Mol Diagn 2013; 13:409-11. [PMID: 23782246 DOI: 10.1586/erm.13.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Ono N, Suzuki S, Furusawa C, Shimizu H, Yomo T. Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarrays. PLoS One 2013; 8:e54571. [PMID: 23382915 PMCID: PMC3557292 DOI: 10.1371/journal.pone.0054571] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/12/2012] [Indexed: 11/18/2022] Open
Abstract
High-density DNA microarrays are useful tools for analyzing sequence changes in DNA samples. Although microarray analysis provides informative signals from a large number of probes, the analysis and interpretation of these signals have certain inherent limitations, namely, complex dependency of signals on the probe sequences and the existence of false signals arising from non-specific binding between probe and target. In this study, we have developed a novel algorithm to detect the single-base substitutions by using microarray data based on a thermodynamic model of hybridization. We modified the thermodynamic model by introducing a penalty for mismatches that represent the effects of substitutions on hybridization affinity. This penalty results in significantly higher detection accuracy than other methods, indicating that the incorporation of hybridization free energy can improve the analysis of sequence variants by using microarray data.
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Affiliation(s)
- Naoaki Ono
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Shingo Suzuki
- Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
| | - Chikara Furusawa
- Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
- * E-mail:
| | - Hiroshi Shimizu
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Tetsuya Yomo
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- ERATO, JST, Suita, Osaka, Japan
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Allegue C, Campuzano O, Castillo S, Coll M, Iglesias A, Brugada R. Nuevas herramientas diagnósticas en la genética de la muerte súbita. REVISTA ESPAÑOLA DE CARDIOLOGÍA SUPLEMENTOS 2013; 13:24-29. [DOI: 10.1016/s1131-3587(13)70063-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
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Longjam N, Deb R, Sarmah AK, Tayo T, Awachat VB, Saxena VK. A Brief Review on Diagnosis of Foot-and-Mouth Disease of Livestock: Conventional to Molecular Tools. Vet Med Int 2011; 2011:905768. [PMID: 21776357 PMCID: PMC3135314 DOI: 10.4061/2011/905768] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/25/2011] [Accepted: 04/20/2011] [Indexed: 12/31/2022] Open
Abstract
Foot-and-mouth disease (FMD) is one of the highly contagious diseases of domestic animals. Effective control of this disease needs sensitive, specific, and quick diagnostic tools at each tier of control strategy. In this paper we have outlined various diagnostic approaches from old to new generation in a nutshell. Presently FMD diagnosis is being carried out using techniques such as Virus Isolation (VI), Sandwich-ELISA (S-ELISA), Liquid-Phase Blocking ELISA (LPBE), Multiplex-PCR (m-PCR), and indirect ELISA (DIVA), and real time-PCR can be used for detection of antibody against nonstructural proteins. Nucleotide sequencing for serotyping, microarray as well as recombinant antigen-based detection, biosensor, phage display, and nucleic-acid-based diagnostic are on the way for rapid and specific detection of FMDV. Various pen side tests, namely, lateral flow, RT-LAMP, Immunostrip tests, and so forth. are also developed for detection of the virus in field condition.
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Affiliation(s)
- Neeta Longjam
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati 781022, India
| | - Rajib Deb
- Division of Animal Biotechnology, Indian Veterinary Research Institute (IVRI), Izatnagar 243122, India
| | - A. K. Sarmah
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati 781022, India
| | - Tilling Tayo
- Division of Animal Nutrition, Indian Veterinary Research Institute (IVRI), Izatnagar 243122, India
| | - V. B. Awachat
- Division of Poultry Science, Central Avian Research Institute (CARI), Izatnagar 243122, India
| | - V. K. Saxena
- Division of Veterinary Biochemistry and Physiology, Central Sheep and Wool Research Institute (CSWRI), Avikanagar, India
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Janvilisri T, Scaria J, Gleed R, Fubini S, Bonkosky MM, Gröhn YT, Chang YF. Development of a microarray for identification of pathogenic Clostridium spp. Diagn Microbiol Infect Dis 2009; 66:140-7. [PMID: 19879710 DOI: 10.1016/j.diagmicrobio.2009.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 09/02/2009] [Accepted: 09/22/2009] [Indexed: 12/25/2022]
Abstract
In recent years, Clostridium spp. have rapidly reemerged as human and animal pathogens. The detection and identification of pathogenic Clostridium spp. is therefore critical for clinical diagnosis and antimicrobial therapy. Traditional diagnostic techniques for clostridia are laborious, are time consuming, and may adversely affect the therapeutic outcome. In this study, we developed an oligonucleotide diagnostic microarray for pathogenic Clostridium spp. The microarray specificity was tested against 65 Clostridium isolates. The applicability of this microarray in a clinical setting was assessed with the use of mock stool samples. The microarray was successful in discriminating at least 4 species with the limit of detection as low as 10(4) CFU/mL. In addition, the pattern of virulence and antibiotic resistance genes of tested strains were determined through the microarrays. This approach demonstrates the high-throughput detection and identification of Clostridium spp. and provides advantages over traditional methods. Microarray-based techniques are promising applications for clinical diagnosis and epidemiologic investigations.
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Affiliation(s)
- Tavan Janvilisri
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853, USA
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Webster DR, Hekele AG, Lauring AS, Fischer KF, Li H, Andino R, DeRisi JL. An enhanced single base extension technique for the analysis of complex viral populations. PLoS One 2009; 4:e7453. [PMID: 19834618 PMCID: PMC2759544 DOI: 10.1371/journal.pone.0007453] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 08/15/2009] [Indexed: 11/24/2022] Open
Abstract
Many techniques for the study of complex populations provide either specific information on a small number of variants or general information on the entire population. Here we describe a powerful new technique for elucidating mutation frequencies at each genomic position in a complex population. This single base extension (SBE) based microarray platform was designed and optimized using poliovirus as the target genotype, but can be easily adapted to assay populations derived from any organism. The sensitivity of the method was demonstrated by accurate and consistent readouts from a controlled population of mutant genotypes. We subsequently deployed the technique to investigate the effects of the nucleotide analog ribavirin on a typical poliovirus population through two rounds of passage. Our results show that this economical platform can be used to investigate dynamic changes occurring at frequencies below 1% within a complex nucleic acid population. Given that many key aspects of the study and treatment of disease are intimately linked to population-level genomic diversity, our SBE-based technique provides a scalable and cost-effective complement to both traditional and next generation sequencing methodologies.
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Affiliation(s)
- Dale R. Webster
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Armin G. Hekele
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Adam S. Lauring
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Kael F. Fischer
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (JLD); (RA)
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (JLD); (RA)
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Bailey DB, Armstrong FD, Kemper AR, Skinner D, Warren SF. Supporting family adaptation to presymptomatic and "untreatable" conditions in an era of expanded newborn screening. J Pediatr Psychol 2009; 34:648-61. [PMID: 18378512 PMCID: PMC2722102 DOI: 10.1093/jpepsy/jsn032] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2007] [Revised: 01/31/2008] [Accepted: 03/08/2008] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE As technology advances, newborn screening will be possible for conditions not screened today. With an expansion of screening, strategies will be needed to support family adaptation to unexpected and possibly uncertain genetic information provided shortly after birth. METHOD Although candidate conditions for expanded newborn screening will typically be associated with increased morbidity or mortality, for most there is no proven medical treatment that must be implemented quickly. Many will have clinical features that gradually emerge and for which the severity of impact is not predictable. Parents will seek guidance on information, support, and treatment possibilities. This article summarizes issues evoked by expanded newborn screening and suggests strategies for supporting families of identified children. RESULTS We propose four components necessary to support family adaptation to pre-symptomatic and "untreatable" conditions in an era of expanded newborn screening: (1) accurate and understandable information; (2) formal and informal support; (3) active surveillance; and (4) general and targeted interventions. We argue that no condition is "untreatable" and that a well-designed program of prevention and support has the potential to maximize benefit and minimize harm. CONCLUSIONS Pediatric psychologists can play important roles in an era of expanded newborn screening by helping families understand genetic information, make informed decisions about genetic testing, and cope with the potential psychosocial consequences of genetic information.
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Affiliation(s)
- Donald B Bailey
- RTI International, Research Triangle Park, NC 27709-2194, USA.
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16
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Microarray-based DNA resequencing using 3' blocked primers. Anal Biochem 2007; 374:41-7. [PMID: 18023400 DOI: 10.1016/j.ab.2007.10.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 10/22/2007] [Accepted: 10/23/2007] [Indexed: 11/22/2022]
Abstract
To exceed the throughput and accuracy of conventional sequencing technologies, we tested a method (pyrophosphorolysis-activated polymerization [PAP]) of nucleic acid amplification that uses 3' blocked primers (P*s). As proof-of-principle, we resequenced a 20-bp region of the factor IX gene with a microarray of P*s. P*s discriminate 3' end mismatches with ultra-high specificity as well as mismatches along their lengths with high specificity. We correctly identified two wild-type samples as well as all mismatches, including three single-base substitutions, one microdeletion, one microinsertion, and one heterozygous mutation. Despite limitations in the primer purity, the signal/noise ratio between the matched and mismatched P*s sometimes exceeded 1000. Thus, PAP resequencing shows great potential for accurate and high-throughput microarray-based resequencing.
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Circulating mutant DNA to assess tumor dynamics. Nat Med 2007; 14:985-90. [PMID: 18670422 DOI: 10.1038/nm.1789] [Citation(s) in RCA: 1896] [Impact Index Per Article: 111.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 05/27/2008] [Indexed: 02/06/2023]
Abstract
The measurement of circulating nucleic acids has transformed the management of chronic viral infections such as HIV. The development of analogous markers for individuals with cancer could similarly enhance the management of their disease. DNA containing somatic mutations is highly tumor specific and thus, in theory, can provide optimum markers. However, the number of circulating mutant gene fragments is small compared to the number of normal circulating DNA fragments, making it difficult to detect and quantify them with the sensitivity required for meaningful clinical use. In this study, we applied a highly sensitive approach to quantify circulating tumor DNA (ctDNA) in 162 plasma samples from 18 subjects undergoing multimodality therapy for colorectal cancer. We found that ctDNA measurements could be used to reliably monitor tumor dynamics in subjects with cancer who were undergoing surgery or chemotherapy. We suggest that this personalized genetic approach could be generally applied to individuals with other types of cancer.
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Wang XW, Zhang L, Jin LQ, Jin M, Shen ZQ, An S, Chao FH, Li JW. Development and application of an oligonucleotide microarray for the detection of food-borne bacterial pathogens. Appl Microbiol Biotechnol 2007; 76:225-33. [PMID: 17492283 DOI: 10.1007/s00253-007-0993-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2007] [Revised: 04/10/2007] [Accepted: 04/11/2007] [Indexed: 01/10/2023]
Abstract
The rapid and accurate detection and identification of food-borne pathogenic bacteria is critical for food safety. In this paper, we describe a rapid (<4 h) high-throughput detection and identification system that uses universal polymerase chain reaction (PCR) primers to amplify a variable region of bacterial the 16S rRNA gene, followed by reverse hybridization of the products to species-specific oligonucleotide probes on a chip. This procedure was successful in discriminating 204 strains of bacteria from pure culture belonging to 13 genera of bacteria. When this method was applied directly to 115 strains of bacteria isolated from foods, 112/115 (97.4%) were correctly identified; two strains were indistinguishable due to weak signal, while one failed to produce a PCR product. The array was used to detect and successfully identify two strains of bacteria from food poisoning outbreak samples, giving results through hybridization that were identical to those obtained by traditional methods. The sensitivity of the microarray assay was 10(2) CFU of bacteria. Thus, the oligonucleotide microarray is a powerful tool for the detection and identification of pathogens from foods.
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Affiliation(s)
- Xin-Wei Wang
- Institute of Environment and Health, No. 1, Dali Road, Tianjin, 300050, People's Republic of China
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Sawada A, Mizufune S, Kaji N, Tokeshi M, Baba Y. Evaluation of amplified cRNA targets for oligonucleotide microarrays. Anal Bioanal Chem 2007; 387:2645-54. [PMID: 17285305 DOI: 10.1007/s00216-007-1125-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 01/03/2007] [Accepted: 01/12/2007] [Indexed: 11/26/2022]
Abstract
Due to their hybridization specificity and capacity for systematic gene discovery, oligonucleotide-based microarray platforms offer numerous advantages over the cDNA microarrays currently widely used for comprehensive analysis of gene expression. Although fluorescently labeled amplified cRNA generated by T7 transcription is generally used in oligonucleotide microarrays, the feasibility of this combination (and that of cDNA microarrays) is yet to be studied systematically. In this paper, we performed a comparative study using a direct labeling method and T7 amplification to evaluate amplified cRNA targets for oligonucleotide microarrays. The efficiency of incorporation of Cy3- and Cy5-CTP into the target preparations, the reproducibility and the number of genes detected were investigated for each labeling approach and compared. The 12 genes that showed different expression profiles in the two labeling methods were evaluated by quantitative real-time PCR. In the 60-mer oligonucleotide microarray, amplified cRNA targets prepared by the T7 amplification method showed higher reproducibility and reliability than targets prepared by the direct labeling method in a comparative analysis of gene expression. This result also suggests the importance of fragmenting cRNA down to lengths of 50-200 bases before the hybridization process.
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Affiliation(s)
- Akihiro Sawada
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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Salvado C, Cram D. Microarray Technology for Mutation Analysis of Low-Template DNA Samples. METHODS IN MOLECULAR MEDICINE™ 2007; 132:153-73. [PMID: 17876083 DOI: 10.1007/978-1-59745-298-4_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Microarrays containing oligonucleotide mutation probes are emerging as useful platforms for the diagnosis of genetic disease. Herein, we describe the development and validation of an in-house microarray suitable for the diagnosis of common cystic fibrosis (CF) mutations in low-template DNA samples such as those taken for preimplantation genetic diagnosis and prenatal diagnosis. The success of the CF microarray was based on the ability to generate sufficient target DNA for hybridization to the array probes using either direct polymerase chain reaction (PCR) amplification or whole-genome amplification followed by PCR. From replicate experiments using target DNA carrying known CF mutations, it was possible to define strict diagnostic parameters for the accurate diagnosis of CF. This protocol serves as a general guide for DNA-testing laboratories to develop other microarray platforms that may eventually replace traditional PCR-based genetic testing in the near future.
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Affiliation(s)
- Chelsea Salvado
- Monash Immunology and Stem Cell Laboraotires, Monash University, Melbourne, Australia
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Kinoshita K, Fujimoto K, Yakabe T, Saito S, Hamaguchi Y, Kikuchi T, Nonaka K, Murata S, Masuda D, Takada W, Funaoka S, Arai S, Nakanishi H, Yokoyama K, Fujiwara K, Matsubara K. Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer. Nucleic Acids Res 2006; 35:e3. [PMID: 17135189 PMCID: PMC1747182 DOI: 10.1093/nar/gkl939] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 10/01/2006] [Accepted: 10/16/2006] [Indexed: 11/14/2022] Open
Abstract
DNA microarrays are routinely used to monitor gene expression profiling and single nucleotide polymorphisms (SNPs). However, for practically useful high performance, the detection sensitivity is still not adequate, leaving low expression genes undetected. To resolve this issue, we have developed a new plastic S-BIO PrimeSurface with a biocompatible polymer; its surface chemistry offers an extraordinarily stable thermal property for a lack of pre-activated glass slide surface. The oligonucleotides immobilized on this substrate are robust in boiling water and show no significant loss of hybridization activity during dissociation treatment. This allowed us to hybridize the templates, extend the 3' end of the immobilized DNA primers on the S-Bio by DNA polymerase using deoxynucleotidyl triphosphates (dNTP) as extender units, release the templates by denaturalization and use the same templates for a second round of reactions similar to that of the PCR method. By repeating this cycle, the picomolar concentration range of the template oligonucleotide can be detected as stable signals via the incorporation of labeled dUTP into primers. This method of Multiple Primer EXtension (MPEX) could be further extended as an alternative route for producing DNA microarrays for SNP analyses via simple template preparation such as reverse transcript cDNA or restriction enzyme treatment of genome DNA.
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Affiliation(s)
- Kenji Kinoshita
- Sumitomo Bakelite Co., Ltd. 1-1-5 Muroya, Nishi-ku, Kobe 651-2241, Japan.
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22
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Chavan P, Joshi K, Patwardhan B. DNA microarrays in herbal drug research. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2006; 3:447-57. [PMID: 17173108 PMCID: PMC1697755 DOI: 10.1093/ecam/nel075] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Accepted: 09/19/2006] [Indexed: 12/18/2022]
Abstract
Natural products are gaining increased applications in drug discovery and development. Being chemically diverse they are able to modulate several targets simultaneously in a complex system. Analysis of gene expression becomes necessary for better understanding of molecular mechanisms. Conventional strategies for expression profiling are optimized for single gene analysis. DNA microarrays serve as suitable high throughput tool for simultaneous analysis of multiple genes. Major practical applicability of DNA microarrays remains in DNA mutation and polymorphism analysis. This review highlights applications of DNA microarrays in pharmacodynamics, pharmacogenomics, toxicogenomics and quality control of herbal drugs and extracts.
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Coppola G, Geschwind DH. Technology Insight: querying the genome with microarrays--progress and hope for neurological disease. ACTA ACUST UNITED AC 2006; 2:147-58. [PMID: 16932541 DOI: 10.1038/ncpneuro0133] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Accepted: 01/09/2006] [Indexed: 01/23/2023]
Abstract
The ability to perform large-scale analysis of the genome at the level of gene sequence, gene copy number and messenger RNA transcript expression characterizes the post-genomic era. In the past decade, the microarray-based approach has emerged as one of the major tools in this area of genome biology, contributing to advances in the understanding of Mendelian and complex neurological disorders. Despite technical issues regarding design, data analysis and validation that have to be addressed in the planning and interpretation of a microarray study, microarray-based approaches for studying transcript expression, single-nucleotide-polymorphism genotyping and gene resequencing are becoming more widely adopted. Genomic microarrays are providing an unprecedented opportunity to dissect the genetic risk for complex neurological disorders. Numerous clinical and preclinical applications are likely to dominate the ambitious microarray agenda within the next decade.
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Affiliation(s)
- Giovanni Coppola
- Neurogenetics Program, Center for Autism Research, University of California Los Angeles, CA 90095, USA
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Abstract
DNA microarrays are a tool for simultaneously assessing the expression levels of thousands of genes in a single experiment, making them well-suited to understanding the complex gene response patterns and the regulatory pathways involved in human disease. This article reviews the basics of array technology and analysis, and highlights its application to pediatric diseases.
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Affiliation(s)
- Martin J Hessner
- The Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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Kim S, Lim GS, Lee SE, Lee JG, Yun K, Park JK. DNA chip replication for a personalized DNA chip. BIOMOLECULAR ENGINEERING 2006; 23:129-34. [PMID: 16527538 DOI: 10.1016/j.bioeng.2006.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/15/2005] [Accepted: 01/03/2006] [Indexed: 05/07/2023]
Abstract
We report the replication technology of DNA chip using by sequence specific localization of nucleic acids via hybridization and electric transfer of the nucleic acids onto a new substrate without losing their array information. The denatured DNA fragments are first spotted and UV-cross-linked on a nylon membrane. The membrane is then immersed and hybridized in a DNA mixture solution that contains all complementary sequences of the nucleic acids to be hybridized with the DNA fragments on the membrane. The hybridized DNA fragments are transferred to another membrane at the denatured condition. After separating two membranes, the transferred membrane contains a complementary array of DNA fragments. This method can be used for the replication of the same copy of DNA chip repeatedly and moreover could be applied for a personalized DNA chip fabrication, where specific information of each spot of DNA chip is originated from the genetic information of a personal sample.
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Affiliation(s)
- Suhyeon Kim
- Bio Electronics Group, LG Electronics Institute of Technology, 16 Woomyeon-dong, Seocho-gu, Seoul 137-724, Republic of Korea
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Martín V, Perales C, Abia D, Ortíz AR, Domingo E, Briones C. Microarray-based identification of antigenic variants of foot-and-mouth disease virus: a bioinformatics quality assessment. BMC Genomics 2006; 7:117. [PMID: 16709242 PMCID: PMC1481559 DOI: 10.1186/1471-2164-7-117] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Accepted: 05/18/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of viral quasispecies can influence viral pathogenesis and the response to antiviral treatments. Mutant clouds in infected organisms represent the first stage in the genetic and antigenic diversification of RNA viruses, such as foot and mouth disease virus (FMDV), an important animal pathogen. Antigenic variants of FMDV have been classically diagnosed by immunological or RT-PCR-based methods. DNA microarrays are becoming increasingly useful for the analysis of gene expression and single nucleotide polymorphisms (SNPs). Recently, a FMDV microarray was described to detect simultaneously the seven FMDV serotypes. These results encourage the development of new oligonucleotide microarrays to probe the fine genetic and antigenic composition of FMDV for diagnosis, vaccine design, and to gain insight into the molecular epidemiology of this pathogen. RESULTS A FMDV microarray was designed and optimized to detect SNPs at a major antigenic site of the virus. A screening of point mutants of the genomic region encoding antigenic site A of FMDV C-S8c1 was achieved. The hybridization pattern of a mutant includes specific positive and negative signals as well as crosshybridization signals, which are of different intensity depending on the thermodynamic stability of each probe-target pair. Moreover, an array bioinformatic classification method was developed to evaluate the hybridization signals. This statistical analysis shows that the procedure allows a very accurate classification per variant genome. CONCLUSION A specific approach based on a microarray platform aimed at distinguishing point mutants within an important determinant of antigenicity and host cell tropism, namely the G-H loop of capsid protein VP1, was developed. The procedure is of general applicability as a test for specificity and discriminatory power of microarray-based diagnostic procedures using multiple oligonucleotide probes.
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Affiliation(s)
- Verónica Martín
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Celia Perales
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - David Abia
- Bioinformatics Unit, Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Angel R Ortíz
- Bioinformatics Unit, Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Carlos Briones
- Centro de Astobiología (CSIC-INTA), Torrejón de Ardoz, 28850, Madrid, Spain
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Kim SY, Park YJ, Song E, Jang H, Kim C, Yoo J, Kang SJ. Evaluation of the CombiChip Mycobacteria™ Drug-Resistance detection DNA chip for identifying mutations associated with resistance to isoniazid and rifampin in Mycobacterium tuberculosis. Diagn Microbiol Infect Dis 2006; 54:203-10. [PMID: 16458476 DOI: 10.1016/j.diagmicrobio.2005.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Accepted: 09/30/2005] [Indexed: 11/17/2022]
Abstract
The CombiChip Mycobacteriatrade mark Drug-Resistance Detection DNA chip, recently developed by GeneIn (Pusan, South Korea), is an oligonucleotide microchip coupled with polymerase chain reaction for the detection of mutations associated with resistance to isoniazid (INH) and rifampin (RIF). This oligonucleotide chip was compared with DNA sequencing and phenotypic drug susceptibility testing with 69 INH- and/or RIF-resistant and 27 all tested drug-susceptible Mycobacterium tuberculosis isolates. Two selected codons (the katG codon 315 and inhA15) allowed identification of 84.1% of INH-resistant isolates and 100% of RIF resistance were detected by screening for 7 codons: rpoB511, rpoB513, rpoB516, rpoB522, rpoB526, rpoB531, and rpoB533. The overall specificity of this oligonucleotide chip for detecting INH and RIF resistance were 100 and 95.3%, respectively. This level of sensitivity and specificity is concordant with that from the determination of M. tuberculosis drug resistance by DNA sequencing. This oligonucleotide chip is a rapid and reliable genotypic method capable of detecting multiple mutations associated with INH and RIF resistance simultaneously in a single microchip slide.
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Affiliation(s)
- Soo-Young Kim
- Department of Clinical Pathology, College of Medicine, The Catholic University of Korea, St. Vincent's Hospital, Suwon 442-723, South Korea
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Wick LM, Rouillard JM, Whittam TS, Gulari E, Tiedje JM, Hashsham SA. On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucleic Acids Res 2006; 34:e26. [PMID: 16478712 PMCID: PMC1369288 DOI: 10.1093/nar/gnj024] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Nucleic acid hybridization serves as backbone for many high-throughput systems for detection, expression analysis, comparative genomics and re-sequencing. Specificity of hybridization between probes and intended targets is always critical. Approaches to ensure and evaluate specificity include use of mismatch probes, obtaining dissociation curves rather than single temperature hybridizations, and comparative hybridizations. In this study, we quantify effects of mismatch type and position on intensity of hybridization signals and provide a new approach based on dissociation rate constants to evaluate specificity of hybridized signals in complex target mixtures. Using an extensive set of 18mer oligonucleotide probes on an in situ synthesized biochip platform, we demonstrate that mismatches in the center of the probe are more discriminating than mismatches toward the extremities of the probe and mismatches toward the attached end are less discriminating than those toward the loose end. The observed destabilizing effect of a mismatch type agreed in general with predictions using the nearest neighbor model. Use of a new parameter, specific dissociation temperature (Td-w, temperature of maximum specific dissociation rate constant), obtained from probe–target duplex dissociation profiles considerably improved the evaluation of specificity. These results have broad implications for hybridization data obtained from complex mixtures of nucleic acids.
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Affiliation(s)
| | | | | | - Erdogan Gulari
- Department of Chemical Engineering, University of MichiganAnn Arbor, MI, USA
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State UniversityEast Lansing, MI, USA
| | - Syed A. Hashsham
- Center for Microbial Ecology, Michigan State UniversityEast Lansing, MI, USA
- Department of Civil and Environmental Engineering, Michigan State UniversityEast Lansing, MI, USA
- To whom correspondence should be addressed. Tel: +1 517 355 8241; Fax: +1 517 355 0250;
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Wu Q, Ma W, Shi R, Zhang B, Mao X, Zheng W. An Activated GOPS-poly- L-Lysine- Coated Glass Surface for the Immobilization of 60mer Oligonucleotides. Eng Life Sci 2005; 5:466-470. [PMID: 32313546 PMCID: PMC7163479 DOI: 10.1002/elsc.200520097] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Revised: 09/10/2005] [Accepted: 09/16/2005] [Indexed: 11/24/2022] Open
Abstract
To explore a method for enhancing the immobilization and hybridization efficiency of oligonucleotides on DNA microarrays, conventional protocols of poly‐L‐lysine coating were modified by means of surface chemistry, namely, the slides were prepared by the covalently coupling of poly‐L‐lysine to a glycidoxy‐modified glass surface. The modified slides were then used to print microarrays for the detection of the SARS coronavirus by means of 60mer oligonucleotide probes. The characteristics of the modified slides concerning immobilization efficiency, hybridization dynamics, and probe stripping cycles were determined. The improved surface exhibited high immobilization efficiency, a good quality uniformity, and satisfactory hybridization dynamics. The spotting concentration of 10 μmol/L can meet the requirements of detection; the spots were approximately 170 nm in diameter; the mean fluorescence intensity of the SARS spots were between 3.2 × 104 and 5.0 × 104 after hybridization. Furthermore, the microarrays prepared by this method demonstrated more resistance to consecutive probe stripping cycles. The activated GOPS‐PLL slide could undergo hybridization stripping cycles for at least three cycles, and the highest loss in fluorescence intensity was found to be only 11.9 % after the third hybridization. The modified slides using the above‐mentioned method were superior to those slides treated with conventional approaches, which theoretically agrees with the fact that modification by surface chemistry attaches the DNA covalently firmly to the slides. This protocol may have great promise in the future for application in large‐scale manufacture. One of the key steps in oligonucleotide microarray fabrication is the immobilization of oligonucleotides on a modified glass slide surface. Conventional protocols of poly‐L‐lysine coating were modified by means of surface chemistry in a way similar to the immobilization of 60mer oligonucleotides by deposition technology. The slides prepared by covalently coupling of poly‐L‐lysine to a glycidoxy‐modified glass surface were used to print microarrays for the detection of the SARS coronavirus.
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Affiliation(s)
- Q Wu
- Southern Medical University, Institute of Molecular Biology, Guangzhou 510515, Guangdong, P.R. China
| | - W Ma
- Southern Medical University, Institute of Molecular Biology, Guangzhou 510515, Guangdong, P.R. China
| | - R Shi
- Southern Medical University, Institute of Molecular Biology, Guangzhou 510515, Guangdong, P.R. China
| | - B Zhang
- Southern Medical University, Institute of Molecular Biology, Guangzhou 510515, Guangdong, P.R. China
| | - X Mao
- Southern Medical University, Institute of Molecular Biology, Guangzhou 510515, Guangdong, P.R. China
| | - W Zheng
- Guangzhou Liu Hua Qiao Hospital, Department of Medical Research, Guangzhou 510010, PR China
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Lee KH, Yim EK, Kim CJ, Namkoong SE, Um SJ, Park JS. Proteomic analysis of anti-cancer effects by paclitaxel treatment in cervical cancer cells. Gynecol Oncol 2005; 98:45-53. [PMID: 15907983 DOI: 10.1016/j.ygyno.2005.04.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 01/29/2005] [Accepted: 04/12/2005] [Indexed: 10/25/2022]
Abstract
OBJECTIVES Paclitaxel (Taxol), a potent drug of natural origin isolated from the bark of the Pacific yew, is widely used in the treatment of ovarian, lung and breast cancer. At present, there is little information regarding the anti-cancer mechanism of paclitaxel against cervical carcinoma cells. We thus tried to show the anti-cancer effect of paclitaxel on cervical carcinoma cell line carrying HPV by using a proteomic analysis and to investigate the mechanism of actions. METHODS We treated paclitaxel to cervical carcinoma cells and then carried out MTT assay to observe the anti-proliferate activity. Using proteomics analysis including two-dimensional (2-DE) gel electrophoresis and MALDI-TOF-MS, we tried to find the anti-proliferate activity-related proteins. Among them, paclitaxel treatment suppressed the expression of the mitotic checkpoint protein BUB3. Functional proteomic analysis by small interfering RNA (siRNA) targeting was tried to illuminate a role of mitotic checkpoint protein BUB3 in cell cycle progression. RESULTS The cytotoxicity effects of paclitaxel were determined in HPV-16 positive CaSki, HPV-18 positive HeLa and HPV-negative C33A cervical carcinoma cell lines. Using efficient proteomics methods including 2-DE/MALDI-TOF-MS, we identified several cellular proteins that are responsive to paclitaxel treatment in HeLa cells. Paclitaxel treatment elevated mainly apoptosis-related, immune response-related and cell cycle check point-related proteins. On the other hand, paclitaxel treatment diminished growth factor/oncogene-related proteins and transcription regulation-related proteins. Paclitaxel showed anti-proliferate activity through the membrane death receptor (DR)-mediated apoptotic pathway involving activation of caspase-8 with a TRAIL-dependent fashion as well as the mitochondrial-mediated pathway involving down-regulation of bcl-2 by cytochrome c release. Furthermore, we found siRNA-induced BUB3 knock down on cell cycle progression blocked by cell cycle arrest after paclitaxel treatment. CONCLUSIONS The proteome profiling technique provided a broad-base and effective approach for the identification of protein changes induced by paclitaxel and showed anti-proliferate activity through the membrane death receptor-mediated apoptotic pathway, the mitochondrial-mediated pathway. This study shows the power of proteomic profiling with functional analysis using RNAi technology for the discovery of novel molecular targets and a better understanding of the actions of paclitaxel at the molecular level in cervical carcinoma cells.
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Affiliation(s)
- Keun-Ho Lee
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Kangnam St. Mary's Hospital, Seoul 137-040, Korea
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Thibault C, Le Berre V, Casimirius S, Trévisiol E, François J, Vieu C. Direct microcontact printing of oligonucleotides for biochip applications. J Nanobiotechnology 2005; 3:7. [PMID: 15992404 PMCID: PMC1184096 DOI: 10.1186/1477-3155-3-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Accepted: 07/01/2005] [Indexed: 11/10/2022] Open
Abstract
Background A critical step in the fabrication of biochips is the controlled placement of probes molecules on solid surfaces. This is currently performed by sequential deposition of probes on a target surface with split or solid pins. In this article, we present a cost-effective procedure namely microcontact printing using stamps, for a parallel deposition of probes applicable for manufacturing biochips. Results Contrary to a previous work, we showed that the stamps tailored with an elastomeric poly(dimethylsiloxane) material did not require any surface modification to be able to adsorb oligonucleotides or PCR products. The adsorbed DNA molecules are subsequently printed efficiently on a target surface with high sub-micron resolution. Secondly, we showed that successive stamping is characterized by an exponential decay of the amount of transferred DNA molecules to the surface up the 4th print, then followed by a second regime of transfer that was dependent on the contact time and which resulted in reduced quality of the features. Thus, while consecutive stamping was possible, this procedure turned out to be less reproducible and more time consuming than simply re-inking the stamps between each print. Thirdly, we showed that the hybridization signals on arrays made by microcontact printing were 5 to 10-times higher than those made by conventional spotting methods. Finally, we demonstrated the validity of this microcontact printing method in manufacturing oligonucleotides arrays for mutations recognition in a yeast gene. Conclusion The microcontact printing can be considered as a new potential technology platform to pattern DNA microarrays that may have significant advantages over the conventional spotting technologies as it is easy to implement, it uses low cost material to make the stamp, and the arrays made by this technology are 10-times more sensitive in term of hybridization signals than those manufactured by conventional spotting technology.
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Affiliation(s)
- C Thibault
- LAAS-CNRS, 7, avenue du Colonel Roche 31077 TOULOUSE Cedex 4
| | - V Le Berre
- Biochips Platform Genopole Toulouse, UMR-CNRS 5504 & INRA 792, 135, avenue de Rangueil, 31077 TOULOUSE Cedex 4
- Laboratoire de Biotechnologie & Bioprocédés, UMR-CNRS 5504 & INRA 792, 135, avenue de Rangueil, 31077 TOULOUSE Cedex 4
| | - S Casimirius
- LAAS-CNRS, 7, avenue du Colonel Roche 31077 TOULOUSE Cedex 4
| | - E Trévisiol
- Biochips Platform Genopole Toulouse, UMR-CNRS 5504 & INRA 792, 135, avenue de Rangueil, 31077 TOULOUSE Cedex 4
- Laboratoire de Biotechnologie & Bioprocédés, UMR-CNRS 5504 & INRA 792, 135, avenue de Rangueil, 31077 TOULOUSE Cedex 4
| | - J François
- Biochips Platform Genopole Toulouse, UMR-CNRS 5504 & INRA 792, 135, avenue de Rangueil, 31077 TOULOUSE Cedex 4
- Laboratoire de Biotechnologie & Bioprocédés, UMR-CNRS 5504 & INRA 792, 135, avenue de Rangueil, 31077 TOULOUSE Cedex 4
| | - C Vieu
- LAAS-CNRS, 7, avenue du Colonel Roche 31077 TOULOUSE Cedex 4
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Bower JJ, Shi X. Environmental health research in the post-genome era: new fields, new challenges, and new opportunities. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2005; 8:71-94. [PMID: 15830463 DOI: 10.1080/10937400590909059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The human genome sequence provides researchers with a genetic framework to eventually understand the relationships of gene-environment interactions. This wealth of information has led to the birth of several related areas of research, including proteomics, functional genomics, pharmacogenomics, and toxicogenomics. Developing techniques such as DNA/protein microarrays, small-interfering RNA (siRNA) applications, two-dimensional gel electrophoresis, and mass spectrometry in conjunction with advanced analysis software and the availability of Internet databases offers a powerful set of tools to investigate an individual's response to specific stimuli. This review summarizes these emerging scientific fields and techniques focusing specifically on their applications to the complexities of gene-environment interactions and their potential role in environ-mental biosecurity.
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Affiliation(s)
- Jacquelyn J Bower
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia, USA
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Karaman MW, Groshen S, Lee CC, Pike BL, Hacia JG. Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays. Nucleic Acids Res 2005; 33:e33. [PMID: 15722479 PMCID: PMC549431 DOI: 10.1093/nar/gni034] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Revised: 01/20/2005] [Accepted: 02/04/2005] [Indexed: 12/02/2022] Open
Abstract
Although oligonucleotide probes complementary to single nucleotide substitutions are commonly used in microarray-based screens for genetic variation, little is known about the hybridization properties of probes complementary to small insertions and deletions. It is necessary to define the hybridization properties of these latter probes in order to improve the specificity and sensitivity of oligonucleotide microarray-based mutational analysis of disease-related genes. Here, we compare and contrast the hybridization properties of oligonucleotide microarrays consisting of 25mer probes complementary to all possible single nucleotide substitutions and insertions, and one and two base deletions in the 9168 bp coding region of the ATM (ataxia telangiectasia mutated) gene. Over 68 different dye-labeled single-stranded nucleic acid targets representing all ATM coding exons were applied to these microarrays. We assess hybridization specificity by comparing the relative hybridization signals from probes perfectly matched to ATM sequences to those containing mismatches. Probes complementary to two base substitutions displayed the highest average specificity followed by those complementary to single base substitutions, single base deletions and single base insertions. In all the cases, hybridization specificity was strongly influenced by sequence context and possible intra- and intermolecular probe and/or target structure. Furthermore, single nucleotide substitution probes displayed the most consistent hybridization specificity data followed by single base deletions, two base deletions and single nucleotide insertions. Overall, these studies provide valuable empirical data that can be used to more accurately model the hybridization properties of insertion and deletion probes and improve the design and interpretation of oligonucleotide microarray-based resequencing and mutational analysis.
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Affiliation(s)
- Mazen W. Karaman
- The Institute for Genetic Medicine, University of Southern CaliforniaLos Angeles, CA 90089, USA
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, University of Southern CaliforniaLos Angeles, CA 90089, USA
| | - Susan Groshen
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, University of Southern CaliforniaLos Angeles, CA 90089, USA
| | - Chi-Chiang Lee
- The Institute for Genetic Medicine, University of Southern CaliforniaLos Angeles, CA 90089, USA
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, University of Southern CaliforniaLos Angeles, CA 90089, USA
| | - Brian L. Pike
- The Institute for Genetic Medicine, University of Southern CaliforniaLos Angeles, CA 90089, USA
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, University of Southern CaliforniaLos Angeles, CA 90089, USA
| | - Joseph G. Hacia
- To whom correspondence should be addressed at The Institute for Genetic Medicine, University of Southern California, 2250 Alcazar Street, IGM 240 Los Angeles, CA 90089, USA. Tel: +1 323 442 3030; Fax: +1 323 442 2764;
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Zhou W, Du W, Cao H, Zhao J, Yang S, Li W, Shen Y, Zhang S, Du W, Zhang X. Detection of gyrA and parC mutations associated with ciprofloxacin resistance in Neisseria gonorrhoeae by use of oligonucleotide biochip technology. J Clin Microbiol 2005; 42:5819-24. [PMID: 15583317 PMCID: PMC535257 DOI: 10.1128/jcm.42.12.5819-5824.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An oligonucleotide biochip that specifically detects point mutations in the gyrA and parC genes of Neisseria gonorrhoeae was designed and subsequently evaluated with 87 untreated clinical specimens. The susceptibilities of the N. gonorrhoeae strains were tested to determine the prevalence of ciprofloxacin-resistant strains in Anhui Province, People's Republic of China. Conventional DNA sequencing was also performed to identify mutations in gyrA and parC and to confirm the biochip data. The study demonstrates that all of the point mutations in the gyrA and parC genes of N. gonorrhoeae were easily discriminated by use of the oligonucleotide biochip. Fifteen different alteration patterns involved in the formation of ciprofloxacin resistance were identified by the biochip assay. Double mutations in both Ser91 and Asp95 of the GyrA protein were seen in all nonsensitive isolates. Double mutations in Ser91 and Asp95 of GyrA plus mutation of Glu91 or Ser87 of the ParC protein lead to significant high-level resistance to ciprofloxacin in N. gonorrhoeae isolates. The results obtained by use of the oligonucleotide biochip were identical to those obtained by use of DNA sequencing. In conclusion, the oligonucleotide biochip technology has potential utility for the rapid and reliable identification of point mutations in the drug resistance genes of N. gonorrhoeae.
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Affiliation(s)
- Wenming Zhou
- Institute of Dermatology, Anhui Medical University, Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, People's Republic of China
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35
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Abstract
Newborn screening (NBS) is a public-health genetic screening programme aimed at early detection and treatment of pre-symptomatic children affected by specific disorders. It currently involves protein-based assays and PCR to confirm abnormal results. We propose that DNA microarray technology might be an improvement over protein assays in the first stage of NBS. This approach has important advantages, such as multiplex analysis, but also has disadvantages, which include a high initial cost and the analysis/storage of large data sets. Determining the optimal technology for NBS will require that technical, public health and ethical considerations are made for the collection and extent of analysis of paediatric genomic data, for privacy and for parental consent.
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Affiliation(s)
- Nancy S Green
- March of Dimes Birth Defect Foundation, 1275 Mamaroneck Avenue, White Plains, New York, 10605, USA.
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36
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Abstract
Transitional cell carcinoma of the bladder is a significant cause of morbidity and mortality worldwide. The diagnosis of bladder cancer is based on the information provided by cystoscopy, the gold standard, in combination with urinary cytology findings. Many tumor markers have been evaluated for detecting and monitoring of the disease in serum, bladder washes, and urinary specimens. However, none of these biomarkers reported to date has shown sufficient sensitivity and specificity for the detection of the whole spectrum of bladder cancer diseases in routine clinical practice. The advent of high-throughput microarrays is accelerating the identification process of the molecular events characteristic of bladder tumors' phenotype and subsequent clinical behavior. The information provided by these analyses is resulting not only in the identification of novel therapeutic targets for bladder cancer, but also in the development of diagnostic tools. This review summarizes the reports utilizing high-throughput microarrays in bladder cancer and the implications of these analyses in the diagnosis and clinical management of patients with bladder cancer.
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MESH Headings
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/urine
- Biomedical Research/trends
- Carcinoma, Transitional Cell/diagnosis
- Carcinoma, Transitional Cell/genetics
- Carcinoma, Transitional Cell/pathology
- Carcinoma, Transitional Cell/urine
- Cystoscopy
- Gene Expression Profiling
- Gene Targeting
- Humans
- Models, Biological
- Oligonucleotide Array Sequence Analysis
- Predictive Value of Tests
- Sequence Analysis, DNA
- Sequence Analysis, Protein
- Transcription, Genetic
- Urinary Bladder Neoplasms/diagnosis
- Urinary Bladder Neoplasms/genetics
- Urinary Bladder Neoplasms/pathology
- Urinary Bladder Neoplasms/urine
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Affiliation(s)
- Marta Sanchez-Carbayo
- Division of Molecular Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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37
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Liu Q, Sommer SS. PAP: detection of ultra rare mutations depends on P* oligonucleotides: "sleeping beauties" awakened by the kiss of pyrophosphorolysis. Hum Mutat 2004; 23:426-36. [PMID: 15108273 DOI: 10.1002/humu.20036] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Pyrophosphorolysis-activated polymerization (PAP) was initially developed to enhance the specificity of allele-specific PCR for detection of known mutations in the presence of a great excess of wild-type allele. The high specificity of PAP derives from the serial coupling of activation of a 3' blocked pyrophosphorolysis-activable oligonucleotide (P(*)) with extension of the unblocked, activated P(*). In theory, PAP can detect a copy of a single base mutation present in 3x10(11) copies of the wild-type allele. In practice, the selectivity of detection is limited by polymerase extension errors, a bypass reaction, from the unblocked oligonucleotide annealed to the opposing strand. Bi-directional PAP allele-specific amplification (Bi-PAP-A) is a derivative of PAP that uses two opposing pyrophosphorolysis activable oligonucleotides (P(*)) with one nucleotide overlap at their 3' termini. This eliminates the problematic bypass reaction. The selectivity of Bi-PAP-A was examined using lambda phage DNA as a model system. Bi-PAP-A selectively detected two copies of a rare mutated allele in the presence of at least 2x10(9) copies of the wild-type lambda phage DNA. We then applied Bi-PAP-A to direct detection of spontaneous somatic mutations in the lacI transgene in BigBlue transgenic mice at a frequency as low as 3x10(-9). A 370-fold variation in the frequency of a specific somatic mutation among different mouse samples was found, implying hyper-Poisson variance and clonal expansion of mutation occurring during early development. Bi-PAP-A is a simple, rapid, and general method capable of automation and particularly suited to detection of ultra rare mutations. We also show that P(*) oligonucleotides have the novel and unexpected property of high specificity to mismatches with the template throughout lengths of the P(*). Thus, PAP also can form the basis of microarray-based scanning or resequencing methods to detect virtually all mutations.
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Affiliation(s)
- Qiang Liu
- Department of Molecular Genetics, City of Hope National Medical Center, Duarte, California 91010-3000, USA
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38
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Abstract
The haemoglobinopathies refer to a diverse group of inherited disorders characterized by a reduced synthesis of one or more globin chains (thalassaemias) or the synthesis of a structurally abnormal haemoglobin (Hb). In prevalent regions, the thalassaemias often coexist with a variety of structural Hb variants giving rise to complex genotypes and an extremely wide spectrum of clinical and haematological phenotypes. An appreciation of these phenotypes is needed to facilitate the definitive diagnosis of the causative mutations to inform management and counselling. Haematological and biochemical investigations, and family studies provide essential clues to the different interactions and are fundamental to DNA diagnostics of the Hb disorders. With the exception of a few rare deletions and rearrangements, the molecular lesions causing haemoglobinopathies are all identifiable by PCR-based techniques. Although a full spectrum of >1000 mutations causing haemoglobinopathies has been documented, in practice only a limited number are associated with disease states and clinical significance. Furthermore, each at-risk ethnic group has its own combination of common Hb variants and thalassaemia mutations. Prior identification of the ethnic origin is thus an important part of the diagnostic strategy which becomes less reliable in the UK because of the large ethnic mix. Although the current approach using a combination of different PCR-based techniques seems to work in most laboratories, practice pressures with the imminent implementation of universal antenatal screening for clinically significant Hb disorders in the UK will require a higher throughput approach for DNA diagnostics in the near future. The complex mutational spectrum and the compactness of the globin genes places them in an ideal position for the different non-gel based analytical platforms.
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Affiliation(s)
- B E Clark
- Department of Haematological Medicine, King's College Hospital and GKT School of Medicine, Denmark Hill, London, UK
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39
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Wade MM, Volokhov D, Peredelchuk M, Chizhikov V, Zhang Y. Accurate mapping of mutations of pyrazinamide-resistant Mycobacterium tuberculosis strains with a scanning-frame oligonucleotide microarray. Diagn Microbiol Infect Dis 2004; 49:89-97. [PMID: 15183857 DOI: 10.1016/j.diagmicrobio.2004.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2003] [Accepted: 01/08/2004] [Indexed: 12/22/2022]
Abstract
The increasing emergence of drug-resistant Mycobacterium tuberculosis poses significant threat to the treatment of tuberculosis. Conventional susceptibility testing for the front-line tuberculosis drug pyrazinamide (PZA) is difficult, because of the requirement for acid pH for the drug to show activity. Resistance to PZA in M. tuberculosis is caused by mutations in the pncA gene, and detection of pncA mutations can be an indicator of PZA resistance. In this study, we examined the feasibility of a microarray-based approach exploiting short overlapping oligonucleotides (sliding-frame array) to rapidly detect pncA mutations (substitutions, deletions, and insertions) in multiple strains of PZA-resistant M. tuberculosis. The genetic mapping of these mutations is necessary to link the gene sequence to the protein function defined by mutant phenotype. Microarray analysis was performed in a blind manner using 57 isolates of M. tuberculosis for which the sequence of the pncA gene was previously determined. Our results showed that all mutations could be unambiguously detected, suggesting that microarray can be a routine and valuable tool for rapid identification of drug-resistant M. tuberculosis isolates. We expect that mutation mapping with a sliding-frame microarray will accelerate the molecular analysis of drug-resistant M. tuberculosis bacteria and the microorganism populations.
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Affiliation(s)
- Mary Margaret Wade
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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40
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Sánchez-Carbayo M, Cordon-Cardo C. Applications of array technology: identification of molecular targets in bladder cancer. Br J Cancer 2004; 89:2172-7. [PMID: 14676790 PMCID: PMC2395269 DOI: 10.1038/sj.bjc.6601406] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
High-throughput microarrays are being used in expression profiling analyses with the objectives of gene and pathway discovery, functional characterization of genes, and tumor subclassification. This review summarizes bladder cancer studies dealing with both in vitro models and clinical specimens, using distinct microarray platforms for target discovery.
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Affiliation(s)
- M Sánchez-Carbayo
- Division of Molecular Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.
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41
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Coleman WB. Cancer Bioinformatics: Addressing the Challenges of Integrated Postgenomic Cancer Research. Cancer Invest 2004. [DOI: 10.1081/cnv-120027591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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42
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Lu M, Knickerbocker T, Cai W, Yang W, Hamers RJ, Smith LM. Invasive cleavage reactions on DNA-modified diamond surfaces. Biopolymers 2004; 73:606-13. [PMID: 15048784 DOI: 10.1002/bip.20007] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recently developed DNA-modified diamond surfaces exhibit excellent chemical stability to high-temperature incubations in biological buffers. The stability of these surfaces is substantially greater than that of gold or silicon surfaces, using similar surface attachment chemistry. The DNA molecules attached to the diamond surfaces are accessible to enzymes and can be modified in surface enzymatic reactions. An important application of these surfaces is for surface invasive cleavage reactions, in which target DNA strands added to the solution may result in specific cleavage of surface-bound probe oligonucleotides, permitting analysis of single nucleotide polymorphisms (SNPs). Our previous work demonstrated the feasibility of performing such cleavage reactions on planar gold surfaces using PCR-amplified human genomic DNA as target. The sensitivity of detection in this earlier work was substantially limited by a lack of stability of the gold surface employed. In the present work, detection sensitivity is improved by a factor of approximately 100 (100 amole of DNA target compared with 10 fmole in the earlier work) by replacing the DNA-modified gold surface with a more stable DNA-modified diamond surface.
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Affiliation(s)
- Manchun Lu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1396, USA
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43
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44
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Affiliation(s)
- Urvashi Bhardwaj
- Department of Pediatrics, 22-412 MDCC, David Geffen School of Medicine at UCLA, 10833 Le Conte Avenue, Los Angeles, CA 90095-1752, USA
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45
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Le Berre V, Trévisiol E, Dagkessamanskaia A, Sokol S, Caminade AM, Majoral JP, Meunier B, François J. Dendrimeric coating of glass slides for sensitive DNA microarrays analysis. Nucleic Acids Res 2003; 31:e88. [PMID: 12907740 PMCID: PMC169980 DOI: 10.1093/nar/gng088] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2003] [Revised: 06/03/2003] [Accepted: 06/03/2003] [Indexed: 11/13/2022] Open
Abstract
Successful use and reliability of microarray technology is highly dependent on several factors, including surface chemistry parameters and accessibility of cDNA targets to the DNA probes fixed onto the surface. Here, we show that functionalisation of glass slides with homemade dendrimers allow production of more sensitive and reliable DNA microarrays. The dendrimers are nanometric structures of size-controlled diameter with aldehyde function at their periphery. Covalent attachment of these spherical reactive chemical structures on amino-silanised glass slides generates a reactive approximately 100 A layer onto which amino-modified DNA probes are covalently bound. This new grafting chemistry leads to the formation of uniform and homogenous spots. More over, probe concentration before spotting could be reduced from 0.2 to 0.02 mg/ml with PCR products and from 20 to 5 micro M with 70mer oligonucleotides without affecting signal intensities after hybridisation with Cy3- and Cy5-labelled targets. More interestingly, while the binding capacity of captured probes on dendrimer-activated glass surface (named dendrislides) is roughly similar to other functionalised glass slides from commercial sources, detection sensitivity was 2-fold higher than with other available DNA microarrays. This detection limit was estimated to 0.1 pM of cDNA targets. Altogether, these features make dendrimer-activated slides ideal for manufacturing cost-effective DNA arrays applicable for gene expression and detection of mutations.
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Affiliation(s)
- Véronique Le Berre
- Transcriptome-Biochips Platform of Genopole Toulouse Midi-Pyrénées, Centre de Bioingénierie Gilbert Durand UMR-CNRS 5504, UMR-INRA 792, Institut National des Sciences Appliquées, F-31077 Toulouse cedex 04, France
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46
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Brightwell G, Wycherley R, Waghorn A. SNP genotyping using a simple and rapid single-tube modification of ARMS illustrated by analysis of 6 SNPs in a population of males with FRAXA repeat expansions. Mol Cell Probes 2003; 16:297-305. [PMID: 12270271 DOI: 10.1006/mcpr.2002.0424] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microsatellites have been used extensively in gene mapping, linkage and association studies but with the near completion of the human genome project (HGP) single nucleotide polymorphisms (SNP) have become the marker of choice. However, for association studies to be useful large numbers of SNPs must be analysed. To make these studies cost effective a simple and non-labour intensive method for SNP genotyping is essential. This work describes a single-tube modification of the amplification refractory mutation system (Biallelic-ARMS). Control amplimers flanking the SNP were amplified in a single-tube multiplex PCR with two SNP specific primers that prime in opposite directions. The SNP allele was identified on the basis of PCR product size after gel electrophoresis. Biallelic-ARMS was used to analyse six SNPs within 300 kb of the FRAXA repeat, two from the HGP SNP Database (ATL1 and FMRb) and four novel SNPs (WEX1, WEX10, WEX17 and WEX28). The study population consisted of 649 males with a range of FRAXA (10 to >200) repeat sizes. Each SNP correlated with distinct haplogroups, as identified by DXS548, FRAXAC1 and FRAXAC2 flanking microsatellite repeat patterns and confirmed the initial choice of haplogroups for FRAXA repeat stability defined by Enniset al.
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Affiliation(s)
- G Brightwell
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, UK.
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47
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Ketomäki K, Hakala H, Kuronen O, Lönnberg H. Hybridization properties of support-bound oligonucleotides: the effect of the site of immobilization on the stability and selectivity of duplex formation. Bioconjug Chem 2003; 14:811-6. [PMID: 12862435 DOI: 10.1021/bc0340058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four 12-mer oligodeoxyribonucleotide sequences were immobilized to uniformly sized (50 microm) polymer particles through C5-tethered thymine and N(4)-tethered cytosine bases at four different sites in each sequence. The effect of the site of immobilization on the efficiency and selectivity of hybridization of the particle-bound probes was quantified by a sandwich-type assay based on a time-resolved fluorometric measurement of an oligonucleotide probe labeled with a photoluminescent europium(III) chelate directly from the surface of a single particle. Immobilization through a base in the central part of the sequence was observed to destablize the duplex more markedly than tethering through a terminal base. The effect of a one-base mismatch on the duplex stability increased with the increasing distance from the site of immobilization.
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Affiliation(s)
- Kaisa Ketomäki
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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48
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Chandler DP, Newton GJ, Small JA, Daly DS. Sequence versus structure for the direct detection of 16S rRNA on planar oligonucleotide microarrays. Appl Environ Microbiol 2003; 69:2950-8. [PMID: 12732571 PMCID: PMC154527 DOI: 10.1128/aem.69.5.2950-2958.2003] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A two-probe proximal chaperone detection system consisting of a species-specific capture probe for the microarray and a labeled, proximal chaperone probe for detection was recently described for direct detection of intact rRNAs from environmental samples on oligonucleotide arrays. In this study, we investigated the physical spacing and nucleotide mismatch tolerance between capture and proximal chaperone detector probes that are required to achieve species-specific 16S rRNA detection for the dissimilatory metal and sulfate reducer 16S rRNAs. Microarray specificity was deduced by analyzing signal intensities across replicate microarrays with a statistical analysis-of-variance model that accommodates well-to-well and slide-to-slide variations in microarray signal intensity. Chaperone detector probes located in immediate proximity to the capture probe resulted in detectable, nonspecific binding of nontarget rRNA, presumably due to base-stacking effects. Species-specific rRNA detection was achieved by using a 22-nt capture probe and a 15-nt detector probe separated by 10 to 14 nt along the primary sequence. Chaperone detector probes with up to three mismatched nucleotides still resulted in species-specific capture of 16S rRNAs. There was no obvious relationship between position or number of mismatches and within- or between-genus hybridization specificity. From these results, we conclude that relieving secondary structure is of principal concern for the successful capture and detection of 16S rRNAs on planar surfaces but that the sequence of the capture probe is more important than relieving secondary structure for achieving specific hybridization.
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MESH Headings
- Base Sequence
- Deltaproteobacteria/genetics
- Deltaproteobacteria/isolation & purification
- Desulfovibrio/genetics
- Desulfovibrio/isolation & purification
- Environmental Microbiology
- Molecular Sequence Data
- Nucleic Acid Conformation
- Oligonucleotide Array Sequence Analysis/methods
- Oligonucleotide Array Sequence Analysis/statistics & numerical data
- Oligonucleotide Probes/genetics
- RNA, Bacterial/analysis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- Sequence Homology, Nucleic Acid
- Shewanella putrefaciens/genetics
- Shewanella putrefaciens/isolation & purification
- Species Specificity
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Affiliation(s)
- Darrell P Chandler
- Biochip Technology Center, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, A-249, Argonne, IL 60439, USA.
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49
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Bates MD. The potential of DNA microarrays for the care of children. J Pediatr 2003; 142:235-9. [PMID: 12640368 DOI: 10.1067/mpd.2003.88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Michael D Bates
- Division of Gastroenterology, Hepatology, and Nutrition, and the Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.
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50
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Wang Y, Vaidya B, Farquar HD, Stryjewski W, Hammer RP, McCarley RL, Soper SA, Cheng YW, Barany F. Microarrays assembled in microfluidic chips fabricated from poly(methyl methacrylate) for the detection of low-abundant DNA mutations. Anal Chem 2003; 75:1130-40. [PMID: 12641233 DOI: 10.1021/ac020683w] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Low-density arrays were assembled into microfluidic channels hot-embossed in poly(methyl methacrylate) (PMMA) to allow the detection of low-abundant mutations in gene fragments (K-ras) that carry point mutations with high diagnostic value for colorectal cancers. Following spotting, the chip was assembled with a cover plate and the array accessed using microfluidics in order to enhance the kinetics associated with hybridization. The array was configured with zip code sequences (24-mers) that were complementary to sequences present on the target. The hybridization targets were generated using an allele-specific ligase detection reaction (LDR), in which two primers (discriminating primer that carriers the complement base to the mutation being interrogated and a common primer) that flank the point mutation and were ligated joined together) only when the particular mutation was present in the genomic DNA. The discriminating primer contained on its 5'-end the zip code complement (directs the LDR product to the appropriate site of the array), and the common primer carried on its 3' end a fluorescent dye (near-IR dye IRD-800). The coupling chemistry (5'-amine-containing oligonucleotide tethered to PMMA surface) was optimized to maximize the loading level of the zip code oligonucleotide, improve hybridization sensitivity (detection of low-abundant mutant DNAs in high copy numbers of normal sequences), and increase the stability of the linkage chemistry to permit re-interrogation of the array. It was found that microfluidic addressing of the array reduced the hybridization time from 3 h for a conventional array to less than 1 min. In addition, the coupling chemistry allowed reuse of the array > 12 times before noticing significant loss of hybridization signal. The array was used to detect a point mutation in a K-ras oncogene at a level of 1 mutant DNA in 10,000 wild-type sequences.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803-1804, USA
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