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Sajid S, Mashkoor M, Jørgensen MG, Christensen LP, Hansen PR, Franzyk H, Mirza O, Prabhala BK. The Y-ome Conundrum: Insights into Uncharacterized Genes and Approaches for Functional Annotation. Mol Cell Biochem 2024; 479:1957-1968. [PMID: 37610616 DOI: 10.1007/s11010-023-04827-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023]
Abstract
The ever-increasing availability of genome sequencing data has revealed a substantial number of uncharacterized genes without known functions across various organisms. The first comprehensive genome sequencing of E. coli K12 revealed that more than 50% of its open reading frames corresponded to transcripts with no known functions. The group of protein-coding genes without a functional description and/or a recognized pathway, beginning with the letter "Y", is classified as the "y-ome". Several efforts have been made to elucidate the functions of these genes and to recognize their role in biological processes. This review provides a brief update on various strategies employed when studying the y-ome, such as high-throughput experimental approaches, comparative omics, metabolic engineering, gene expression analysis, and data integration techniques. Additionally, we highlight recent advancements in functional annotation methods, including the use of machine learning, network analysis, and functional genomics approaches. Novel approaches are required to produce more precise functional annotations across the genome to reduce the number of genes with unknown functions.
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Affiliation(s)
- Salvia Sajid
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Maliha Mashkoor
- Department of Surgery, Center for Surgical Sciences, Zealand University Hospital, Lykkebækvej 1, 4600, Køge, Denmark
| | - Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Lars Porskjær Christensen
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Bala Krishna Prabhala
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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Wiwanitkit V. Utilization of multiple "omics" studies in microbial pathogeny for microbiology insights. Asian Pac J Trop Biomed 2015; 3:330-3. [PMID: 23620861 DOI: 10.1016/s2221-1691(13)60073-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 02/20/2013] [Indexed: 11/28/2022] Open
Abstract
In the present day, bioinformatics becomes the modern science with several advantages. Several new "omics" sciences have been introduced for a few years and those sciences can be applied in biomedical work. Here, the author will summarize and discuss on important applications of omics studies in microbiology focusing on microbial pathogeny. It can be seen that genomics and proteinomics can be well used in this area of biomedical studies.
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Fakruddin M, Mannan KSB, Chowdhury A, Mazumdar RM, Hossain MN, Islam S, Chowdhury MA. Nucleic acid amplification: Alternative methods of polymerase chain reaction. J Pharm Bioallied Sci 2014; 5:245-52. [PMID: 24302831 PMCID: PMC3831736 DOI: 10.4103/0975-7406.120066] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 02/24/2013] [Accepted: 08/16/2013] [Indexed: 01/05/2023] Open
Abstract
Nucleic acid amplification is a valuable molecular tool not only in basic research but also in application oriented fields, such as clinical medicine development, infectious diseases diagnosis, gene cloning and industrial quality control. A comperehensive review of the literature on the principles, applications, challenges and prospects of different alternative methods of polymerase chain reaction (PCR) was performed. PCR was the first nucleic acid amplification method. With the advancement of research, a no of alternative nucleic acid amplification methods has been developed such as loop mediated isothermal amplification, nucleic acid sequence based amplification, strand displacement amplification, multiple displacement amplification. Most of the alternative methods are isothermal obviating the need for thermal cyclers. Though principles of most of the alternate methods are relatively complex than that of PCR, they offer better applicability and sensitivity in cases where PCR has limitations. Most of the alternate methods still have to prove themselves through extensive validation studies and are not available in commercial form; they pose the potentiality to be used as replacements of PCR. Continuous research is going on in different parts of the world to make these methods viable technically and economically.
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Affiliation(s)
- Md Fakruddin
- Industrial Microbiology Laboratory, Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
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Wang J, Aki M, Onoshima D, Arinaga K, Kaji N, Tokeshi M, Fujita S, Yokoyama N, Baba Y. Microfluidic biosensor for the detection of DNA by fluorescence enhancement and the following streptavidin detection by fluorescence quenching. Biosens Bioelectron 2014; 51:280-5. [DOI: 10.1016/j.bios.2013.07.058] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/16/2013] [Accepted: 07/30/2013] [Indexed: 12/11/2022]
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Brückner K, Schwarz K, Beck S, Linscheid MW. DNA Quantification via ICP-MS Using Lanthanide-Labeled Probes and Ligation-Mediated Amplification. Anal Chem 2013; 86:585-91. [DOI: 10.1021/ac402668p] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kathrin Brückner
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Kathleen Schwarz
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Sebastian Beck
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Michael W. Linscheid
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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Pipkorn R, Rawer S, Wiessler M, Waldeck W, Koch M, Schrenk HH, Braun K. SPPS resins impact the PNA-syntheses' improvement. Int J Med Sci 2013; 10:331-7. [PMID: 23423830 PMCID: PMC3575629 DOI: 10.7150/ijms.5374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/19/2012] [Indexed: 01/07/2023] Open
Abstract
The personalized medicine, also documented as "individualized medicine", is an effective and therapeutic approach. It is designed to treat the disease of the individual patient whose precise differential gene expression profile is well known. The trend in the biomedical and biophysical research shows important consequences for the pharmaceutical drug and diagnostics research. It requires a high variability in the design and safety of target-specific pharmacologically active molecules and diagnostic components for imaging of metabolic processes. A key technology which may fulfill the highest demands during synthesis of these individual drugs and diagnostics is the solid phase synthesis which is congenial to automated manufacturing. Additionally the choice of tools like resins and reagents is pivotal to synthesize drugs and diagnostics in high quality and yields. Here we demonstrate the solid phase synthesis effects dependent on the choice of resin and of the deprotection agent.
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Affiliation(s)
- Rüdiger Pipkorn
- German Cancer Research Center, Peptide Synthesis Core Facility, INF 280, D-69120 Heidelberg, Germany.
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Kalyanasundaram D, Kim JH, Yeo WH, Oh K, Lee KH, Kim MH, Ryew SM, Ahn SG, Gao D, Cangelosi GA, Chung JH. Rapid extraction and preservation of genomic DNA from human samples. Anal Bioanal Chem 2013; 405:1977-83. [PMID: 23307121 DOI: 10.1007/s00216-012-6637-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/24/2012] [Accepted: 12/06/2012] [Indexed: 11/29/2022]
Abstract
Simple and rapid extraction of human genomic DNA remains a bottleneck for genome analysis and disease diagnosis. Current methods using microfilters require cumbersome, multiple handling steps in part because salt conditions must be controlled for attraction and elution of DNA in porous silica. We report a novel extraction method of human genomic DNA from buccal swab and saliva samples. DNA is attracted onto a gold-coated microchip by an electric field and capillary action while the captured DNA is eluted by thermal heating at 70 °C. A prototype device was designed to handle four microchips, and a compatible protocol was developed. The extracted DNA using microchips was characterized by qPCR for different sample volumes, using different lengths of PCR amplicon, and nuclear and mitochondrial genes. In comparison with a commercial kit, an equivalent yield of DNA extraction was achieved with fewer steps. Room-temperature preservation for 1 month was demonstrated for captured DNA, facilitating straightforward collection, delivery, and handling of genomic DNA in an environment-friendly protocol.
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Affiliation(s)
- D Kalyanasundaram
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA
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McBride CM, Wade CH, Kaphingst KA. Consumers' views of direct-to-consumer genetic information. Annu Rev Genomics Hum Genet 2010; 11:427-46. [PMID: 20690815 DOI: 10.1146/annurev-genom-082509-141604] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this report, we describe the evolution and types of genetic information provided directly to consumers, discuss potential advantages and disadvantages of these products, and review research evaluating consumer responses to direct-to-consumer (DTC) genetic testing. The available evidence to date has focused on predictive tests and does not suggest that individuals, health care providers, or health care systems have been harmed by a DTC provision of genetic information. An understanding of consumer responses to susceptibility tests has lagged behind. The Multiplex Initiative is presented as a case study of research to understand consumers' responses to DTC susceptibility tests. Three priority areas are recommended for accelerated research activities to inform public policy regarding DTC genetic information: (a) exploring consumer's long-term responses to DTC genetic testing on a comprehensive set of outcomes, (b) evaluating optimal services to support decision making about genetic testing, and (c) evaluating best practices in promoting genetic competencies among health providers.
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Affiliation(s)
- Colleen M McBride
- Social and Behavioral Research Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA.
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Silva LB, Veigas B, Doria G, Costa P, Inácio J, Martins R, Fortunato E, Baptista PV. Portable optoelectronic biosensing platform for identification of mycobacteria from the Mycobacterium tuberculosis complex. Biosens Bioelectron 2010; 26:2012-7. [PMID: 20875731 DOI: 10.1016/j.bios.2010.08.078] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 08/27/2010] [Accepted: 08/31/2010] [Indexed: 11/17/2022]
Abstract
In this paper we report on the fabrication and performance of a portable and low cost optoelectronic platform integrating a double color tuned light emitting diode as light source, an amorphous/nanocrystalline silicon photodetector with a flat spectral response in the wavelength range from 520 nm to 630 nm and integrated electronic for signal acquisition and conditioning constituted by current to voltage converter, a filter and an amplification stage, followed by an analog to digital converter, with appropriate software for full automation to minimize human error. Incorporation of the double color tuned light emitting diode provides for a simple yet innovative solution to signal acquisition independently from the light intensity and/or solution concentration, while considerably decreasing production costs. Detection based on Au-nanoprobes constitutes the biorecognition step and allowed identification of specific sequences of Mycobacterium tuberculosis complex, namely Mycobacterium bovis and M. tuberculosis in biological samples.
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Affiliation(s)
- Leonardo Bione Silva
- CENIMAT/I3N, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa and CEMOP-UNINOVA, 2829-516 Caparica, Portugal
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Abstract
Transfusion safety relating to blood-transmissible agents is a major public health concern, particularly when faced with the continuing emergence of new infectious agents. These include new viruses appearing alongside other known reemerging viruses (West Nile virus, Chikungunya) as well as new strains of bacteria and parasites (Plasmodium falciparum, Trypanosoma cruzi) and finally pathologic prion protein (variant Creutzfeldt-Jakob disease). Genomic mutations of known viruses (hepatitis B virus, hepatitis C virus, human immunodeficiency virus) can also be at the origin of variants susceptible to escaping detection by diagnostic tests. New technologies that would allow the simultaneous detection of several blood-transmissible agents are now needed for the development and improvement of screening strategies. DNA microarrays have been developed for use in immunohematology laboratories for blood group genotyping. Their application in the detection of infectious agents, however, has been hindered by additional technological hurdles. For instance, the variability among and within genomes of interest complicate target amplification and multiplex analysis. Advances in biosensor technologies based on alternative detection strategies have offered new perspectives on pathogen detection; however, whether they are adaptable to diagnostic applications testing biologic fluids is under debate. Elsewhere, current nanotechnologies now offer new tools to improve the sample preparation, target capture, and detection steps. Second-generation devices combining micro- and nanotechnologies have brought us one step closer to the potential development of innovative and multiplexed approaches applicable to the screening of blood for transmissible agents.
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Affiliation(s)
- Chantal Fournier-Wirth
- Laboratoire de R&D-Agents Transmissibles par Transfusion (R&D-ATT), Etablissement Français du Sang Pyrénées-Méditerranée, Montpellier, France.
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12
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Lutz S, Weber P, Focke M, Faltin B, Hoffmann J, Müller C, Mark D, Roth G, Munday P, Armes N, Piepenburg O, Zengerle R, von Stetten F. Microfluidic lab-on-a-foil for nucleic acid analysis based on isothermal recombinase polymerase amplification (RPA). LAB ON A CHIP 2010; 10:887-93. [PMID: 20300675 DOI: 10.1039/b921140c] [Citation(s) in RCA: 243] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
For the first time we demonstrate a self-sufficient lab-on-a-foil system for the fully automated analysis of nucleic acids which is based on the recently available isothermal recombinase polymerase amplification (RPA). The system consists of a novel, foil-based centrifugal microfluidic cartridge including prestored liquid and dry reagents, and a commercially available centrifugal analyzer for incubation at 37 degrees C and real-time fluorescence detection. The system was characterized with an assay for the detection of the antibiotic resistance gene mecA of Staphylococcus aureus. The limit of detection was <10 copies and time-to-result was <20 min. Microfluidic unit operations comprise storage and release of liquid reagents, reconstitution of lyophilized reagents, aliquoting the sample into < or = 30 independent reaction cavities, and mixing of reagents with the DNA samples. The foil-based cartridge was produced by blow-molding and sealed with a self-adhesive tape. The demonstrated system excels existing PCR based lab-on-a-chip platforms in terms of energy efficiency and time-to-result. Applications are suggested in the field of mobile point-of-care analysis, B-detection, or in combination with continuous monitoring systems.
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Affiliation(s)
- Sascha Lutz
- HSG-IMIT, Wilhelm-Schickard-Strasse 10, D-78052, Villingen-Schwenningen, Germany.
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13
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Lau A, Chen S, Sleiman S, Sorrell T. Current status and future perspectives on molecular and serological methods in diagnostic mycology. Future Microbiol 2009; 4:1185-222. [DOI: 10.2217/fmb.09.70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.
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Affiliation(s)
- Anna Lau
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia
| | - Sharon Chen
- Centre for Infectious Diseases & Microbiology, University of Sydney, Sydney, Australia and Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sue Sleiman
- Centre for Infectious Diseases & Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Tania Sorrell
- Centre for Infectious Diseases & Microbiology, Westmead Hospital, Darcy and Hawkesbury Roads, Westmead, NSW 2145, Australia
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Raymaekers M, Smets R, Maes B, Cartuyvels R. Checklist for optimization and validation of real-time PCR assays. J Clin Lab Anal 2009; 23:145-51. [PMID: 19455629 DOI: 10.1002/jcla.20307] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Real-time polymerase chain reaction (PCR) is a frequently used technique in molecular diagnostics. To date, practical guidelines for the complete process of optimization and validation of commercial and in-house developed molecular diagnostic methods are scare. Therefore, we propose a practical guiding principle for the optimization and validation of real-time PCR assays. Based on literature, existing guidelines, and personal experience, we created a checklist that can be used in different steps of the development and validation process of commercial and in-house developed real-time PCR assays. Furthermore, determination of target values and reproducibility of internal quality controls are included, which allows a statistical follow-up of the performance of the assay. Recently, we used this checklist for the development of various qualitative and quantitative assays for microbiological and hematological applications, for which accreditation according to ISO 15189:2007 was obtained. In our experience, the use of the proposed guidelines leads to a more efficient and standardized optimization and validation. Ultimately, this results in reliable and robust molecular diagnostics. The proposed checklist is independent of environment, equipment, and specific applications and can be used in other laboratories. A worldwide consensus on this kind of checklist should be aimed at.
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Affiliation(s)
- Marijke Raymaekers
- Molecular Biology, Clinical Laboratory, Virga Jesse Hospital, Hasselt, Belgium.
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15
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Hansen RR, Johnson LM, Bowman CN. Visual, base-specific detection of nucleic acid hybridization using polymerization-based amplification. Anal Biochem 2009; 386:285-7. [DOI: 10.1016/j.ab.2008.12.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 12/05/2008] [Accepted: 12/09/2008] [Indexed: 11/30/2022]
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Kraytsberg Y, Bodyak N, Myerow S, Nicholas A, Ebralidze K, Khrapko K. Quantitative analysis of somatic mitochondrial DNA mutations by single-cell single-molecule PCR. Methods Mol Biol 2009; 554:329-69. [PMID: 19513684 DOI: 10.1007/978-1-59745-521-3_21] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial genome integrity is an important issue in somatic mitochondrial genetics. Development of quantitative methods is indispensable to somatic mitochondrial genetics as quantitative studies are required to characterize heteroplasmy and mutation processes, as well as their effects on phenotypic developments. Quantitative studies include the identification and measurement of the load of pathogenic and non-pathogenic clonal mutations, screening mitochondrial genomes for mutations in order to determine the mutation spectra and characterize an ongoing mutation process. Single-molecule PCR (smPCR) has been shown to be an effective method that can be applied to all areas of quantitative studies. It has distinct advantages over conventional vector-based cloning techniques avoiding the well-known PCR-related artifacts such as the introduction of artificial mutations, preferential allelic amplifications, and "jumping" PCR. smPCR is a straightforward and robust method, which can be effectively used for molecule-by-molecule mutational analysis, even when mitochondrial whole genome (mtWG) analysis is involved. This chapter describes the key features of the smPCR method and provides three examples of its applications in single-cell analysis: di-plex smPCR for deletion quantification, smPCR cloning for clonal point mutation quantification, and smPCR cloning for whole genome sequencing (mtWGS).
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Affiliation(s)
- Yevgenya Kraytsberg
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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Morisset D, Dobnik D, Hamels S, Zel J, Gruden K. NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs. Nucleic Acids Res 2008; 36:e118. [PMID: 18710880 PMCID: PMC2566881 DOI: 10.1093/nar/gkn524] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 07/30/2008] [Accepted: 07/31/2008] [Indexed: 11/12/2022] Open
Abstract
We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1-25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification.
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Affiliation(s)
- Dany Morisset
- Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 111, Ljubljana 1000, Slovenia and Eppendorf Array Technologies SA, Rue du séminaire 20, B-5000 Namur, Belgium.
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18
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Kranaster R, Ketzer P, Marx A. Mutant DNA polymerase for improved detection of single-nucleotide variations in microarrayed primer extension. Chembiochem 2008; 9:694-7. [PMID: 18247447 DOI: 10.1002/cbic.200700609] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ramon Kranaster
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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19
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Alternative DNA amplification methods to PCR and their application in GMO detection: a review. Eur Food Res Technol 2008. [DOI: 10.1007/s00217-008-0850-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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20
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Feasibility of transferring fluorescent in situ hybridization probes to an 18S rRNA gene phylochip and mapping of signal intensities. Appl Environ Microbiol 2008; 74:2814-21. [PMID: 18326673 DOI: 10.1128/aem.02122-07] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA microarray technology offers the possibility to analyze microbial communities without cultivation, thus benefiting biodiversity studies. We developed a DNA phylochip to assess phytoplankton diversity and transferred 18S rRNA probes from dot blot or fluorescent in situ hybridization (FISH) analyses to a microarray format. Similar studies with 16S rRNA probes have been done determined that in order to achieve a signal on the microarray, the 16S rRNA molecule had to be fragmented, or PCR amplicons had to be <150 bp in length to minimize the formation of a secondary structure in the molecule so that the probe could bind to the target site. We found different results with the 18S rRNA molecule. Four out of 12 FISH probes exhibited false-negative signals on the microarray; eight exhibited strong but variable signals using full-length 18S RNA molecules. A systematic investigation of the probe's accessibility to the 18S rRNA gene was made using Prymenisum parvum as the target. Fourteen additional probes identical to this target covered the regions not tested with existing FISH probes. Probes with a binding site in the first 900 bp of the gene generated positive signals. Six out of nine probes binding in the last 900 bp of the gene produced no signal. Our results suggest that although secondary structure affected probe binding, the effect is not the same for the 18S rRNA gene and the 16S rRNA gene. For the 16S rRNA gene, the secondary structure is stronger in the first half of the molecule, whereas in the 18S rRNA gene, the last half of the molecule is critical. Probe-binding sites within 18S rRNA gene molecules are important for the probe design for DNA phylochips because signal intensity appears to be correlated with the secondary structure at the binding site in this molecule. If probes are designed from the first half of the 18S rRNA molecule, then full-length 18S rRNA molecules can be used in the hybridization on the chip, avoiding the fragmentation and the necessity for the short PCR amplicons that are associated with using the 16S rRNA molecule. Thus, the 18S rRNA molecule is a more attractive molecule for use in environmental studies where some level of quantification is desired. Target size was a minor problem, whereas for 16S rRNA molecules target size rather than probe site was important.
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METFIES KATJA, BORSUTZKI PHILIPP, GESCHER CHRISTINE, MEDLIN LINDAK, FRICKENHAUS STEPHAN. phylochipanalyser — a program for analysing hierarchical probe sets. Mol Ecol Resour 2008; 8:99-102. [DOI: 10.1111/j.1471-8286.2007.01927.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Plummer PJ. Molecular diagnostics for the food animal practitioner. Vet Clin North Am Food Anim Pract 2007; 23:481-501, vi. [PMID: 17920458 DOI: 10.1016/j.cvfa.2007.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Molecular diagnostics are becoming widely used as routine diagnostic tests performed by food animal practitioners. This article discusses the variations of several commonly performed molecular assays with regard to their molecular basis and the appropriate interpretation of the results. Applications of these methods are discussed in the context of infectious disease testing and genetic testing of food animal species.
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Affiliation(s)
- Paul J Plummer
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1710 Veterinary Medicine Complex, Ames, IA 50011-1250, USA.
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METFIES KATJA, BERZANO MARCO, MAYER CHRISTIAN, ROOSKEN PAUL, GUALERZI CLAUDIO, MEDLIN LINDA, MUYZER GERARD. An optimized protocol for the identification of diatoms, flagellated algae and pathogenic protozoa with phylochips. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01799.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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24
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Rant U, Arinaga K, Scherer S, Pringsheim E, Fujita S, Yokoyama N, Tornow M, Abstreiter G. Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets. Proc Natl Acad Sci U S A 2007; 104:17364-9. [PMID: 17951434 PMCID: PMC2077262 DOI: 10.1073/pnas.0703974104] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Indexed: 11/18/2022] Open
Abstract
We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 x 10(8) bound targets per cm(2) sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format.
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Affiliation(s)
- Ulrich Rant
- Walter Schottky Institut, Technische Universität München, 85748 Garching, Germany.
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25
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Akhras MS, Unemo M, Thiyagarajan S, Nyrén P, Davis RW, Fire AZ, Pourmand N. Connector inversion probe technology: a powerful one-primer multiplex DNA amplification system for numerous scientific applications. PLoS One 2007; 2:e915. [PMID: 17878950 PMCID: PMC1976392 DOI: 10.1371/journal.pone.0000915] [Citation(s) in RCA: 29] [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: 07/19/2007] [Accepted: 08/20/2007] [Indexed: 01/26/2023] Open
Abstract
We combined components of a previous assay referred to as Molecular Inversion Probe (MIP) with a complete gap filling strategy, creating a versatile powerful one-primer multiplex amplification system. As a proof-of-concept, this novel method, which employs a Connector Inversion Probe (CIPer), was tested as a genetic tool for pathogen diagnosis, typing, and antibiotic resistance screening with two distinct systems: i) a conserved sequence primer system for genotyping Human Papillomavirus (HPV), a cancer-associated viral agent and ii) screening for antibiotic resistance mutations in the bacterial pathogen Neisseria gonorrhoeae. We also discuss future applications and advances of the CIPer technology such as integration with digital amplification and next-generation sequencing methods. Furthermore, we introduce the concept of two-dimension informational barcodes, i.e. “multiplex multiplexing padlocks” (MMPs). For the readers' convenience, we also provide an on-line tutorial with user-interface software application CIP creator 1.0.1, for custom probe generation from virtually any new or established primer-pairs.
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Affiliation(s)
- Michael S. Akhras
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
- Department of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Magnus Unemo
- National Reference Laboratory for Pathogenic Neisseria, Department of Clinical Microbiology, Örebro University Hospital, Örebro, Sweden
| | - Sreedevi Thiyagarajan
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Pål Nyrén
- Department of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Ronald W. Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Andrew Z. Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nader Pourmand
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
- Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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26
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Biologie moléculaire et microbiologie clinique en 2007. IMMUNO-ANALYSE & BIOLOGIE SPÉCIALISÉE 2007. [PMCID: PMC7148721 DOI: 10.1016/j.immbio.2006.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
La biologie moléculaire est omniprésente en biologie médicale et plus particulièrement en microbiologie. De nombreux articles démontrent son importance tant dans le domaine du diagnostic que du pronostic, de l'évaluation thérapeutique, de l'épidémiologie ou des risques biologiques naturels ou non. La quantité considérable d'articles sur ce sujet n'apporte pas toujours une réponse évidente sur le rôle de la biologie moléculaire dans un laboratoire de microbiologie qu'il soit hospitalier ou non. Cette revue constitue une synthèse des apports de cette discipline en microbiologie. À partir de cet état des lieux, certaines questions se posent, par exemple : la biologie moléculaire constitue-t-elle un réel apport en microbiologie ? Dans quelles indications prescrire un examen de biologie moléculaire ? Les réponses ne sont pas toujours simples. Elles sont évidentes dans certains cas (l'hépatite C par exemple) et le sont moins dans d'autres, la tuberculose par exemple. Dans la première partie de l'article, nous avons parlé des généralités appliquées à la microbiologie. Dans cette deuxième partie, nous abordons certaines applications, reflets de l'importance prise par la biologie moléculaire en microbiologie.
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27
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Akhras MS, Thiyagarajan S, Villablanca AC, Davis RW, Nyrén P, Pourmand N. PathogenMip assay: a multiplex pathogen detection assay. PLoS One 2007; 2:e223. [PMID: 17311101 PMCID: PMC1794193 DOI: 10.1371/journal.pone.0000223] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 01/26/2007] [Indexed: 01/15/2023] Open
Abstract
The Molecular Inversion Probe (MIP) assay has been previously applied to a large-scale human SNP detection. Here we describe the PathogenMip Assay, a complete protocol for probe production and applied approaches to pathogen detection. We have demonstrated the utility of this assay with an initial set of 24 probes targeting the most clinically relevant HPV genotypes associated with cervical cancer progression. Probe construction was based on a novel, cost-effective, ligase-based protocol. The assay was validated by performing pyrosequencing and Microarray chip detection in parallel experiments. HPV plasmids were used to validate sensitivity and selectivity of the assay. In addition, 20 genomic DNA extracts from primary tumors were genotyped with the PathogenMip Assay results and were in 100% agreement with conventional sequencing using an L1-based HPV genotyping protocol. The PathogenMip Assay is a widely accessible protocol for producing and using highly discriminating probes, with experimentally validated results in pathogen genotyping, which could potentially be applied to the detection and characterization of any microbe.
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Affiliation(s)
- Michael S. Akhras
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
- Department of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Sreedevi Thiyagarajan
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Andrea C. Villablanca
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Ronald W. Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Pål Nyrén
- Department of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Nader Pourmand
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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28
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Yang YG, Kim JY, Song YH, Kim DS. A novel buffer system, AnyDirect, can improve polymerase chain reaction from whole blood without DNA isolation. Clin Chim Acta 2007; 380:112-7. [PMID: 17331487 DOI: 10.1016/j.cca.2007.01.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Revised: 01/16/2007] [Accepted: 01/17/2007] [Indexed: 01/08/2023]
Abstract
BACKGROUND Polymerase chain reaction (PCR) using DNA from blood samples is a valuable tool in the field of medical diagnostics. However, DNA isolation from blood is a laborious and sample-consuming step, and hampers the automation of PCR for large-scale studies. Attempts to perform PCR from blood without DNA isolation have been difficult to achieve, since numerous endogenous and exogenous blood constituents may inhibit PCR. METHODS We used a novel buffer system, 'AnyDirect', that conserves the enzymatic activity of DNA polymerases for effective use in direct PCR from whole blood under various conditions. RESULTS Using AnyDirect, DNA amplification was achieved from whole blood with a variety of thermostable DNA polymerases. Amplification occurred regardless of target size (up to 1.7 kb), presence of various known PCR inhibitors, and high target GC content. Importantly, low copy number DNA targets were effectively amplified from whole blood. CONCLUSIONS AnyDirect buffer allows direct PCR from whole blood and may facilitate detection of genetic diseases or infections by eliminating the time and effort for DNA extraction. The use of AnyDirect could facilitate the development of high-throughput PCR for large-scale diagnostic screening or investigation of various medical conditions.
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Affiliation(s)
- Young Geun Yang
- Department of Biochemistry, College of Science, Yonsei University, Seoul 120-749, Republic of Korea
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29
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Gaster J, Rangam G, Marx A. Increased single nucleotide discrimination in arrayed primer elongation by 4'C-modified primer probes. Chem Commun (Camb) 2007:1692-4. [PMID: 17457410 DOI: 10.1039/b616129d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Herein we describe the beneficial impact of immobilized 4'C-modified primer probes on detecting single nucleotide variations in arrayed primer extension by a DNA polymerase.
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Affiliation(s)
- Jens Gaster
- Universität Konstanz, Fachbereich Chemie, Universitätsstr. 10, 78457 Konstanz, Germany
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30
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Abstract
The need for low-cost DNA sequence detection in clinical applications is driving development of new technologies. We demonstrate a method for detection of mutations in a DNA sequence purely by electronic means, and without need for fluorescent labeling. Our method uses an array of nanopores to perform synchronized single-molecule force spectroscopy measurements over many molecules in parallel, yielding detailed information on the kinetics of hundreds of molecule dissociations in a single measurement.
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Affiliation(s)
- Carolina Tropini
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
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31
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Bullerdiek J. [Research into the human genome driven by improved methods]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2006; 49:989-94. [PMID: 17013777 DOI: 10.1007/s00103-006-0044-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The enormous progress made by research of the human genome is mainly driven by newly established or improved methods for the analysis of nucleic acids and proteins. Among the methods that have gained a wide-spread use within a comparably short time are fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR) including methods for quantitative PCR, and the use of short interfering RNA (siRNA) molecules aimed at gene silencing. The increasing significance of the analysis of secondary modifications of nucleic acids and proteins (genomic imprinting by DNA methylation, posttranslational protein modification) is reflected by an increasing use of mass spectrometry for the analysis and characterization of these biomolecules. Overall, in the future the research into the human genome and the interpretation of data will further benefit from these and other refined tools.
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Affiliation(s)
- J Bullerdiek
- Zentrum für Humangenetik, Universität Bremen, Leobener Strasse ZHG, 28359 Bremen, BRD.
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32
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Ralser M, Querfurth R, Warnatz HJ, Lehrach H, Yaspo ML, Krobitsch S. An efficient and economic enhancer mix for PCR. Biochem Biophys Res Commun 2006; 347:747-51. [PMID: 16842759 DOI: 10.1016/j.bbrc.2006.06.151] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Accepted: 06/27/2006] [Indexed: 11/19/2022]
Abstract
Polymerase chain reaction (PCR) has become a fundamental technique in molecular biology. Nonetheless, further improvements of the existing protocols are required to broaden the applicability of PCR for routine diagnostic purposes, to enhance the specificity and the yield of PCRs as well as to reduce the costs for high-throughput applications. One known problem typically reported in PCR experiments is the poor amplification of GC-rich DNA sequences. Here we designed and tested a novel effective and low-cost PCR enhancer, a concentration-dependent combination of betaine, dithiothreitol, and dimethyl sulfoxide that broadly enhanced the quantitative and/or qualitative output of PCRs. Additionally, we showed that the performances of this enhancer mix are comparable to those of commercially available PCR additives and highly effective with different DNA polymerases. Thus, we propose the routine application of this PCR enhancer mix for low- and high-throughput experiments.
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Affiliation(s)
- Markus Ralser
- Max Planck Institute for Molecular Genetics, Berlin, Germany
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33
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Tsongalis GJ, Silverman LM. Molecular diagnostics: A historical perspective. Clin Chim Acta 2006; 369:188-92. [PMID: 16701603 DOI: 10.1016/j.cca.2006.02.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 02/27/2006] [Indexed: 10/24/2022]
Abstract
The rapid growth in molecular diagnostic testing, which has averaged between 10% and 20% per year for the past 5 years, is largely attributable to both breakthroughs in our basic understanding (i.e., the Human Genome Project) and in applied technology. In the past decade, molecular applications have moved from labor-intensive and manual to rapid and automated due to improvements in sample extraction, target amplification, and sensitive and specific detection schema. This review describes some of the more significant technological milestones of the past 10 years and, when tied to basic and applied research, how these have led to important clinical applications. The next decade promises even more exciting technologies and applications for the field of molecular laboratory medicine.
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Affiliation(s)
- Gregory J Tsongalis
- Department of Pathology, Dartmouth Medical School and Dartmouth-Hitchcock Medical Center, One Medical Center Drive, Lebanon, NH 03756, USA.
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34
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Abstract
The landmark sequencing of the human genome has ushered in a new field of large-scale research. Advances in understanding the molecular basis of disease have opened up new opportunities to develop genomics-based tools to diagnose, predict disease onset or recurrence, tailor treatment options, and assess treatment response. Although still in the early stages of research and development, genomic biomarker research has the capability of providing a comprehensive insight into pathophysiological processes as well as more precise predictors of outcome not previously attainable with traditional biomarkers. Before genomic biomarkers are incorporated into clinical practice, several issues will need to be addressed in order to generate the necessary levels of evidence to demonstrate analytical and clinical validity and utility. In addition, efforts will be needed to educate health professionals and the public about genomics-based tools, revise regulatory oversight mechanisms, and ensure privacy safeguards of the information generated from these new tests.
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Affiliation(s)
- Geoffrey S Ginsburg
- Center for Genomic Medicine, Institute for Genome Sciences & Policy, Duke University, Box 3382, Durham, NC 27708, USA.
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