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Nucleic Acid Amplification Techniques (3):
Recent article
Nucleic Acid Amplification Techniques
Abstract
We present a systematic review of published microsatellite primer notes and show that, on average, about half of all candidate loci are lost due to insufficient PCR amplification, monomorphism or multicopy status in the genome, no matter what isolation strategy is used. Thus, the screening of candid...
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PMID: 21847526
PDF is available here.
PDF is available here.
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Abstract
Cauliflower-like DNAs are stem-loop DNAs that are fabricated periodically in inverted repetitions from deoxyribonucleic acid phosphates (dNTPs) by loop-mediated isothermal amplification (LAMP). Cauliflower-like DNAs have ladder-shape behaviors on gel electrophoresis, and increasing t...
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PMID: 21738438
PDF is available here.
PDF is available here.
Abstract
To evaluate GenoType MTBDRplus (Hain Lifescience, Germany) for its capacity to detect the resistance of rifampicin (RFP) and isoniazid (INH).
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PMID: 21922778
PDF is available here.
PDF is available here.
Abstract
We describe how to analyze genome-wide replication timing (RT) in mammalian cells. Asynchronously cycling cells are pulse labeled with the nucleotide analog 5-bromo-2-deoxyuridine (BrdU) and sorted into S-phase fractions on the basis of DNA content using flow cytometry. BrdU-labeled DNA from each fr...
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PMID: 21637205
PDF is available here.
PDF is available here.
Abstract
TB is a major public health problem causing 9 million cases, of which 10%-15% occur in children each year. Historically, children have received lower priority within TB control activities because they are considered less infectious than smear-positive adults. This review argues that TB is a public he...
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PMID: 21188551
PDF is available here.
PDF is available here.
Abstract
New DNA amplification methods are continuously developed for sensitive detection and quantification of specific DNA target sequences for, e.g. clinical, environmental or food applications. These new applications often require the use of long DNA oligonucleotides as probes for target...
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PMID: 21404441
PDF is available here.
PDF is available here.
Abstract
We designed and tested an integrated nucleic acid extraction and amplification device employing a loop-mediated isothermal amplification (LAMP) or reverse transcriptase-LAMP assay. Our system provides a screening tool with polymerase-chain-reaction-level sensitivity and specificity for outbreak dete...
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PMID: 21342806
PDF is available here.
PDF is available here.
Abstract
We explored the feasibility (user friendliness) and test characteristics (sensitivity and specificity) of a new prototype device to detect Chlamydia in adolescent women by using small numbers of subjects and rapid communication with the manufacturer. We compared cervical POC test results to the gold...
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PMID: 20934941
PDF is available here.
PDF is available here.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] (27)2 2011
Abstract
Cancer Biology & Therapy (10)12 2011
Abstract
Due to the small volume and high density of breast tissue in Asian women, particularly younger women, mammographic diagnosis is sometimes non-conclusive, with a Breast Imaging Reporting and Data System (BI-RADS) result of 0. No alternative based on blood biomarkers has yet succeeded...
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PMID: 20930549
PDF is available here.
PDF is available here.
Voprosy Virusologii (56)1 2011
Abstract
The paper describes a simple, rapid screening of samples potentially containing Crimean-Congo hemorrhagic fever (CCHF) virus strains, by applying the restriction analysis of amplicones, for the differentiation of CCHF virus genotypes that are characteristic of Europe from virus biovariants uncharacte...
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PMID: 21427952
PDF is available here.
PDF is available here.
Amplification of unknown RNAs and RNA mixtures based on unique restriction enzyme cleavage in vitro.
Abstract
We have developed a novel method to amplify target RNA. The amplification procedure was carried out by sequential RT-PCR, effective separation, restriction enzymatic cleavage of cDNA strand, and run-off transcription in vitro of target RNA from its cDNA. Introduction of a unique stem-loop linker int...
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PMID: 21106769
PDF is available here.
PDF is available here.
Abstract
Leptospira borgpetersenii serovar Arborea is an emerging cause of leptospirosis in Australia. It was not previously recognized as an endemic serovar before the 1990s, but at that point, human infections with the serovar increased significantly. Using fluorescent-amplified fragment-length polymorphism...
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PMID: 20889871
PDF is available here.
PDF is available here.
Abstract
To update the reader on the latest developments in the laboratory diagnosis of intestinal protozoa.
Correct identification of a diarrhoea causing pathogens is essential for the choice of treatment in an individual patient as well as to map the aetiology of diarrhoea in a variety of patient populatio...
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PMID: 20683263
PDF is available here.
PDF is available here.
Genetics in Medicine (12)10 2010
Abstract
Abstract
The conference Applications of Nucleic Acids Technologies in Molecular Diagnostics (part of TIDES) consisted of four sessions: Regulatory Pathways and Quality Strategies, Manufacturing and Business Considerations for Successful Launch in the Clinical Market, Analytical Methods and Validation, and Ne...
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PMID: 20964604
PDF is available here.
PDF is available here.
Abstract
A loop-mediated isothermal amplification (LAMP) assay was developed specifically for detection and differentiation of pseudorabies virus (PRV). One group of primers was designed to detect wild-type strains (i.e., strains with the gE gene) and the other group of primers was designed to detect both PR...
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PMID: 20691214
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (135)8 2010
Abstract
We have developed a Cyclic Enzymatic Amplification Method (CEAM) for sensitive and selective detection of nucleic acids. In this design, the displacing probe is non-fluorescent on its own and cannot be digested by Exo III until displacement hybridization by a target sequence, leading to release of f...
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PMID: 20563332
PDF is available here.
PDF is available here.
Abstract
We can conclude that the LAMP assay provides us an accurate and highly sensitive test method to detect C. parvum oocyst and cyst of G. lamblia, in place of labor-intensive and experience-dependent microscopic examination, in clinical laboratories....
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PMID: 20860168
PDF is available here.
PDF is available here.
Abstract
We developed a completely homogeneous duplex loop-mediated isothermal amplification (LAMP) method. The present LAMP method employed a combination of a 6-carboxyfluorescein (FAM)-labeled primer (donor) for one target gene, a non-labeled primer for the other, and an intercalator ethidium bromide (EtBr...
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PMID: 20230890
PDF is available here.
PDF is available here.
Abstract
We report two JBS patients from China out of a total of 451 patients with unexplained DD/MR. The genotypes of these patients were compared with earlier reported patients in North America and Europe. Both patients presented with severe DD, microcephaly and facial dysmorphism; one patient had a low bi...
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PMID: 20520618
PDF is available here.
PDF is available here.
Abstract
An external quality assessment (EQA) panel consisting of a total of 13 samples in broncho alveolar lavage (BAL) or transport medium was prepared to assess the proficiency of laboratories in the correct detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae by nucleic acid amplification tech...
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PMID: 20493214
PDF is available here.
PDF is available here.
Abstract
We developed a new technology to display the parallel genomic DNA fragment massively based on two-step reaction with capital EF, Phi29 DNA polymerase. The genomic DNA fragments were firstly amplified by rolling-circle amplification (RCA) reaction in liquid phase, and then amplified further on the ch...
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PMID: 20602923
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)13 2010
Abstract
Little is known about the regulation of nitrogenase genes in cyanobacteria. Transcription of the nifH1 and vnfH genes, encoding dinitrogenase reductases for the heterocyst-specific Mo-nitrogenase and the alternative V-nitrogenase, respectively, was studied by using a lacZ reporter. Despite evidence...
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PMID: 20435734
PDF is available here.
PDF is available here.
Abstract
We describe a paired-end sequencing strategy, which enables more robust mapping and characterization of capped transcripts. We used this strategy to explore the transcription initiation landscape in the Drosophila melanogaster embryo. Extending the previous findings in mammals, we found that fly pro...
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PMID: 20495556
PDF is available here.
PDF is available here.
Abstract
IGF1R (insulin-like growth factor 1 receptor) haploinsufficiency is a rare event causing difficulties in defining clear genotype-phenotype correlations, although short stature is its well established hallmark. Several pure 15q26 monosomies (n=22) have been described in the literature...
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PMID: 19955558
PDF is available here.
PDF is available here.
Abstract
We developed detects novel influenza A (H1N1) of swine origin and seasonal influenza A (H1N1 and H3N2) viruses. Individual primer sets targeting the HA gene for novel H1N1, H1N1, and H3N2 were newly designed to specifically detect these subtypes. No cross-reactions occurred among novel H1N1, H1N1, a...
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PMID: 20715552
PDF is available here.
PDF is available here.
Abstract
The objective was to determine the occurrence of four urethral pathogens in urine specimens from symptomatic men using transcription mediated amplification (TMA) assay. Urethral swab and urine specimens from 300 men presenting to a family practitioner were Gram stained and tested for Neisseria gonor...
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PMID: 20852197
PDF is available here.
PDF is available here.
Abstract
Abstract
Several potential biomarkers of tuberculous pleurisy have been evaluated, but none have been found to be clearly superior to pleural fluid level of ADA or IFN-gamma. The majority of recent studies confirm the high diagnostic utility of pleural fluid ADA and IFN-gamma measurement; hence, these marker...
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PMID: 20473171
PDF is available here.
PDF is available here.
British Journal of Cancer (103)1 2010
Abstract
The MGMT protein was detected in all TMZ-resistant cell lines, whereas no MGMT protein could be detected in cell lines that were TMZ sensitive. The MS-MLPA results were able to predict TMZ sensitivity in 9 out of 16 cell lines (56%). The qMSP results matched well with TMZ sensitivity in 11 out of 12...
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PMID: 20517307
PDF is available here.
PDF is available here.
Abstract
The introduction of endobronchial ultrasound increases the diagnostic yield of the nucleic acid amplification tests, acid-fast bacillus smear, and M tuberculosis culture from bronchioalveolar lavage fluid in patients with pulmonary tuberculosis who have negative sputum smear or no sputum production....
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PMID: 20494195
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (135)6 2010
Abstract
We review the cumulative efforts to develop rapid and ultrasensitive diagnostic systems, especially for the infectious agent, Bacillus anthracis, as a model system. This Minireview focuses on demonstrating the features of various probes for target molecule detection and recent methods of signal gene...
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PMID: 20498871
PDF is available here.
PDF is available here.
Abstract
We have investigated whether LAMP can be used to detect small numbers of enteroaggregative Escherichia coli (EAEC) cells contaminated in food samples. Primers for LAMP reaction were designed with EAEC aggR gene sequences (available in GenBank). LAMP specificity with these primers was the same as tha...
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PMID: 20537261
PDF is available here.
PDF is available here.
Future Microbiology (5)6 2010
Abstract
Respiratory tract viral infections are responsible for an incredible amount of morbidity and mortality throughout the world. Older diagnostic methods, such as tissue culture and serology, have been replaced with more advanced molecular techniques, such as PCR and reverse-transcriptase PCR, nucleic a...
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PMID: 20521935
PDF is available here.
PDF is available here.
Abstract
We estimated variability of sequence-related amplified polymorphism (SRAP) markers in 77 accessions of 22 sea buckthorn cultivars to seek markers associated with DSD resistance and help to identify potential breeding cultivars. Seventeen SRAP primer combinations generated 289 bands, with a mean of 1...
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PMID: 20555434
PDF is available here.
PDF is available here.
Abstract
We assessed in detail the variables contributing to interobserver interpretive reproducibility of HER2 SISH among 10 pathologists. HER2 was quantified using the ratio of HER2 to CHR17 signals using the conventional historical interpretation scale and also by the American Society of Clinical Oncology...
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PMID: 20421783
PDF is available here.
PDF is available here.
Genetics in Medicine (12)6 2010
Abstract
We identified four unbalanced rearrangements: one del 18pter/amp 5pter, one del 9pter, one 15q11q13 microdeletion, and one 22q11 microdeletion with atypical presentation. After genetic counseling, two of the pregnancies were terminated. CONCLUSION: Multiplex ligation probe amplification analysis was...
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PMID: 20453657
PDF is available here.
PDF is available here.
Abstract
A colorimetric loop-mediated isothermal amplification (LAMP) assay with hydroxy naphthol blue was designed to amplify a region in the outer membrane lipoprotein (oprL) gene of Pseudomonas aeruginosa. The LAMP assay showed 100% specificity for the serogroup and other bacteria, and the sensitivity was...
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PMID: 20298724
PDF is available here.
PDF is available here.
Lab On a Chip (10)10 2010
Abstract
We set out to create an integrated microchemical chip that benefits from microfluidic chip technology in terms of sensitivity and a strong detection methodology provided jointly by padlock probes and rolling circle amplification (RCA). Here, we have integrated padlock probes and RCA into a microchip...
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PMID: 20445878
PDF is available here.
PDF is available here.
Clinical Biochemistry (43)7-8 2010
Abstract
DNA sequencing combined with MLPA allows reliable and simplified genotyping of SDHB, SDHC and SDHD.
2010 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved....
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PMID: 20153743
PDF is available here.
PDF is available here.
Clinica Chimica Acta (411)9-10 2010
Abstract
Abstract
We have developed two loop-mediated isothermal amplification (LAMP) assays for specific detection of Trypanosoma cruzi and Trypanosoma rangeli based on the 18S ribosomal RNA (rRNA) and the small nucleolar RNA (snoRNA) genes, respectively. The detection limit of the assays is 100 fg and 1 pg for T. c...
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PMID: 20439966
PDF is available here.
PDF is available here.
Abstract
To establish a simple and rapid molecular detection for Legionella pneumophila.
The loop-mediated isothermal amplification (LAMP) was applied for detection of Legionella pneumophila. A set of primers were designed to identify six special areas in mip gene of Legionella pneumophila. Genomic DNAs from...
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PMID: 20544994
PDF is available here.
PDF is available here.
Abstract
We evaluated respiratory and nonrespiratory clinical specimens using a new automated Mycobacterium tuberculosis complex (MTBC) rRNA detection kit (TRCRapid M.TB; Tosoh Bioscience, Tokyo, Japan), which is based on the transcription-reverse transcription concerted reaction (TRC). TRC enables the rapid...
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PMID: 20200296
PDF is available here.
PDF is available here.
Abstract
It is uncertain which methods for the diagnosis of rectal gonococcal and chlamydial infection are optimal. This study evaluated the performance of culture and nucleic acid amplification tests (NAATs) for rectal chlamydial and gonococcal diagnosis. From July 2003 until February 2007, 441 rectal test...
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PMID: 20335410
PDF is available here.
PDF is available here.
Abstract
DBS EasyQ VL assays provide an accurate option for early infant diagnosis in low resource settings.
Copyright 2010 Elsevier B.V. All rights reserved....
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PMID: 20211580
PDF is available here.
PDF is available here.
Abstract
The AMPLICOR HPV Test can be successfully and reproducibly performed from DNA isolated from residual SurePath cervical cytology specimens stored at ambient temperature for at least 21 days. This provides clinical laboratories flexible storage conditions for residual SurePath cytology specimens.
Copy...
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PMID: 20233675
PDF is available here.
PDF is available here.
Abstract
Clinical specificity, analytical and clinical sensitivities, reproducibility, and subtype/genotype coverage of the cobas TaqScreen MPX Test, a multiplex nucleic acid test with expanded coverage of HIV variants, were determined. A total of 72,281 blood donations were evaluated. The 95% limit of detec...
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PMID: 20152864
PDF is available here.
PDF is available here.
Abstract
We present a sequencing strategy which we call an extension-quenching-extension sequencing on a microarray based on a two-primer hyperbranched rolling circle amplification (HRCA). The microarray is a high throughput and low-cost tool. The template on a microarray for SBS was prepared by HRCA. The Cy...
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PMID: 20188940
PDF is available here.
PDF is available here.
Parasitology (137)4 2010
Abstract
Salivarian trypanosomes pose a substantial threat to livestock, but their full diversity is not known. To survey trypanosomes carried by tsetse in Tanzania, DNA samples from infected proboscides of Glossina pallidipes and G. swynnertoni were identified using fluorescent fragment length barcoding (FF...
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PMID: 19961657
PDF is available here.
PDF is available here.
Clinical Biochemistry (43)6 2010
Abstract
Our MLPA allows rapid and precise OCRL1 gene quantification. Moreover this study provides no further evidence for the hypothesis that duplications and deletion somatic mosaic deletions account for the fraction of patients who have no detectible mutation after the usual screening procedures.
Copyrigh...
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PMID: 20043897
PDF is available here.
PDF is available here.
Abstract
The use of whole genome amplification and analysis of viruses is of increasing importance, as data generated using these methods are currently used for clinical diagnostics, epidemiological studies, phylogenetic analyses, and studies of genome organization and evolution. The best known amplification...
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PMID: 20360369
PDF is available here.
PDF is available here.
Biological Bulletin (218)2 2010
Abstract
We detected telomerase activity in host nuclear extracts prepared from two scleractinian corals, Madracis auretenra and Madracis decactis, and also in cultured Symbiodinium, the symbiotic algae that live within corals. Sequencing the TRAP reaction products indicated that the telomeric DNA repeat seq...
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PMID: 20413788
PDF is available here.
PDF is available here.
Abstract
The aim of the study was to evaluate the sensitivity of patients' self-sampled vaginal specimens, first-catch urine (FCU), combined vaginal/FCU specimens and endocervical specimens for detecting chlamydial infection in women. Women attending sexually transmitted disease clinics, youth clinics and a...
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PMID: 20378903
PDF is available here.
PDF is available here.
Abstract
Abstract
The aim of this study was to determine how widespread the use is of dual nucleic acid amplification tests (NAATs) for the diagnosis of both Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) in England and Wales. A structured telephone questionnaire was used to collect information on the meth...
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PMID: 20378894
PDF is available here.
PDF is available here.
Transfusion Medicine (20)2 2010
Abstract
West Nile virus (WNV), a mosquito-borne flavivirus, has increasingly become a concern in both America and Europe due to its complex and unpredictable lifecycle. Transfusion-associated transmission of the WNV has been well documented during the last few years. This study aimed to dete...
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PMID: 19719473
PDF is available here.
PDF is available here.
Abstract
We describe here our procedure for qRT-PCR analysis of circulating miRNAs as biomarkers, and discuss relevant issues of sample preparation, experimental design and data analysis.
Copyright 2010 Elsevier Inc. All rights reserved....
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PMID: 20146939
PDF is available here.
PDF is available here.
Abstract
We present a statistical approach based on multivariate analysis of the amplification response data generated in real-time. The amplification trajectory in its most resolved and dynamic phase is fitted with a suitable model. Two parameters of this model, related to amplification efficiency, are then...
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PMID: 20109549
PDF is available here.
PDF is available here.