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Amplicon detection
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Circulating tumour DNA (ctDNA) detection and monitoring have enormous potential clinical utility in oncology. We describe here a fast, flexible and cost-effective method to profile multiple genes simultaneously in low input cell-free DNA (cfDNA).
14p
vibransone
28-03-2024
5
2
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Here, we describe a novel approach for rapid discovery of a set of tumor-specific genomic structural variants (SVs), based on a combination of low coverage cancer genome sequencing using Oxford Nanopore with an SV calling and filtering pipeline. We applied the method to tumor samples of high-grade ovarian and prostate cancer patients and validated on average ten somatic SVs per patient with breakpoint-spanning PCR mini-amplicons.
14p
vibransone
28-03-2024
3
2
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Part 1 book "Molecular diagnostic PCR handbook" includes content: Background; PCR – the basic reaction; amplicon detection, analysis and PCR evaluation; limitations and troubleshooting, specific types of PCR assays.
118p
oursky06
17-10-2023
5
1
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Part 2 book "PCR Protocols" includes content: Linking emulsion PCR haplotype analysis, the many faces of MLPA, assessing gene specific methylation using HRM-Based analysis, asynchronous PCR, enhanced solid phase PCR for increased loading of amplicon onto solid support, application of blocking oligonucleotides to improve signal to noise ratio in a PCR,...and other contents.
179p
oursky06
17-10-2023
3
1
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We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore Sequencing.
17p
viarchimedes
26-01-2022
9
0
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Amplicon deep sequencing permits sensitive detection of minority clones and improves discriminatory power for genotyping multi-clone Plasmodium falciparum infections. New amplicon sequencing and data analysis protocols are needed for genotyping in epidemiological studies and drug efficacy trials of P. falciparum.
13p
vilarryellison
29-10-2021
21
1
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The state-of-the-art in nucleic acid based biodetection continues to be polymerase chain reaction (PCR), and many real-time PCR assays targeting biodefense pathogens for biosurveillance are in widespread use.
21p
vijeeni2711
24-07-2021
15
0
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The identity of the causal virus was established on the basis of symptomatology and molecular assays. Primers designed against coat protein (CP) gene resulted in obtaining a desired amplicon of ~162 bp confirming the isolate to be of Cucumber mosaic virus
7p
chauchaungayxua10
19-03-2021
16
1
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Next-generation sequencing (NGS) is rapidly becoming common practice in clinical diagnostics and cancer research. In addition to the detection of single nucleotide variants (SNVs), information on copy number variants (CNVs) is of great interest.
9p
vikentucky2711
26-11-2020
15
0
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Amplicon re-sequencing based on the automated Sanger method remains popular for detection of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels) for a spectrum of genetics applications.
8p
vioklahoma2711
19-11-2020
6
1
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The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS.
18p
vicolorado2711
22-10-2020
6
0
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Detection of bovine papillomavirus in cutaneous lesions by polymerase chain reaction (PCR) in cattle
Bovine papillomavirus (BPV) causes benign tumours in the mucosal and cutaneous epithelium and is characterized by the presence of warts. The present study includes the molecular identification of BPV strains in samples of warts using degenerate polymerase chain reaction (PCR) primers FAP59/64. Wart samples were collected from the cattle having typical lesions on various parts of the body. The present study showed that PCR amplification with the primers FAP59/64, which partially amplify the L1 gene and showed the 470bp amplicon size, indicating BPV.
6p
angicungduoc6
22-07-2020
7
1
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In lung cancer, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor sensitizing mutations co-existing with rare minor EGFR mutations are known as compound mutations. These minor EGFR mutations can lead to acquired resistance after EGFR tyrosine kinase inhibitor treatment, so determining the mutation status of patients is important.
9p
viputrajaya2711
22-06-2020
14
1
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The present study was designed to find variations among Staphylococcus aureus on the basis of cultural and biochemical properties. From 59 samples of cattle clinical mastitic milk, 28 isolates were obtained and confirmed by species specific primers targeted against 23S rRNA with an amplicon of 1250bp. The genotypically confirmed isolates were subjected to determine phenotypic variations among them. In our study total seven biotypes were detected with variations in pigment production, haemolysis pattern and coagulase production.
7p
kethamoi5
03-06-2020
12
0
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The present study was carried out for the isolation, identification and molecular characterization of Brucella species. A total of 50 samples were collected from cattle and buffalo suffering from abortions and other reproductive disorders in and around Ludhiana, Punjab. Out of the 50 samples of fetal stomach contents (25), uterine discharges (10), vaginal mucus (8) and placenta (7) processed for isolation of Brucella of which a total of four isolate were obtained and identified biochemically. All the 4 isolates were typed as biotype 1.
5p
trinhthamhodang1213
29-05-2020
6
0
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Micropropagation is a highly sought after technique in the commercial production of orchid plants. This has the advantage of providing large number of plants in a short period of time. But a major constrain in the in vitro propagation technique is the somaclonal variation. It is important to produce true to type planting materials especially in case of the hybrids as they are more prone to variations. The true to type nature of the micropropagated plantlets can be confirmed by genetic fidelity analysis.
9p
caygaocaolon3
27-02-2020
12
2
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Black spot of papaya caused by Asperisporium caricae incidence was recorded in five different localities viz., Pasur, Telungupalayam, Thondamuthur, Vedapatti and TNAU orchard of Coimbatore district. Per cent disease severity (PDS) ranged from 1 to 29 per cent on leaves. The fungal pathogen associated with black spot of papaya was isolated and identified as Asperisporium caricae based on morphological characters. Severe disease incidence was observed from November to January and no disease incidence was recorded during summer.
7p
chauchaungayxua3
07-02-2020
26
1
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The study was undertaken with an objective to evaluate a rapid PCR based method for detection of adulteration of buffalo milk in cow milk at minimum level of detection. This method utilizes primers targeting the mitochondrial encoded 12S rRNA gene as the target for species identification. PCR assay involve use of three different primers. Reverse primers specific for cow and buffalo complementary to the gene fragment of 12S rRNA along with the common forward primer. The cow specific primer, along with the common forward primer, yields a cow specific amplicon of 346 bp in the 12S rRNA gene.
7p
kethamoi2
15-12-2019
11
1
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The present study was carried out to know the sap transmission nature of sunflower necrosis virus and detection by serological and molecular means. The disease was successfully transmitted through mechanical sap using 0.05 M potassium phosphate buffer. A maximum transmission of 52.33 per cent on cultivar KBSH-44, 51.33 per cent on KBSH-1, and 48.33 per cent on Morden. Under artificial inoculation, the newly emerged leaves showed slight downward curling, puckering and chlorosis followed by necrosis.
6p
cothumenhmong1
11-12-2019
13
1
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PCR detection of blaIMP gene in Metallo-β-Lactamase resistant E. coli isolated from clinical samples
PCR detection of blaIMP gene in Imipenem resistant E. coli is the aim ot this study. Total of n=66 of n=23 Imipenem resistant E. coli were selected for the present study based on the drug resistance pattern and their MIC to Imipenem. Phenotypic detection of MBL production was carried out and subsequently, PCR amplification of blaIMP was carried out. Among selected (n=23) Imipenem resistant E. coli (IREC), 100% (n=23) strains were positive for Imipenem mediated MBL production. Twenty-three MBL positive IREC isolates were shown presence of Plasmid DNA, with size measured about approx. 6kb.
6p
cothumenhmong1
11-12-2019
11
0
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