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Breast Surgery
Published in Tjun Tang, Elizabeth O'Riordan, Stewart Walsh, Cracking the Intercollegiate General Surgery FRCS Viva, 2020
Gaural Patel, Lucy Kate Satherley, Animesh JK Patel, Georgina SA Phillips
How is HER2 measured?Immunohistochemistry – antibodies directed against the HER2 protein are visualised with chromogenic detection. This is a widely available method. Score is 0, 1+, 2+ or 3+. There is a 10% false-negative rate. Equivocal results (2+) are retested by FISH.FISH is a quantitative measurement of gene amplification. It requires specialist equipment and is relatively expensive.CISH (chromogenic in situ hybridisation) and SISH (silver in situ hybridisation) are quantitative measurements using immunohistochemical techniques to visualise HER2 expression directly; CISH is lower cost than FISH, with similar sensitivity and specificity to the FISH technique.38
The N-Myc Oncogene in Pediatric Tumors: Diagnostic, Prognostic and Biological Aspects
Published in John T. Kemshead, Pediatric Tumors: Immunological and Molecular Markers, 2020
As mentioned above, gene amplification is one of the mechanisms by which proto-oncogenes can become activated. In lower organisms, such as amphibians and Drosophila, selective increase in gene copy number (i.e., amplification) occurs normally during certain stages of development.17 Even in mammals, the phenomenon is not exclusively associated with the neoplastic process, but may be seen when cells are placed under a variety of selective conditions.12,18 The best known example of this is the amplification of the dihy-drofolate reductase gene, leading to drug-resistance in response to methotrexate exposure.19 At the cytological level, amplified genes are associated with characteristic karyotype abnormalities known as homogenously staining chromosomal regions (HSRs) and extrachro-mosomal double minute chromatin bodies (DMs). HSRs (so called because they tend to stain uniformly with Giemsa in G-band preparations) are relatively stable structures but DMs lack centromeres, are thus comparatively unstable and may disappear from cells altogether or participate in the formation of HSRs by chromosomal reintegration.18
Oncogenes and Cancer
Published in Pimentel Enrique, Oncogenes, 2020
Amplification of oncogenes, or other cellular genes, might be related to some stages of the oncogenic process because during the process of gene amplification multiple DNA rearrangements occur that generate new combinations of DNA sequences.111 Each amplified unit has a unique structure and, at the time of formation of the units, pieces of DNA from different parts of the genome are joined together to form novel structures. Thus, gene amplification could contribute to the production of DNA molecular rearrangements that occur in many tumor cells.
Loop-mediated isothermal amplification for Candida species surveillance in under-resourced setting: a review of evidence
Published in Expert Review of Molecular Diagnostics, 2022
Oloche Owoicho, Charles Ochieng’ Olwal, Edward Jenner Tettevi, Bernard Ortwer Atu, Ernest Uzodimma Durugbo
Typically, gene amplification occurs by repetition of two types of elongation reactions that occur via loop regions. Each of the inner primers has a sequence complementary to one chain of the amplification region at the 3’ terminal and is identical to the inner region of the same chain at the 5’ terminal. The elongation is sequentially repeated by DNA polymerase-mediated strand-displacement synthesis using the stem loop regions as a stage [17]. This method is premised on the principle of the production of lots of DNA amplification products with a mutually complementary sequence and an alternating repeated structure. LAMP amplifies a few copies of DNA to 109 copies within an hour under isothermal condition with great specificity (reviewed in [33]). The LAMP output is then visualized by the naked eye through magnesium pyrophosphate, a turbid by-product of the amplification. Amplification can also be visualized by adding different dyes like SYBR green, hydroxynaphthol blue, and calcein [27]. Moreover, other methods of detecting LAMP amplicons include the use of fluorogenic primers and probes, and heterogeneous or homogeneous particles, which have been well reviewed [20,21].
Dietary Pattern, Genomic Stability and Relative Cancer Risk in Asian Food Landscape
Published in Nutrition and Cancer, 2022
Razinah Sharif, Suzana Shahar, Nor Fadilah Rajab, Michael Fenech
Telomeres consist of a conserved hexanucleotide repeat sequence (TTAGGG) that caps the ends of chromosomes and protects them from recombining with each other and thus preventing chromosomal end-to-end fusions. Degradation of telomeres has been shown to lead to chromosomal instability, via telomere end fusions resulting in generation of abnormal dicentric chromosomes and breakage-fusion-bridge cycles within these abnormal chromosomes (75, 76). This leads to gene amplification and gene dosage imbalance which is an important risk factor for cancer. Accelerated telomere shortening and telomere end fusions can result in a persistent DNA damage response leading to cell cycle arrest and apoptosis. Although telomere shortening has been proposed as one of the fundamental mechanisms that determine chromosomal instability, and increased cancer risk, studies on the relationship between dietary factors and telomere biology have mainly focused on western diets such as the Mediterranean diet which is protective but knowledge remains limited with respect to Asian dietary patterns (77, 78).
Higher accuracy of genotypic identification compared to phenotyping in the diagnosis of coagulase-negative staphylococcus infection in orthopedic surgery
Published in Infectious Diseases, 2020
Gema Muñoz-Gamito, Eva Cuchí, Jordi Roigé, Lucía Gómez, Àngels Jaén, Alfredo Matamala, M. Lluïsa Pedro-Botet, Josep Anton Capdevila, Francesc Anglès, Josefa Pérez
All isolated CoNS strains were grouped in a surgical episode. Bacterial DNA was extracted using the QIAcube automated system (Qiagen, Hilden, Germany), and the rep-PCR technique (DiversiLab System, bioMérieux Marcy-l'Étoile, France) was carried out according to the manufacturer’s instructions. Gene amplification used specific primers and conditions for each reaction. The PCR products were separated, visualised, and the results were evaluated using 5 different methods: dendrogram analysis, analysis of the similarity matrix (similarity percentage between paired samples), visual inspection of the DNA band patterns in the sample graphs (define differences between samples), analysis of the graphs (overlapping graphs can reveal small differences), and analysis of the dispersion diagram, which provides a general view of the grouping in clusters.