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Fluorescence in-situ hybridization

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https://www.readbyqxmd.com/read/29352719/prognostic-testing-patterns-and-outcomes-of-chronic-lymphocytic-leukemia-patients-stratified-by-fluorescence-in-situ-hybridization-cytogenetics-a-real-world-clinical-experience-in-the-connect-cll-registry
#1
Anthony Mato, Chadi Nabhan, Neil E Kay, Nicole Lamanna, Thomas J Kipps, David L Grinblatt, Christopher R Flowers, Charles M Farber, Matthew S Davids, Pavel Kiselev, Arlene S Swern, Shriya Bhushan, Kristen Sullivan, E Dawn Flick, Jeff P Sharman
INTRODUCTION: Prognostic genetic testing is recommended for patients with chronic lymphocytic leukemia (CLL) to guide clinical management. Specific abnormalities, such as del(17p), del(11q), and unmutated IgHV, can predict the depth and durability of the response to CLL therapy. PATIENTS AND METHODS: In the present analysis of the Connect CLL Registry (ClinicalTrials.gov identifier, NCT01081015), a prospective observational cohort study of patients treated across 199 centers, the patterns of prognostic testing and outcomes of patients with unfavorable-risk genetics were analyzed...
December 6, 2017: Clinical Lymphoma, Myeloma & Leukemia
https://www.readbyqxmd.com/read/29352306/prognostic-and-predictive-role-of-egfr-pathway-alterations-in-biliary-cancer-patients-treated-with-chemotherapy-and-anti-egfr
#2
Caterina Peraldo-Neia, Giuliana Cavalloni, Elisabetta Fenocchio, Celeste Cagnazzo, Loretta Gammaitoni, Stefano Cereda, Guglielmo Nasti, Maria Antonietta Satolli, Giuseppe Aprile, Michele Reni, Antonio Avallone, Rosella Spadi, Tiziana Venesio, Vittoria Martin, Claudio Doglioni, Milo Frattini, Massimo Aglietta, Francesco Leone
The association of anti-EGFR to gemcitabine and oxaliplatin (GEMOX) chemotherapy did not improve survival in biliary tract carcinoma (BTC) patients. Multiple mechanisms might be involved in the resistance to anti-EGFR. Here, we explored the mutation profile of EGFR extracellular domain (ECD), of tyrosine kinase domain (TKD), and its amplification status. EGFR mutational status of exons 12, 18-21 was analyzed in 57 tumors by Sanger sequencing. EGFR amplification was evaluated in 37 tumors by Fluorescent In Situ Hybridization (FISH)...
2018: PloS One
https://www.readbyqxmd.com/read/29344579/prognostic-significance-of-cytogenetic-heterogeneity-in-patients-with-newly-diagnosed-multiple-myeloma
#3
Maximilian Merz, Anna Jauch, Thomas Hielscher, Tilmann Bochtler, Stefan Olaf Schönland, Anja Seckinger, Dirk Hose, Uta Bertsch, Kai Neben, Marc Steffen Raab, Jens Hillengass, Hans Salwender, Igor Wolfgang Blau, Hans-Walter Lindemann, Ingo G H Schmidt-Wolf, Christof Scheid, Mathias Haenel, Katja C Weisel, Hartmut Goldschmidt
We investigated subclonal cytogenetic aberrations (CA) detected by interphase fluorescence in situ hybridization (iFISH) in patients with newly diagnosed multiple myeloma (MM) enrolled in the Haemato Oncology Foundation for Adults in the Netherlands (HOVON)-65/German-Speaking MM Group (GMMG)-HD4 phase 3 trial. Patients were either treated with 3 cycles of vincristine, Adriamycin, and dexamethasone or bortezomib, Adriamycin, and dexamethasone and then thalidomide or bortezomib maintenance after tandem autologous transplantation...
January 9, 2018: Blood Advances
https://www.readbyqxmd.com/read/29344493/comparison-of-gene-expression-profiling-and-chromosome-3-analysis-by-fluorescent-in-situ-hybridization-and-multiplex-ligation-probe-amplification-in-fine-needle-aspiration-biopsy-specimens-of-uveal-melanoma
#4
Michael A Klufas, Elizabeth Richter, Sujit Itty, Christian Moreno, Colin A McCannel, Tara A McCannel
Purpose: The aim of this paper was to assess the concordance between results of DecisionDx-UM specific gene expression profiling (GEP) and fluorescence in situ hybridization (FISH) for chromosome 3 analysis, and between DecisionDx-UM GEP and multiplex ligation probe amplification (MLPA) in uveal melanoma undergoing intraoperative fine-needle aspiration biopsy (FNAB) for metastatic prognostication during brachytherapy. Methods: We retrospectively reviewed consecutive patients diagnosed with posterior uveal melanoma who underwent intraoperative FNAB prior to placement of an iodine-125 radioactive plaque between 2012 and 2014...
December 2017: Ocular Oncology and Pathology
https://www.readbyqxmd.com/read/29344131/a-novel-variant-translocation-1-9-p22-q34-resulting-in-a-dek-nup214-fusion-gene-in-a-patient-with-acute-myeloid-leukemia-a-case-report
#5
Qishan Hao, Qi Zhang, Chengwen Li, Shuning Wei, Qinghua Li, Yang Song, Yingchang Mi
The present case report describes a 46-year-old female patient diagnosed with M4 acute myeloid leukemia (AML), accompanied with a t(1;9)(p22;q34) chromosomal abnormality. Transcriptome sequencing identified a DEK proto-oncogene (DEK)/nucleoporin (NUP)214 fusion gene, which results from the t(6;9)(p23;q34) chromosomal translocation. Polymerase chain reaction analysis and fluorescence in situ hybridization were used to verify the existence of the DEK/NUP214 fusion gene. Few patients with AML with the t(6;9)(p23;q34) chromosomal translocation have been reported to have other chromosomal or karyotype changes...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343880/novel-application-of-loop-mediated-isothermal-amplification-for-rapid-detection-of-gene-translocation
#6
Ibu Matsuzaki, Hideto Iguchi, Yurina Mikasa, Hiromu Morishita, Katsuya Okuda, Keita Nakaguchi, Yuki Mori, Yoshifumi Iwahashi, Kenji Warigaya, Masakazu Fujimoto, Fumiyoshi Kojima, Shin-Ichi Murata
Identification of fusion genes in cancer is essential for pathological diagnosis and clinical therapy. Although methods for detection of fusion genes, such as fluorescence in situ hybridization (FISH) and real-time polymerase chain reaction (PCR), have been developed in last two decades, these methods are not ideal for detection of these genetic alterations owing to their high cost and time-consuming procedures. In this study, we developed novel application for detection of gene translocations using loop-mediated isothermal amplification (LAMP)...
December 26, 2017: Acta Histochemica et Cytochemica
https://www.readbyqxmd.com/read/29342995/-pediatric-myeloid-neoplasms-associated-with-eosinophilia-and-platelet-derived-growth-factor-receptor-beta-gene-rearrangement-a-case-report-and-literature-review
#7
X Y Zhang, T F Liu, C W Li, Q H Li, X F Zhu
Objective: To investigate the clinical features and therapeutic strategies of childhood myeloid neoplasms associated with eosinophilia and platelet-derived growth factor receptor beta (PDGFRB) gene rearrangement. Methods: Clinical data of myeloid neoplasms associated with eosinophilia and t (1;5) (q21;q33) chromosomal translocation of PDGFRB gene rearrangement in a child hospitalized in Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences on May 2015 was collected and analyzed...
January 2, 2018: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29341473/somatic-mosaic-deletions-involving-scn1a-cause-dravet-syndrome
#8
Tojo Nakayama, Atsushi Ishii, Takeshi Yoshida, Hirosato Nasu, Keiko Shimojima, Toshiyuki Yamamoto, Shigeo Kure, Shinichi Hirose
Somatic mosaicism in single nucleotide variants of SCN1A is known to occur in a subset of parents of children with Dravet syndrome (DS). Here, we report recurrent somatic mosaic microdeletions involving SCN1A in children diagnosed with DS. Through the evaluation of 237 affected individuals with DS who did not show SCN1A or PCHD19 mutations in prior sequencing analyzes, we identified two children with mosaic microdeletions covering the entire SCN1A region. The allele frequency of the mosaic deletions estimated by multiplex ligation-dependent probe amplification and array comparative genomic hybridization was 25-40%, which was comparable to the mosaic ratio in lymphocytes and buccal mucosa cells observed by fluorescence in situ hybridization analysis...
January 17, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29340254/response-of-methane-production-via-propionate-oxidation-to-carboxylated-multiwalled-carbon-nanotubes-in-paddy-soil-enrichments
#9
Jianchao Zhang, Xingxuan Xia, Siliang Li, Wei Ran
Carboxylated multiwalled carbon nanotubes (MWCNTs-COOH) have become a growing concern in terms of their fate and toxicity in aqueous environments. Methane (CH4) is a major product of organic matter degradation in waterlogged environments. In this study, we determined the effect of MWCNTs-COOH on the production of CH4 from propionate oxidation in paddy soil enrichments. The results showed that the methanogenesis from propionate degradation was accelerated in the presence of MWCNTs-COOH. In addition, the rates of CH4 production and propionate degradation increased with increasing concentrations of MWCNTs-COOH...
2018: PeerJ
https://www.readbyqxmd.com/read/29339834/use-of-multicolor-fluorescence-in-situ-hybridization-to-detect-deletions-in-clinical-tissue-sections
#10
REVIEW
Maisa Yoshimoto, Olga Ludkovski, Jennifer Good, Ciro Pereira, Robert J Gooding, Jean McGowan-Jordan, Alexander Boag, Andrew Evans, Ming-Sound Tsao, Paulo Nuin, Jeremy A Squire
A variety of laboratory methods are available for the detection of deletions of tumor suppressor genes and losses of their proteins. The clinical utility of fluorescence in situ hybridization (FISH) for the identification of deletions of tumor suppressor genes has previously been limited by difficulties in the interpretation of FISH signal patterns. The first deletion FISH assays using formalin-fixed paraffin-embedded tissue sections had to deal with a significant background level of signal losses affecting nuclei that are truncated by the cutting process of slide preparation...
January 16, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29338072/targeting-her2-in-colorectal-cancer-the-landscape-of-amplification-and-short-variant-mutations-in-erbb2-and-erbb3
#11
Jeffrey S Ross, Marwan Fakih, Siraj M Ali, Julia A Elvin, Alexa B Schrock, James Suh, Jo-Anne Vergilio, Shakti Ramkissoon, Eric Severson, Sugganth Daniel, David Fabrizio, Garrett Frampton, James Sun, Vincent A Miller, Philip J Stephens, Laurie M Gay
BACKGROUND: In contrast to lung cancer, few precision treatments are available for colorectal cancer (CRC). One rapidly emerging treatment target in CRC is ERBB2 (human epidermal growth factor receptor 2 [HER2]). Oncogenic alterations in HER2, or its dimerization partner HER3, can underlie sensitivity to HER2-targeted therapies. METHODS: In this study, 8887 CRC cases were evaluated by comprehensive genomic profiling for genomic alterations in 315 cancer-related genes, tumor mutational burden, and microsatellite instability...
January 16, 2018: Cancer
https://www.readbyqxmd.com/read/29335461/pixelated-spatial-gene-expression-analysis-from-tissue
#12
A Ganguli, A Ornob, N Spegazzini, Y Liu, G Damhorst, T Ghonge, B Thornton, C J Konopka, W Dobrucki, S E Clare, R Bhargava, A M Smith, F Kosari, R Bashir
Here, we present a technique that performs on-chip picoliter real-time reverse transcriptase loop mediated isothermal amplification (RT-LAMP) reactions on a histological tissue section without any analyte purification while preserving the native spatial location of the nucleic acid molecules. We demonstrate this method by amplifying TOP2A messenger RNA (mRNA) in a prostate cancer xenograft with 100 µm spatial resolution and by visualizing the variation in threshold time of amplification across the tissue...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29335378/comparison-of-telomere-length-measurement-methods
#13
REVIEW
Tsung-Po Lai, Woodring E Wright, Jerry W Shay
The strengths and limitations of the major methods developed to measure telomere lengths (TLs) in cells and tissues are presented in this review. These include Q-PCR (Quantitative Polymerase Chain Reaction), TRF (Terminal Restriction Fragment) analysis, a variety of Q-FISH (Quantitative Fluorescence In Situ Hybridization) methods, STELA (Single TElomere Length Analysis) and TeSLA (Telomere Shortest Length Assay). For each method, we will cover information about validation studies, including reproducibility in independent laboratories, accuracy, reliability and sensitivity for measuring not only the average but also the shortest telomeres...
March 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29335281/high-throughput-identification-of-rna-nuclear-enrichment-sequences
#14
Chinmay J Shukla, Alexandra L McCorkindale, Chiara Gerhardinger, Keegan D Korthauer, Moran N Cabili, David M Shechner, Rafael A Irizarry, Philipp G Maass, John L Rinn
In the post-genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNAs (lncRNAs), and a cadre of small peptides. These ever-growing catalogs require high-throughput assays to test their functionality at scale. Massively parallel reporter assays have greatly enhanced the understanding of noncoding DNA elements en masse Here, we present a massively parallel RNA assay (MPRNA) that can assay 10,000 or more RNA segments for RNA-based functionality...
January 15, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29330722/location-of-low-copy-genes-in-chromosomes-of-brachiaria-spp
#15
Thaís Furtado Nani, James C Schnable, Jacob D Washburn, Patrice Albert, Welison Andrade Pereira, Fausto Souza Sobrinho, James A Birchler, Vânia Helena Techio
Repetitive DNA sequences have been widely used in cytogenetic analyses. The use of gene sequences with a low-copy-number, however, is little explored especially in plants. To date, the karyotype details in Brachiaria spp. are limited to the location of rDNA sites. The challenge lies in developing new probes based on incomplete sequencing data for the genus or complete sequencing of related species, since there are no model species with a sequenced genome in Brachiaria spp. The present study aimed at the physical location of conserved genes in chromosomes of Brachiaria ruziziensis, Brachiaria brizantha, and Brachiaria decumbens using RNAseq data, as well as sequences of Setaria italica and Sorghum bicolor through the fluorescent in situ hybridization technique...
January 12, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29330459/a-novel-ultra-stable-monomeric-green-fluorescent-protein-for-direct-volumetric-imaging-of-whole-organs-using-clarity
#16
Daniel J Scott, Natalie J Gunn, Kelvin J Yong, Verena C Wimmer, Nicholas A Veldhuis, Leesa M Challis, Mouna Haidar, Steven Petrou, Ross A D Bathgate, Michael D W Griffin
Recent advances in thick tissue clearing are enabling high resolution, volumetric fluorescence imaging of complex cellular networks. Fluorescent proteins (FPs) such as GFP, however, can be inactivated by the denaturing chemicals used to remove lipids in some tissue clearing methods. Here, we solved the crystal structure of a recently engineered ultra-stable GFP (usGFP) and propose that the two stabilising mutations, Q69L and N164Y, act to improve hydrophobic packing in the core of the protein and facilitate hydrogen bonding networks at the surface, respectively...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330187/acquisition-of-a-novel-sulfur-oxidizing-symbiont-in-the-gutless-marine-worm-inanidrilus-exumae
#17
C Bergin, C Wentrup, N Brewig, A Blazejak, C Erséus, O Giere, M Schmid, P De Wit, N Dubilier
Gutless phallodrilines are marine annelid worms without a mouth or gut, which live in an obligate association with multiple bacterial endosymbionts that supply them with nutrition. In this study, we discovered an unusual symbiont community in the gutless phallodriline Inanidrilus exumae that differs markedly from the microbiome of all other 22 examined host species. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization revealed that I. exumae harboured co-occurring gamma-, alpha- and deltaproteobacterial symbionts, while all other known host species harbour gamma- and either alpha- or deltaproteobacterial symbionts...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29327717/combined-mutation-and-copy-number-variation-detection-by-targeted-next-generation-sequencing-in-uveal-melanoma
#18
Kyra N Smit, Natasha M van Poppelen, Jolanda Vaarwater, Robert Verdijk, Ronald van Marion, Helen Kalirai, Sarah E Coupland, Sophie Thornton, Neil Farquhar, Hendrikus-Jan Dubbink, Dion Paridaens, Annelies de Klein, Emine Kiliç
Uveal melanoma is a highly aggressive cancer of the eye, in which nearly 50% of the patients die from metastasis. It is the most common type of primary eye cancer in adults. Chromosome and mutation status have been shown to correlate with the disease-free survival. Loss of chromosome 3 and inactivating mutations in BAP1, which is located on chromosome 3, are strongly associated with 'high-risk' tumors that metastasize early. Other genes often involved in uveal melanoma are SF3B1 and EIF1AX, which are found to be mutated in intermediate- and low-risk tumors, respectively...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29327716/genomic-heterogeneity-of-alk-fusion-breakpoints-in-non-small-cell-lung-cancer
#19
Jason N Rosenbaum, Ryan Bloom, Jason T Forys, Jeff Hiken, Jon R Armstrong, Julie Branson, Samantha McNulty, Priya D Velu, Kymberlie Pepin, Haley Abel, Catherine E Cottrell, John D Pfeifer, Shashikant Kulkarni, Ramaswamy Govindan, Eric Q Konnick, Christina M Lockwood, Eric J Duncavage
In lung adenocarcinoma, canonical EML4-ALK inversion results in a fusion protein with a constitutively active ALK kinase domain. Evidence of ALK rearrangement occurs in a minority (2-7%) of lung adenocarcinoma, and only ~60% of these patients will respond to targeted ALK inhibition by drugs such as crizotinib and ceritinib. Clinically, targeted anti-ALK therapy is often initiated based on evidence of an ALK genomic rearrangement detected by fluorescence in situ hybridization (FISH) of interphase cells in formalin-fixed, paraffin-embedded tissue sections...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29327482/streptococcus-oralis-maintains-homeostasis-in-supragingival-biofilms-by-antagonizing-cariogenic-pathogen-streptococcus-mutans
#20
Thomas Thurnheer, Georgios N Belibasakis
Bacteria residing in oral biofilms live in a state of dynamic equilibrium with one another. The intricate synergistic or antagonistic interactions between them are crucial for determining this balance. Using the 6-species Zürich "supragingival" biofilm model, this study aimed to investigate interactions regarding growth and localization of the constituent species. As control, an inoculum containing all six strains was used, whereas in each of the further five inocula one of the bacterial species was absent, and in the last both streptococci were absent...
January 11, 2018: Molecular Oral Microbiology
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