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FFPE sequencing

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https://www.readbyqxmd.com/read/28545165/highly-recurrent-h3f3a-mutations-with-additional-epigenetic-regulator-alterations-in-giant-cell-tumor-of-bone
#1
Koichi Ogura, Fumie Hosoda, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Shoko Ohashi, Hirofumi Rokutan, Erina Takai, Shinichi Yachida, Akira Kawai, Sakae Tanaka, Tatsuhiro Shibata
Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next-generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) for clinical diagnosis have not been assessed...
May 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28545022/a-high-throughput-method-to-detect-rna-profiling-by-integration-of-rt-mlpa-with-next-generation-sequencing-technology
#2
Jing Wang, Xue Yang, Haofeng Chen, Xuewei Wang, Xiangyu Wang, Yi Fang, Zhenyu Jia, Jidong Gao
RNA in formalin-fixed and paraffin-embedded (FFPE) tissues provides large amount of information indicating disease stages, histological tumor types and grades, as well as clinical outcomes. However, Detection of RNA expression levels in formalin-fixed and paraffin-embedded samples is extremely difficult due to poor RNA quality. Here we developed a high-throughput method, Reverse Transcription-Multiple Ligation-dependent Probe Sequencing (RT-MLPSeq), to determine expression levels of multiple transcripts in FFPE samples...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28532404/use-of-the-qiagen-genereader-ngs-system-for-detection-of-kras-mutations-validated-by-the-qiagen-therascreen-pcr-kit-and-alternative-ngs-platform
#3
Agus Darwanto, Anne-Mette Hein, Sascha Strauss, Yi Kong, Andrew Sheridan, Dan Richards, Eric Lader, Monika Ngowe, Timothy Pelletier, Danielle Adams, Austin Ricker, Nishit Patel, Andreas Kühne, Simon Hughes, Dan Shiffman, Dirk Zimmermann, Kai Te Kaat, Thomas Rothmann
BACKGROUND: The detection of somatic mutations in primary tumors is critical for the understanding of cancer evolution and targeting therapy. Multiple technologies have been developed to enable the detection of such mutations. Next generation sequencing (NGS) is a new platform that is gradually becoming the technology of choice for genotyping cancer samples, owing to its ability to simultaneously interrogate many genomic loci at massively high efficiency and increasingly lower cost. However, multiple barriers still exist for its broader adoption in clinical research practice, such as fragmented workflow and complex bioinformatics analysis and interpretation...
May 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28502004/somatic-dna-mutation-analysis
#4
Anthony O'Grady, Robert Cummins
Somatic mutations in patient tumor DNA samples can be readily detected based on mass spectrometry. The MassARRAY system is a high-throughput matrix-assisted laser desorption time-of-flight (MALDI) mass spectrometer for detection of nucleic acids. The technique is based on single-nucleotide base extension. A series of PCR assays amplify specific DNA regions of interest harboring mutations. A third primer is then introduced into the reaction which corresponds to the DNA template immediately in front of the mutation site...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28498833/assessment-of-the-quality-of-dna-from-various-formalin-fixed-paraffin-embedded-ffpe-tissues-and-the-use-of-this-dna-for-next-generation-sequencing-ngs-with-no-artifactual-mutation
#5
Naoki Einaga, Akio Yoshida, Hiroko Noda, Masaaki Suemitsu, Yuki Nakayama, Akihisa Sakurada, Yoshiko Kawaji, Hiromi Yamaguchi, Yasushi Sasaki, Takashi Tokino, Mariko Esumi
Formalin-fixed, paraffin-embedded (FFPE) tissues used for pathological diagnosis are valuable for studying cancer genomics. In particular, laser-capture microdissection of target cells determined by histopathology combined with FFPE tissue section immunohistochemistry (IHC) enables precise analysis by next-generation sequencing (NGS) of the genetic events occurring in cancer. The result is a new strategy for a pathological tool for cancer diagnosis: 'microgenomics'. To more conveniently and precisely perform microgenomics, we revealed by systematic analysis the following three details regarding FFPE DNA compared with paired frozen tissue DNA...
2017: PloS One
https://www.readbyqxmd.com/read/28489587/ngs-based-identification-of-mutational-hotspots-for-targeted-therapy-in-anaplastic-thyroid-carcinoma
#6
Vera Tiedje, Saskia Ting, Thomas Herold, Sarah Synoracki, Soeren Latteyer, Lars C Moeller, Denise Zwanziger, Martin Stuschke, Dagmar Fuehrer, Kurt Werner Schmid
CONTEXT: Anaplastic thyroid carcinoma (ATC) represents one of the most aggressive carcinomas with no consistent survival benefit when treated with conventional radiochemotherapy. Approaches targeting "oncogene addiction" of ATC are increasingly explored and first promising results have been reported in single case studies. OBJECTIVE: To determine the prevalence of mutations in known thyroid oncogenes and signalling pathways amendable to targeted therapy in a large cohort of ATC...
April 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28477007/tissue-recommendations-for-precision-cancer-therapy-using-next-generation-sequencing-a-comprehensive-single-cancer-center-s-experiences
#7
Minho Cho, Soomin Ahn, Mineui Hong, Heejin Bang, Michael Van Vrancken, Seungtae Kim, Jeeyun Lee, Se Hoon Park, Joon Oh Park, Young Suk Park, Ho Yeong Lim, Won Ki Kang, Jong-Mu Sun, Se Hoon Lee, Myung-Ju Ahn, Keunchil Park, Duk Hwan Kim, Seunggwan Lee, Woongyang Park, Kyoung-Mee Kim
To generate accurate next-generation sequencing (NGS) data, the amount and quality of DNA extracted is critical. We analyzed 1564 tissue samples from patients with metastatic or recurrent solid tumor submitted for NGS according to their sample size, acquisition method, organ, and fixation to propose appropriate tissue requirements.Of the 1564 tissue samples, 481 (30.8%) consisted of fresh-frozen (FF) tissue, and 1,083 (69.2%) consisted of formalin-fixed paraffin-embedded (FFPE) tissue. We obtained successful NGS results in 95...
April 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28460486/small-rna-sequencing-reveals-metastasis-related-micrornas-in-lung-adenocarcinoma
#8
Iben Daugaard, Morten T Venø, Yan Yan, Tina E Kjeldsen, Philippe Lamy, Henrik Hager, Jørgen Kjems, Lise Lotte Hansen
The majority of lung cancer deaths are caused by metastatic disease. MicroRNAs (miRNAs) are posttranscriptional regulators of gene expression and miRNA dysregulation can contribute to metastatic progression. Here, small RNA sequencing was used to profile the miRNA and piwi-interacting RNA (piRNA) transcriptomes in relation to lung cancer metastasis. RNA-seq was performed using RNA extracted from formalin-fixed paraffin embedded (FFPE) lung adenocarcinomas (LAC) and brain metastases from 8 patients, and LACs from 8 patients without detectable metastatic disease...
April 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28460011/the-immune-microenvironment-of-hpv-negative-oral-squamous-cell-carcinoma-from-never-smokers-and-never-drinkers-patients-suggests-higher-clinical-benefit-of-ido1-and-pd1-pd-l1-blockade
#9
J-P Foy, C Bertolus, M-C Michallet, S Deneuve, R Incitti, N Bendriss-Vermare, M-A Albaret, S Ortiz-Cuaran, E Thomas, A Colombe, C Py, N Gadot, J-P Michot, J Fayette, A Viari, B Van den Eynde, P Goudot, M Devouassoux-Shisheboran, A Puisieux, C Caux, P Zrounba, S Lantuejoul, P Saintigny
Background: : Never-smokers and never-drinkers patients (NSND) suffering from oral squamous cell carcinoma (OSCC) are epidemiologically different from smokers drinkers (SD). We therefore hypothesized that they harbored distinct targetable molecular alterations. Patients and methods: Data from The Cancer Genome Atlas (TCGA) (discovery set), Gene Expression Omnibus and Centre Léon Bérard (CLB) (3 validation sets) with available gene expression profiles of HPV-negative OSCC from NSND and SD were mined...
April 28, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28449808/validation-of-quantitative-pcr-based-assays-for-detection-of-gene-copy-number-aberrations-in-formalin-fixed-paraffin-embedded-solid-tumor-samples
#10
Meenakshi Mehrotra, Rajyalakshmi Luthra, Ronald Abraham, Bal Mukund Mishra, Shumaila Virani, Hui Chen, Mark J Routbort, Keyur P Patel, L Jeffrey Medeiros, Rajesh R Singh
Gene copy number changes are important somatic alterations in cancers. A number of high throughput methods, such as next generation sequencing, are capable of detecting copy number aberrations, but their use can be challenging and cost prohibitive for screening a small number of markers. Furthermore, detection of CNAs by high throughput platforms needs confirmation by an orthogonal technique, especially in cases with low level CNAs. Here, we have validated TaqMan based quantitative PCR (qPCR) assays to detect CNAs in genes of high clinical importance in formalin-fixed, paraffin-embedded (FFPE) samples...
April 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28432840/detection-of-egfr-mutations-in-patients-with-non-small-cell-lung-cancer-by-high-resolution-melting-comparison-with-other-methods
#11
Carlos Martínez-Carretero, Fernando Iguaz Pascual, Antonio Rus, Ivan Bernardo
BACKGROUND: The discovery of mutations in the epidermal growth factor receptor gene (EGFR) related to the clinical response to tyrosine kinase inhibitors, has transformed the management of non-small cell lung cancer (NSCLC). Several methods have been developed for determination of mutations in EGFR, with different sensitivity and potential ability to detect a different number of mutations. METHODS: We developed a screening method by high resolution melting (HRM) to detect EGFR mutations, and compared the results of 123 fixed in formalin and paraffin embedded (FFPE) tumor tissue samples with the detection of mutations by allele-specific PCR...
April 22, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28427242/epidermal-growth-factor-receptor-variant-iii-in-head-and-neck-squamous-cell-carcinoma-is-not-relevant-for-targeted-therapy-and-irradiation
#12
Dominik Thomas Koch, Anja Pickhard, Lena Gebel, Anna Maria S Buchberger, Murat Bas, Carolin Mogler, Rudolf Reiter, Guido Piontek, Markus Wirth
BACKGROUND: The epidermal growth factor receptor (EGFR) is an important regulator of cell growth and survival, and is highly variable in tumor cells. The most prevalent variation of the EGFR extracellular domain is the EGFR variant III (EGFRvIII). Some studies imply that EGFRvIII may be responsible for the poor response to the monoclonal EGFR-antibody Cetuximab, used therapeutically in head and neck squamous cell carcinoma (HNSCC). Due to inconsistent data in the literature regarding EGFRvIII prevalence and clinical relevance in HNSCC, especially its predictive value, we examined EGFRvIII-transfected cell lines and patient tissue samples...
May 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28416765/lolopicker-detecting-low-allelic-fraction-variants-from-low-quality-cancer-samples
#13
Jian Carrot-Zhang, Jacek Majewski
INTRODUCTION: Although several programs are designed to identify variants with low allelic-fraction, further improvement is needed, especially to push the detection limit of low allelic-faction variants in low-quality, "noisy" tumor samples. RESULTS: We developed LoLoPicker, an efficient tool dedicated to calling somatic variants from next-generation sequencing (NGS) data of tumor sample against the matched normal sample plus a user-defined control panel of additional normal samples...
March 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/28404952/high-throughput-detection-of-clinically-targetable-alterations-using-next-generation-sequencing
#14
Julie A Vendrell, David Grand, Isabelle Rouquette, Valérie Costes, Samira Icher, Janick Selves, Marion Larrieux, Aurore Barbe, Pierre Brousset, Jérôme Solassol
Next-generation sequencing (NGS) has revolutionized the therapeutic care of patients by allowing high-throughput and parallel sequencing of large numbers of genes in a single run. However, most of available commercialized cancer panels target a large number of mutations that do not have direct therapeutic implications and that are not fully adapted to low quality formalin-fixed, paraffin-embedded (FFPE) samples. Here, we designed an amplicon-based NGS panel assay of 16 currently actionable genes according to the most recent recommendations of the French National Cancer Institute (NCI)...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28376728/comparison-of-triple-negative-breast-cancer-molecular-subtyping-using-rna-from-matched-fresh-frozen-versus-formalin-fixed-paraffin-embedded-tissue
#15
Bojana Jovanović, Quanhu Sheng, Robert S Seitz, Kasey D Lawrence, Stephan W Morris, Lance R Thomas, David R Hout, Brock L Schweitzer, Yan Guo, Jennifer A Pietenpol, Brian D Lehmann
BACKGROUND: Triple negative breast cancer (TNBC) is a heterogeneous disease that lacks unifying molecular alterations that can guide therapy decisions. We previously identified distinct molecular subtypes of TNBC (TNBCtype) using gene expression data generated on a microarray platform using frozen tumor specimens. Tumors and cell lines representing the identified subtypes have distinct enrichment in biologically relevant transcripts with differing sensitivity to standard chemotherapies and targeted agents...
April 4, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28371134/strandadvantage-test-for-early-line-and-advanced-stage-treatment-decisions-in-solid-tumors
#16
Manimala Sen, Shanmukh Katragadda, Aarthi Ravichandran, Gouri Deshpande, Minothi Parulekar, Swetha Nayanala, Vikram Vittal, Weiming Shen, Melanie Phooi Nee Yong, Jemima Jacob, Sravanthi Parchuru, Kalpana Dhanuskodi, Kenneth Eyring, Pooja Agrawal, Smita Agarwal, Ashwini Shanmugam, Satish Gupta, Divya Vishwanath, Kiran Kumari, Arun K Hariharan, Sai A Balaji, Qiaoling Liang, Belen Robolledo, Vijayashree Gauribidanur Raghavendrachar, Mohammed Oomer Farooque, Cary J Buresh, Preveen Ramamoorthy, Urvashi Bahadur, Kalyanasundaram Subramanian, Ramesh Hariharan, Vamsi Veeramachaneni, Satish Sankaran, Vaijayanti Gupta
Comprehensive genetic profiling of tumors using next-generation sequencing (NGS) is gaining acceptance for guiding treatment decisions in cancer care. We designed a cancer profiling test combining both deep sequencing and immunohistochemistry (IHC) of relevant cancer targets to aid therapy choices in both standard-of-care (SOC) and advanced-stage treatments for solid tumors. The SOC report is provided in a short turnaround time for four tumors, namely lung, breast, colon, and melanoma, followed by an investigational report...
May 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28346123/panfungal-polymerase-chain-reaction-for-identification-of-fungal-pathogens-in-formalin-fixed-animal-tissues
#17
Courtney Meason-Smith, Erin E Edwards, Caitlin E Older, Mackenzie Branco, Laura K Bryan, Sara D Lawhon, Jan S Suchodolski, Gabriel Gomez, Joanne Mansell, Aline Rodrigues Hoffmann
Identification of fungal organisms often poses a problem for pathologists because the histomorphology of some fungal organisms is not specific, fresh tissues may not be available, and isolation and identification in culture may take a long time. The purpose of this study was to validate the use of panfungal polymerase chain reaction (PCR) to identify fungal organisms from formalin-fixed paraffin-embedded (FFPE) tissues. Formalin-fixed paraffin-embedded curls were tested from 128 blocks containing canine, feline, equine, and bovine tissues with cutaneous, nasal, pulmonary, and systemic fungal infections, identified by the presence of fungi in histologic sections...
January 1, 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/28335433/evaluation-and-adaptation-of-a-laboratory-based-cdna-library-preparation-protocol-for-retrospective-sequencing-of-archived-micrornas-from-up-to-35-year-old-clinical-ffpe-specimens
#18
Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert Greenlee, Deborah Multerer, Stacey Honda, Yihe Daida, Heather Spencer Feigelson, Andrew Glass, Fergus J Couch, Thomas Rohan, Iddo Z Ben-Dov
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28334446/molecular-glycopathology-by-capillary-electrophoresis-analysis-of-the-n-glycome-of-formalin-fixed-paraffin-embedded-mouse-tissue-samples
#19
Boglarka Donczo, Mate Szarka, Jozsef Tovari, Gyorgyi Ostoros, Eszter Csanky, Andras Guttman
Capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection was used to analyze endoglycosidase released and fluorophore-labeled N-glycans from formalin-fixed paraffin-embedded (FFPE) mouse tissue samples of lung, brain, heart, spleen, liver, kidney and intestine. The FFPE samples were first deparaffinized followed by solubilization and glycoprotein retrieval. PNGase F mediated release of the N-linked oligosaccharides was followed by labeling with aminopyrene trisulfonate. After CE-LIF glycoprofiling of the FFPE mouse tissues, the N-glycan pool of the lung specimen was subject to further investigation by exoglycosidase array based carbohydrate sequencing...
March 23, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28323122/exome-analysis-of-the-evolutionary-path-of-hepatocellular-adenoma-carcinoma-transition-vascular-invasion-and-brain-dissemination
#20
Sílvia Vilarinho, E Zeynep Erson-Omay, Kisha Mitchell-Richards, Charles Cha, Carol Nelson-Williams, Akdes Serin Harmancı, Katsuhito Yasuno, Murat Günel, Tamar H Taddei
Hepatocellular adenoma (HCA) is a rare benign liver tumor, predominantly seen in young women. Its major complications are malignant transformation, spontaneous hemorrhage, and rupture. We describe a case of a young female with no underlying liver disease who presented with acute abdominal pain and was found to have a 17cm heterogeneous mass in the left lobe of the liver. She underwent left hepatectomy and pathology revealed a 14cm moderately differentiated hepatocellular carcinoma (HCC) arising in a shell of a HCA...
March 18, 2017: Journal of Hepatology
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