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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
#1
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
#2
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...
March 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28416765/lolopicker-detecting-low-allelic-fraction-variants-from-low-quality-cancer-samples
#3
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
#4
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
#5
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
#6
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...
April 3, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28346123/panfungal-polymerase-chain-reaction-for-identification-of-fungal-pathogens-in-formalin-fixed-animal-tissues
#7
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
#8
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
#9
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
#10
Sílvia Vilarinho, 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 17 cm heterogeneous mass in the left lobe of the liver. She underwent left hepatectomy and pathology revealed a 14 cm moderately differentiated hepatocellular carcinoma (HCC) arising in a shell of a HCA...
March 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28315738/pulmonary-sarcomatoid-carcinomas-commonly-harbor-either-potentially-targetable-genomic-alterations-or-high-tumor-mutational-burden-as-observed-by-comprehensive-genomic-profiling
#11
Alexa B Schrock, Shuyu D Li, Garrett M Frampton, James Suh, Eduardo Braun, Ranee Mehra, Steven Buck, Jose A Bufill, Nir Peled, Nagla Abdel Karim, Cynthia Hsieh, Manuel Doria, James Knost, Rong Chen, Sai-Hong Ignatius Ou, Jeffrey S Ross, Philip J Stephens, Paul Fishkin, Vincent A Miller, Siraj M Ali, Balazs Halmos, Jane J Liu
BACKGROUND: Pulmonary sarcomatoid carcinoma (PSC) is a high-grade non-small cell lung carcinoma (NSCLC) characterized by poor prognosis and resistance to chemotherapy. Development of targeted therapeutic strategies for PSC has been hampered due to limited and inconsistent molecular characterization. METHODS: Hybrid-capture based comprehensive genomic profiling (CGP) was performed on DNA from 15,867 FFPE NSCLCs including 125 PSCs (0.8%). Tumor mutational burden (TMB) was calculated from 1...
March 15, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28314930/non-reproducible-sequence-artifacts-in-ffpe-tissue-an-experience-report
#12
Richard Ofner, Cathrin Ritter, Selma Ugurel, Lorenzo Cerroni, Mathias Stiller, Thomas Bogenrieder, Flavio Solca, David Schrama, Jürgen C Becker
BACKGROUND: Recent advances in sequencing technologies supported the development of molecularly targeted therapy in cancer patients. Thus, genomic analyses are becoming a routine part in clinical practice and accurate detection of actionable mutations is essential to assist diagnosis and therapy choice. However, this is often challenging due to major problems associated with DNA from formalin-fixed paraffin-embedded tissue which is usually the primary source for genetic testing. OBJECTIVES: Here we want to share our experience regarding major problems associated with FFPE DNA used for PCR-based sequencing as illustrated by the mutational analysis of ERBB4 in melanoma...
March 17, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28274512/practical-use-and-utility-of-fluorescence-in-situ-hybridization-in-the-pathological-diagnosis-of-soft-tissue-and-bone-tumors
#13
Shintaro Sugita, Tadashi Hasegawa
During routine pathological examination, fluorescence in situ hybridization (FISH) plays a significant role in the genetic analysis of samples. FISH can detect genetic abnormalities such as chromosomal translocations, gene amplifications, and deletions in formalin-fixed, paraffin-embedded (FFPE) specimens. Due to its practical advantages, FISH is already used in many pathology laboratories. It is especially useful for the diagnosis of translocation-related sarcomas (TRSs), which comprise about 25% of soft tissue sarcomas...
March 5, 2017: Journal of Orthopaedic Science: Official Journal of the Japanese Orthopaedic Association
https://www.readbyqxmd.com/read/28269754/evaluation-of-pik3ca-mutations-as-a-biomarker-in-chinese-breast-carcinomas-from-western-china
#14
Jingliang Cheng, Shangyi Fu, Chunli Wei, Mousumi Tania, Asaduzzaman Khan, Saber Imani, Baixu Zhou, Hanchun Chen, Xiuli Xiao, Jingbo Wu, Junjiang Fu
BACKGROUND: PIK3CA gene encodes the p110 α catalytic subunit of the oncoprotein phosphatidylinositol 3-kinase (PI3 K) which regulates many biological processes such as cell proliferation, differentiation, migration and survival through the activation of various signaling pathways. OBJECTIVE: In this study, we have investigated the possible somatic mutations in PIK3CA gene in invasive ductal breast carcinomas of Chinese women from Western China. METHODS: Genomic DNA was extracted from the formalin-fixed paraffin-embedded (FFPE) tissue samples...
February 27, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28246590/the-utilization-of-formalin-fixed-paraffin-embedded-specimens-in-high-throughput-genomic-studies
#15
REVIEW
Pan Zhang, Brian D Lehmann, Yu Shyr, Yan Guo
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28245386/-diagnostic-significance-of-biomed-2-standardized-gene-rearran-gement-system-in-patients-with-non-hodgkin-s-lymphoma
#16
Yan Zhang, Ning Xu, Bao-Jun Dong, Ge Song, Qing-Hua Li, Gang An, Xiao-Fei Ai
OBJECTIVE: To detect the immunoglobulin(Ig) and T cell receptor(TCR) gene rearrangement in bone marrow of non-Hodgkin's lymphoma(NHL) patients by using BIOMED-2 standardized system, and to explore the potential clinical significance of Ig/TCR gene rearrangement. METHODS: DNA was extracted in bone marrow and Formalin-fixed and Paraffin-embedded(FFPE) samples of NHL patients, the Ig/TCR gene rearrangements were analyzed by using BIOMED-2 multiple primers system and multiplex PCR assay...
February 2017: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/28228113/validation-of-an-ngs-mutation-detection-panel-for-melanoma
#17
Anne Reiman, Hugh Kikuchi, Daniela Scocchia, Peter Smith, Yee Wah Tsang, David Snead, Ian A Cree
BACKGROUND: Knowledge of the genotype of melanoma is important to guide patient management. Identification of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are driver oncogene mutations in NRAS, GNAQ or GNA11 as these patients may benefit from alternative strategies such as immunotherapy. METHODS: While polymerase chain reaction (PCR) methods are often used to detect BRAF mutations, next generation sequencing (NGS) is able to determine all of the necessary information on several genes at once, with potential advantages in turnaround time...
February 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28201998/clinical-performance-evaluation-of-a-sensitive-rapid-low-throughput-test-for-kras-mutation-analysis-using-formalin-fixed-paraffin-embedded-tissue-samples
#18
Christine Weyn, Sofie Van Raemdonck, Robina Dendooven, Vincent Maes, Karen Zwaenepoel, Suzan Lambin, Patrick Pauwels
BACKGROUND: Testing for KRAS mutations in metastatic colorectal cancer (mCRC) on formalin-fixed, paraffin embedded (FFPE) tumor tissue has become standard of care. Different molecular methods exist to determine hotspot KRAS mutations in exon 2, 3 and 4, but testing is often limited by the sensitivity and the speed of analysis. The aim of this retrospective study was to establish the clinical performance of the Idylla™ KRAS Mutation Test on FFPE tumor samples of patients with mCRC. METHODS: KRAS mutation analysis was performed using the therascreen KRAS on the RotorGene Q platform (CE-IVD; Qiagen) and results were subsequently compared to the Idylla™ KRAS Mutation Test...
February 16, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28196074/clinical-applicability-and-cost-of-a-46-gene-panel-for-genomic-analysis-of-solid-tumours-retrospective-validation-and-prospective-audit-in-the-uk-national-health-service
#19
Angela Hamblin, Sarah Wordsworth, Jilles M Fermont, Suzanne Page, Kulvinder Kaur, Carme Camps, Pamela Kaisaki, Avinash Gupta, Denis Talbot, Mark Middleton, Shirley Henderson, Anthony Cutts, Dimitrios V Vavoulis, Nick Housby, Ian Tomlinson, Jenny C Taylor, Anna Schuh
BACKGROUND: Single gene tests to predict whether cancers respond to specific targeted therapies are performed increasingly often. Advances in sequencing technology, collectively referred to as next generation sequencing (NGS), mean the entire cancer genome or parts of it can now be sequenced at speed with increased depth and sensitivity. However, translation of NGS into routine cancer care has been slow. Healthcare stakeholders are unclear about the clinical utility of NGS and are concerned it could be an expensive addition to cancer diagnostics, rather than an affordable alternative to single gene testing...
February 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28192086/variant-call-concordance-between-two-laboratory-developed-solid-tumor-targeted-genomic-profiling-assays-using-distinct-workflows-and-sequencing-instruments
#20
Ken J Hampel, Francine B de Abreu, Nikoletta Sidiropoulos, Jason D Peterson, Gregory J Tsongalis
Targeted genomic profiling (TGP) using massively parallel DNA sequencing is becoming the standard methodology in clinical laboratories for detecting somatic variants in solid tumors. The variety of methodologies and sequencing platforms in the marketplace for TGP has resulted in a variety of clinical TGP laboratory developed tests (LDT). The variability of LDTs is a challenge for test-to-test and laboratory-to-laboratory reliability. At the University of Vermont Medical Center (UVMMC), we validated a TGP assay for solid tumors which utilizes DNA hybridization capture and complete exon and selected intron sequencing of 29 clinically actionable genes...
February 10, 2017: Experimental and Molecular Pathology
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