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FFPE sequencing

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https://www.readbyqxmd.com/read/29215764/an-evaluation-of-the-challenges-to-developing-tumour-brca1-and-brca2-testing-methodologies-for-clinical-practice
#1
Gillian Ellison, Miika Ahdesmäki, Sally Luke, Paul M Waring, Andrew Wallace, Ronnie Wright, Benno Röthlisberger, Katja Ludin, Sabine Merkelbach-Bruse, Carina Heydt, Marjolijn J L Ligtenberg, Arjen R Mensenkamp, David Gonzalez Castro, Thomas Jones, Ana Vivancos, Olga Kondrashova, Patrick Pauwels, Christine Weyn, Eric Hahnen, Jan Hauke, Richie Soong, Zhongwu Lai, Brian Dougherty, T Hedley Carr, Justin Johnson, John Mills, J Carl Barrett
Ovarian cancer patients with germline or somatic pathogenic variants benefit from treatment with PARP inhibitors. Tumour BRCA1/2 testing is more challenging than germline testing as the majority of samples are formalin fixed paraffin embedded (FFPE), the tumour genome is complex and the allelic fraction of somatic variants can be low. We collaborated with 10 laboratories testing BRCA1/2 in tumours to compare different approaches to identify clinically important variants within FFPE tumour DNA samples. This was not a proficiency study but an inter-laboratory comparison to identify common issues...
December 7, 2017: Human Mutation
https://www.readbyqxmd.com/read/29212158/rnascope-in-situ-hybridization-confirms-mrna-integrity-in-formalin-fixed-paraffin-embedded-cancer-tissue-samples
#2
Victoria Bingham, Leanne McIlreavey, Christine Greene, Edwina O'Doherty, Rebecca Clarke, Stephanie Craig, Manuel Salto-Tellez, Stephen McQuaid, Claire Lewis, Jacqueline James
Immunohistochemistry remains the overwhelming technique of choice for test biomarker evaluation in both clinical or research settings when using formalin-fixed, paraffin embedded tissue sections. However, validations can be complex with significant issues about specificity, sensitivity and reproducibility. The vast array of commercially available antibodies from many vendors may also lead to non-standard approaches which are difficult to cross-reference. In contrast mRNA detection, by in situ hybridization (ISH) with sequence specific probes, offers a realistic alternative, with less validation steps and more stringent and reproducible assessment criteria...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29210102/the-use-of-droplet-digital-pcr-in-liquid-biopsies-a-highly-sensitive-technique-for-myd88-p-l265p-detection-in-cerebrospinal-fluid
#3
Laura S Hiemcke-Jiwa, Monique C Minnema, Joyce H Radersma-van Loon, N Mehdi Jiwa, Mirthe de Boer, Roos J Leguit, Roel A de Weger, Manon M H Huibers
The gold standard for diagnosis of central nervous system lymphomas still regards a stereotactic brain biopsy, with the risk of major complications for the patient. As tumor cells can be detected in cerebrospinal fluid (CSF), CSF analysis can be used as an alternative. In this respect, mutation analysis in CSF can be of added value to other diagnostic parameters such a cytomorphology and clonality analysis. A well-known example of targeted mutation analysis entails MYD88 p.(L265P) detection, which is present in the majority of Bing Neel syndrome and primary central nervous system lymphoma (PCNSL) patients...
December 6, 2017: Hematological Oncology
https://www.readbyqxmd.com/read/29180174/formalin-fixed-paraffin-embedded-sample-conditions-for-deep-next-generation-sequencing
#4
Masayuki Nagahashi, Yoshifumi Shimada, Hiroshi Ichikawa, Satoru Nakagawa, Nobuaki Sato, Koji Kaneko, Keiichi Homma, Takashi Kawasaki, Keisuke Kodama, Stephen Lyle, Kazuaki Takabe, Toshifumi Wakai
INTRODUCTION: Precision medicine is only possible in oncology practice if targetable genes in fragmented DNA, such as DNA from formalin-fixed paraffin-embedded (FFPE) samples, can be sequenced using next generation sequencing (NGS). The aim of this study was to examine the quality and quantity of DNA from FFPE cancerous tissue samples from surgically resected and biopsy specimens. METHODS: DNA was extracted from unstained FFPE tissue sections prepared from surgically resected specimens of breast, colorectal and gastric cancer, and biopsy specimens of breast cancer...
December 2017: Journal of Surgical Research
https://www.readbyqxmd.com/read/29177603/impact-of-multi-gene-mutational-profiling-on-clinical-trial-outcomes-in-metastatic-breast-cancer
#5
Rossanna C Pezo, Tom W Chen, Hal K Berman, Anna M Mulligan, Albiruni A Razak, Lillian L Siu, David W Cescon, Eitan Amir, Christine Elser, David G Warr, Srikala S Sridhar, Celeste Yu, Lisa Wang, Tracy L Stockley, Suzanne Kamel-Reid, Philippe L Bedard
PURPOSE: Next-generation sequencing (NGS) has identified recurrent genomic alterations in metastatic breast cancer (MBC); however, the clinical utility of incorporating routine sequencing to guide treatment decisions in this setting is unclear. We examine the frequency of genomic alterations in MBC patients from academic and community hospitals and correlate with clinical outcomes. METHODS: MBC patients with good performance status were prospectively recruited at the Princess Margaret Cancer Centre (PM) in Canada...
November 24, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29175301/a-straightforward-assay-to-evaluate-dna-integrity-and-optimize-next-generation-sequencing-for-clinical-diagnosis-in-oncology
#6
Fabiana Bettoni, Fernanda Christtanini Koyama, Paola de Avelar Carpinetti, Pedro Alexandre Favoretto Galante, Anamaria Aranha Camargo, Paula Fontes Asprino
Next generation sequencing (NGS) has become an informative tool to guide cancer treatment and conduce a personalized approach in oncology. The biopsy collected for pathologic analysis is usually stored as formalin-fixed paraffin-embedded (FFPE) blocks and then availed for molecular diagnostic, resulting in DNA molecules that are invariably fragmented and chemically modified. In an attempt to improve NGS based diagnostics in oncology we developed a straightforward DNA integrity assessment assay based on qPCR, defining clear parameters to whether NGS sequencing results is accurate or when it should be analyzed with caution...
November 21, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/29161047/mapping-extracellular-matrix-proteins-in-formalin-fixed-paraffin-embedded-tissues-by-maldi-imaging-mass-spectrometry
#7
Peggi M Angel, Susana Comte-Walters, Lauren E Ball, Kacey Talbot, Anand Mehta, Kelvin G M Brockbank, Richard R Drake
Collagens and elastin form the fundamental framework of all tissues and organs and their expression and post-translational processing are tightly regulated in disease and health. Due to their unique structural composition and properties, it is a recognized challenge to access these protein structures within the complex tissue microenvironment to understand how localized changes modulate tissue health. We describe a new workflow using a combination of matrix-assisted laser desorption /ionization imaging mass spectrometry (MALDI IMS) with collagenase and matrix metalloproteinase (MMP) enzymes to access and report on spatial localization of collagen and elastin sequences in formalin-fixed, paraffin-embedded (FFPE) tissues...
November 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29147610/host-immune-response-index-in-gastric-cancer-identified-by-comprehensive-analyses-of-tumor-immunity
#8
Charny Park, Junhun Cho, Jeeyun Lee, So Young Kang, Ji Yeong An, Min Gew Choi, Jun Ho Lee, Tae Sung Sohn, Jae Moon Bae, Sung Kim, Seung Tae Kim, Se Hoon Park, Joon Oh Park, Won Ki Kang, Insuk Sohn, Sin Ho Jung, Myung-Soo Kang, Kyoung-Mee Kim
Tumor infiltrating lymphocytes (TIL) in Epstein-Barr virus (EBV)-associated/microsatellite-unstable (MSI) gastric carcinomas (GC) constitute immune-active principal cellular components of tumor microenvironment and contribute to better prognosis. With the remarkable success of cancer immunotherapies, there is an urgent need for a comprehensive understanding of tumor-immune interactions in patients with GC in the context of host immune response. To identify GC subtype-specific immune response gene set, we tested differentially expressed genes for MSI and EBV+ GC subtypes in randomly selected test set (n = 278) in merged ACRG-SMC microarray and TCGA RNA sequencing data set...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/29145794/analysis-of-bacterial-and-fungal-nucleic-acid-in-canine-sterile-granulomatous-and-pyogranulomatous-dermatitis-and-panniculitis
#9
Fabio B Rosa, Caitlin E Older, Courtney Meason-Smith, Jan S Suchodolski, Sonia Lingsweiler, Joanne E Mansell, Aline Rodrigues Hoffmann
Next generation sequencing (NGS) studies are revealing a diverse microbiota on the skin of dogs. The skin microbiota of canine sterile granulomatous and pyogranulomatous dermatitis (SGPD) has yet to be investigated using NGS techniques. NGS targeting the 16S rRNA and ITS-1 region of bacterial and fungal DNA, respectively, were used to investigate if bacterial and fungal DNA were associated with skin lesions in cases of canine SGPD. The study included 20 formalin-fixed paraffin-embedded (FFPE) skin samples and 12 fresh samples from SGPD-affected dogs, and 10 FFPE and 10 fresh samples from healthy dogs...
January 1, 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/29137436/tumor-biopsy-stratification-based-on-mtor-pathway-activity-and-functional-mutations-in-the-upstream-genes-pik3ca-and-pten
#10
Jean-François Laes, Sebastien Sauvage, Gregori Ghitti
The mechanistic target of the rapamycin (mTOR) pathway is frequently activated in human cancers. Our objective was to evaluate relationships between mTOR-pathway activity and functional mutations in the upstream genes PIK3CA and PTEN in solid-tumor biopsies from a broad selection of cancer types. Formalin-fixed paraffin-embedded (FFPE) tumor samples were analyzed by immunohistochemistry (IHC) and next-generation sequencing (NGS). TOR-pathway activation was identified by expression (by IHC) of the downstream effector p-4E-BP1...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29130105/tumor-molecular-profiling-of-nsclc-patients-using-next-generation-sequencing
#11
Nikolaos Tsoulos, Eirini Papadopoulou, Vasiliki Metaxa-Mariatou, Georgios Tsaousis, Chrisoula Efstathiadou, Georgia Tounta, Aikaterini Scapeti, Eugenia Bourkoula, Pavlos Zarogoulidis, George Pentheroudakis, Stylianos Kakolyris, Ioannis Boukovinas, Pavlos Papakotoulas, Elias Athanasiadis, Theofanis Floros, Anna Koumarianou, Vasileios Barbounis, Anca Dinischiotu, George Nasioulas
Non‑small cell lung cancer (NSCLC) is the most common type of lung cancer and a tumor with a broad spectrum of targeted therapies already available or in clinical trials. Thus, molecular characterization of the tumor using next generation sequencing (NGS) technology, has become a key tool for facilitating treatment decisions and the clinical management of NSCLC patients. The performance of a custom 23 gene multiplex amplification hot spot panel, based on Ion AmpliSeq™ technology, was evaluated for the analysis of tumor DNA extracted from formalin-fixed and paraffin-embedded (FFPE) tissues...
December 2017: Oncology Reports
https://www.readbyqxmd.com/read/29089060/actionable-gene-based-classification-toward-precision-medicine-in-gastric-cancer
#12
Hiroshi Ichikawa, Masayuki Nagahashi, Yoshifumi Shimada, Takaaki Hanyu, Takashi Ishikawa, Hitoshi Kameyama, Takashi Kobayashi, Jun Sakata, Hiroshi Yabusaki, Satoru Nakagawa, Nobuaki Sato, Yuki Hirata, Yuko Kitagawa, Toshiyuki Tanahashi, Kazuhiro Yoshida, Ryota Nakanishi, Eiji Oki, Dana Vuzman, Stephen Lyle, Kazuaki Takabe, Yiwei Ling, Shujiro Okuda, Kohei Akazawa, Toshifumi Wakai
BACKGROUND: Intertumoral heterogeneity represents a significant hurdle to identifying optimized targeted therapies in gastric cancer (GC). To realize precision medicine for GC patients, an actionable gene alteration-based molecular classification that directly associates GCs with targeted therapies is needed. METHODS: A total of 207 Japanese patients with GC were included in this study. Formalin-fixed, paraffin-embedded (FFPE) tumor tissues were obtained from surgical or biopsy specimens and were subjected to DNA extraction...
October 31, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29079036/apela-promotes-tumour-growth-and-cell-migration-in-ovarian-cancer-in-a-p53-dependent-manner
#13
Yuyin Yi, Shu-Huei Tsai, Jung-Chien Cheng, Evan Y Wang, Michael S Anglesio, Dawn R Cochrane, Megan Fuller, Ewan A Gibb, Wei Wei, David G Huntsman, Aly Karsan, Pamela A Hoodless
OBJECTIVE: APELA is a small, secreted peptide that can function as a ligand for the G-protein coupled receptor, Apelin Receptor (APLNR, APJ). APELA plays an essential role in endoderm differentiation and cardiac development during embryogenesis. We investigated whether APELA exerts any functions in cancer progression. METHODS: The Cancer Genome Atlas (TCGA) RNA sequencing datasets, microarray from an OCCC mouse model, and RNA isolated from fresh frozen and FFPE patient tissue were used to assess APELA expression...
October 24, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29073243/rna-seq-transcriptome-analysis-of-formalin-fixed-paraffin-embedded-canine-meningioma
#14
Jennifer K Grenier, Polly A Foureman, Erica A Sloma, Andrew D Miller
Meningiomas are the most commonly reported primary intracranial tumor in dogs and humans and between the two species there are similarities in histology and biologic behavior. Due to these similarities, dogs have been proposed as models for meningioma pathobiology. However, little is known about specific pathways and individual genes that are involved in the development and progression of canine meningioma. In addition, studies are lacking that utilize RNAseq to characterize gene expression in clinical cases of canine meningioma...
2017: PloS One
https://www.readbyqxmd.com/read/29066670/-clinical-application-of-ngs-based-clinical-sequencing
#15
Kazuto Nishio, Kazuko Sakai
Cancer Clinical Sequencing is a method for making the treatment decision for each cancer patient. Implication of the clinical sequencing is rapidly in progress in Japan. In general, the tumor FFPE samples obtained by biopsy or operatory resection are subjected to amplicon sequencing. The process was divided into pre-analysis, analysis, and post-analysis processes. Quality assurance and control are necessary for all process. In addition, the expert members for clinical sequencing team is essential to make clinical sequencing reports based on the NGS analysis...
October 2017: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/29061374/analytical-validation-of-a-next-generation-sequencing-assay-to-monitor-immune-responses-in-solid-tumors
#16
Jeffrey M Conroy, Sarabjot Pabla, Sean T Glenn, Blake Burgher, Mary Nesline, Antonios Papanicolau-Sengos, Jonathan Andreas, Vincent Giamo, Felicia L Lenzo, Fiona C L Hyland, Angela Omilian, Wiam Bshara, Moachun Qin, Ji He, Igor Puzanov, Marc S Ernstoff, Mark Gardner, Lorenzo Galluzzi, Carl Morrison
We have developed a next-generation sequencing assay to quantify biomarkers of the host immune response in formalin-fixed, paraffin-embedded (FFPE) tumor specimens. This assay aims to provide clinicians with a comprehensive characterization of the immunologic tumor microenvironment as a guide for therapeutic decisions on patients with solid tumors. The assay relies on RNA-sequencing (seq) to semiquantitatively measure the levels of 43 transcripts related to anticancer immune responses and 11 transcripts that reflect the relative abundance of tumor-infiltrating lymphocytes, as well as on DNA-seq to estimate mutational burden...
October 20, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29044880/targeted-deep-sequencing-of-effusion-cytology-samples-is-feasible-informs-spatiotemporal-tumor-evolution-and-has-clinical-and-diagnostic-utility
#17
Jonas Leichsenring, Anna-Lena Volckmar, Martina Kirchner, Daniel Kazdal, Mark Kriegsmann, Fabian Stögbauer, Teresa Bockmayr, Frederick Klauschen, Felix J F Herth, Roland Penzel, Arne Warth, Peter Schirmacher, Volker Endris, Albrecht Stenzinger
During the course of disease, many cancer patients eventually present with metastatic disease including peritoneal or pleural spread. In this context, cytology specimens derived from ascites or pleural effusion may help to differentiate malignant from benign conditions and sometimes yield diagnosis of a malignancy. However, even when supported by immunohistochemistry, cytological interpretation can be challenging, especially if tumor cellularity is low. Here, we investigated whether targeted deep sequencing of formalin-fixed and paraffin embedded (FFPE) cytology specimens of cancer patients is feasible, and has diagnostic and clinical impact...
October 16, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29032825/line-1-retrotransposon-mediated-dna-transductions-in-endometriosis-associated-ovarian-cancers
#18
Zhouchunyang Xia, Dawn R Cochrane, Michael S Anglesio, Yi Kan Wang, Tayyebeh Nazeran, Basile Tessier-Cloutier, Melissa K McConechy, Janine Senz, Amy Lum, Ali Bashashati, Sohrab P Shah, David G Huntsman
OBJECTIVE: Endometrioid (ENOC) and clear cell ovarian carcinoma (CCOC) share a common precursor lesion, endometriosis, hence the designation endometriosis associated ovarian cancers (EAOC). Long interspersed nuclear element 1 (LINE-1 or L1), is a family of mobile genetic elements activated in many cancers capable of moving neighboring DNA through 3' transductions. Here we investigated the involvement of specific L1-mediated transductions in EAOCs. METHODS: Through whole genome sequencing, we identified active L1-mediated transductions originating within the TTC28 gene in 34% (10/29) of ENOC and 31% (11/35) of CCOC cases...
October 9, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29024530/fna-smears-of-pancreatic-ductal-adenocarcinoma-are-superior-to-formalin-fixed-paraffin-embedded-tissue-as-a-source-of-dna-comparison-of-targeted-kras-amplification-and-genotyping-in-matched-preresection-and-postresection-samples
#19
Christopher P Hartley, Aparna M Mahajan, Suzanne M Selvaggi, William M Rehrauer
BACKGROUND: The current study was conducted to compare DNA yield, including normalization to nuclear area, DNA amplification functionality, and detection of KRAS mutations between matched fine-needle aspiration (FNA) specimens and pancreatic resections diagnostic of pancreatic ductal adenocarcinoma. METHODS: A retrospective sample of 30 matched single FNA smears and macrodissected formalin-fixed, paraffin-embedded (FFPE) curls (2 5-μm curls) were compared by measuring the following: nuclear area (via digital image analysis), DNA yield (via NanoDrop spectrophotometry and Quantus fluorometry), and polymerase chain reaction threshold cycles for KRAS amplifications...
November 2017: Cancer
https://www.readbyqxmd.com/read/29022941/genome-wide-mapping-of-dnase-i-hypersensitive-sites-in-rare-cell-populations-using-single-cell-dnase-sequencing
#20
James Cooper, Yi Ding, Jiuzhou Song, Keji Zhao
Increased chromatin accessibility is a feature of cell-type-specific cis-regulatory elements; therefore, mapping of DNase I hypersensitive sites (DHSs) enables the detection of active regulatory elements of transcription, including promoters, enhancers, insulators and locus-control regions. Single-cell DNase sequencing (scDNase-seq) is a method of detecting genome-wide DHSs when starting with either single cells or <1,000 cells from primary cell sources. This technique enables genome-wide mapping of hypersensitive sites in a wide range of cell populations that cannot be analyzed using conventional DNase I sequencing because of the requirement for millions of starting cells...
November 2017: Nature Protocols
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