keyword
MENU ▼
Read by QxMD icon Read
search

FFPE

keyword
https://www.readbyqxmd.com/read/27913155/early-molecular-stratification-of-high-risk-primary-biliary-cholangitis
#1
Claire Hardie, Kile Green, Laura Jopson, Ben Millar, Barbara Innes, Sarah Pagan, Dina Tiniakos, Jessica Dyson, Muzlifah Haniffa, Venetia Bigley, David E Jones, John Brain, Lucy J Walker
High-risk primary biliary cholangitis (PBC), defined by inadequate response at one year to Ursodeoxycholic acid (UDCA), is associated with disease progression and liver transplantation. Stratifying high-risk patients early would facilitate improved approaches to care. Using long-term follow-up data to define risk at presentation, 6 high-risk PBC patients and 8 low-risk patients were identified from biopsy, transplant and biochemical archival records. Formalin-fixed paraffin-embedded (FFPE) liver biopsies taken at presentation were graded (Scheuer and Nakanuma scoring) and gene expression analysed using the NanoString® nCounter PanCancer Immunity 770-gene panel...
November 21, 2016: EBioMedicine
https://www.readbyqxmd.com/read/27911273/robust-detection-of-immune-transcripts-in-ffpe-samples-using-targeted-rna-sequencing
#2
Benjamin E Paluch, Sean T Glenn, Jeffrey M Conroy, Antonios Papanicolau-Sengos, Wiam Bshara, Angela R Omilian, Elizabeth Brese, Mary Nesline, Blake Burgher, Jonathan Andreas, Kunle Odunsi, Kevin Eng, Ji He, Maochun Qin, Mark Gardner, Lorenzo Galluzzi, Carl D Morrison
Current criteria for identifying cancer patients suitable for immunotherapy with immune checkpoint blockers (ICBs) are subjective and prone to misinterpretation, as they mainly rely on the visual assessment of CD274 (best known as PD-L1) expression levels by immunohistochemistry (IHC). To address this issue, we developed a RNA sequencing (RNAseq)-based approach that specifically measures the abundance of immune transcripts in formalin-fixed paraffin embedded (FFPE) specimens. Besides exhibiting superior sensitivity as compared to whole transcriptome RNAseq, our assay requires little starting material, implying that it is compatible with RNA degradation normally caused by formalin...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27910019/fluorescence-in-situ-hybridization-on-tissue-sections
#3
Alvin S T Lim, Tse Hui Lim
Formalin-fixed paraffin-embedded (FFPE) tissues are typically the specimens available for FISH analysis of solid tissues, particularly of tumor specimens. Occasionally, tissue cores constructed as tissue microarrays from several patients are presented for simultaneous evaluation. FFPE sections can also be prepared from cell blocks derived from cell suspensions. The interphase fluorescence in situ hybridization assay employs specific nucleic acid sequences (probes) that target complementary sequences of interest to detect gains or losses of genes/gene loci or a fusion gene within the tissue...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27899965/increased-expression-of-long-non-coding-rna-xist-predicts-favorable-prognosis-of-cervical-squamous-cell-carcinoma-subsequent-to-definitive-chemoradiation-therapy
#4
Reiko Kobayashi, Ryu Miyagawa, Hideomi Yamashita, Teppei Morikawa, Kae Okuma, Masashi Fukayama, Kuni Ohtomo, Keiichi Nakagawa
The present retrospective study aimed to examine the association between the expression of long non-protein-coding RNAs (lncRNAs) and clinical prognosis in the pretreatment formalin-fixed, paraffin-embedded (FFPE) tissue samples of cervical squamous cell carcinoma patients that underwent platinum-based chemoradiation therapy. Between 2001 and 2013, 49 consecutive patients with squamous cell cervical carcinoma were selected for the present study (median follow-up period, 44.1 months). The patients possessed an International Federation of Gynecology and Obstetrics stage of IB1/IIA1 (with pelvic lymph node metastasis), IB2 or IIA2-IVA, and had been treated with definitive chemoradiation therapy...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27896758/phenotyping-multiple-subsets-of-immune-cells-in-situ-in-ffpe-tissue-sections-an-overview-of-methodologies
#5
James R Mansfield
The recent clinical success of new cancer immunotherapy agents and methods is driving the need to understand the role of immune cells in solid tissues, especially tumors. Immune cell phenotyping via flow cytometry, while a cornerstone of immunology, is not spatially resolved and cannot analyze immune cell subsets in situ in clinical biopsy sections or to determine their interrelationships. To address this problem, a number of methodologies have been developed in attempts to phenotype immune and other cells in images acquired from tissue sections and to assess their organization in the tumor and its microenvironment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895798/exploring-the-impact-of-egfr-t790m-neighboring-snps-on-arms-based-t790m-mutation-assay
#6
Sanpeng Xu, Yaqi Duan, Liping Lou, Fengjuan Tang, Juan Shou, Guoping Wang
The present study aimed to explore the influence of T790M neighboring single nucleotide polymorphism (SNP) on the sensitivity of amplification refractory mutation system (ARMS)-based T790M mutation assay. Three ARMS-quantitative polymerase chain reaction (qPCR) systems (system 1 had a forward ARMS primer without rs1050171, system 2 included a forward ARMS primer with rs1050171 and system 3 contained the above two forward ARMS primers) were used to detect the T790M mutation in two series plasmid samples and genomic DNA (gDNA) of the cell line H1975...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27895580/increased-levels-of-mirna-146a-in-serum-and-histologic-samples-of-patients-with-uveal-melanoma
#7
Andrea Russo, Rosario Caltabiano, Antonio Longo, Teresio Avitabile, Livio M Franco, Vincenza Bonfiglio, Lidia Puzzo, Michele Reibaldi
Purpose: To analyze MiRs expression in serum of UM patients, respect to healthy donors, and to compare this data with MiRs expressed in formalin-fixed, paraffin-embedded UM samples. Methods: Expression profile of 754 miRNAs was performed in serum of patients with uveal melanoma who underwent primary enucleation. The level of miRNAs increased in serum was individually analyzed on FFPE UM samples and compared to choroidal melanocytes from unaffected eyes. Results: Fourteen patients with uveal melanoma were included in the study...
2016: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/27890680/the-putative-role-of-maldi-msi-in-the-study-of-membranous-nephropathy
#8
Andrew Smith, Vincenzo L'Imperio, Elena Ajello, Franco Ferrario, Niccolò Mosele, Martina Stella, Manuel Galli, Clizia Chinello, Federico Pieruzzi, Goce Spasovski, Fabio Pagni, Fulvio Magni
Membranous Nephropathy (MN) is an immunocomplex mediated renal disease that represents the leading cause of nephrotic syndrome in adults and is one of the most frequent glomerulopathies worldwide. This glomerular disease can manifest as primary (idiopathic) or secondary and this distinction is crucial when choosing the most appropriate management of patients. In secondary cases, the best strategy consists in treating the underlying disease whereas in primary forms, the possible identification of confirmatory markers of the idiopathic etiology underlining the process is requested by clinicians...
November 23, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27889928/elucidating-the-role-of-cyclooxygenase-2-in-the-pathogenesis-of-oral-lichen-planus-an-immunohistochemical-study-with-supportive-histochemical-analysis
#9
Pratyush Singh, Jasleen Grover, Aditi Amit Byatnal, Vasudeva Guddattu, Raghu Radhakrishnan, Monica Charlotte Solomon
OBJECTIVE: Oral lichen planus (OLP) is a chronic, inflammatory disorder that affects the oral mucous membrane. During an inflammatory response, several chemokines and cytokines are released by the cells of the immune system. Activation of MMPs, along with mast cell-derived chymase and tryptase, degrades the basement membrane structural proteins, resulting in basement membrane breaks. AIM: To investigate the association between the COX-2 expressions, presence of intact or degranulating mast cells within the connective tissue and the extent of basement membrane discontinuity in OLP cases...
November 7, 2016: Journal of Oral Pathology & Medicine
https://www.readbyqxmd.com/read/27879019/screening-for-alk-abnormalities-in-central-nervous-system-metastases-of-non-small-cell-lung-cancer-alk-abnormalities-in-cns-metastases-of-nsclc
#10
Marcin Nicoś, Bożena Jarosz, Paweł Krawczyk, Kamila Wojas-Krawczyk, Tomasz Kucharczyk, Marek Sawicki, Juliusz Pankowski, Tomasz Trojanowski, Janusz Milanowski
Anaplastic lymphoma kinase (ALK) gene rearrangement was reported in 3-7% of primary non-small-cell lung cancer (NSCLC) and its presence is commonly associated with adenocarcinoma (AD) type and non-smoking history. ALK tyrosine kinase inhibitors (TKIs) such as crizotinib, alectinib and ceritinib showed efficiency in patients with primary NSCLC harboring ALK gene rearrangement. Moreover, response to ALK TKIs was observed in central nervous system (CNS) metastatic lesions of NSCLC. However, there are no reports concerning the frequency of ALK rearrangement in CNS metastases...
November 23, 2016: Brain Pathology
https://www.readbyqxmd.com/read/27873160/prognostic-significance-of-cd44-and-orthopedia-homeobox-protein-otp-expression-in-pulmonary-carcinoid-tumours
#11
George Papaxoinis, Daisuke Nonaka, Ciara O'Brien, Benjamin Sanderson, Piotr Krysiak, Wasat Mansoor
CD44 and orthopedia homeobox protein (OTP) expressions have shown to be predictive of overall survival in pulmonary carcinoid (PC) tumours. The scope of the present study was to validate their role in PC patients and investigate potential application in clinical practice. Data was collected from patients presenting to a tertiary cancer centre diagnosed with PC between 2003 and 2015. Diagnosis was confirmed by central pathology review. Formalin-fixed paraffin-embedded (FFPE) tissue samples collected at diagnosis were scored using immunohistochemistry (H score) for standard CD44 and nuclear and cytoplasmic OTP protein expression...
November 21, 2016: Endocrine Pathology
https://www.readbyqxmd.com/read/27869447/-testing-of-mutations-in-brca1-and-brca2-genes-in-tumor-tissues-possibilities-and-limitations
#12
Hana Vošmiková, Aleš Ryška, Kateřina Sieglová, Jan Laco
Development of targeted cancer therapy is accompanied by a search for markers allowing prediction of response to the particular treatment. Recently, the interest is focused, among other neoplasms, also on the therapy of ovarian cancer using new inhibitors of poly (ADP-ribose) polymerase (PARP) proteins, nuclear enzymes involved in the repair of single-stranded DNA breaks. The greatest benefit from the administration of PARP inhibitors have patients with a deleterious or potentially deleterious germ-line or somatic mutation of BRCA1 or BRCA2, two genes responsible for repair of double stranded DNA breaks...
2016: Ceskoslovenská Patologie
https://www.readbyqxmd.com/read/27863259/validation-of-a-gene-expression-test-for-mesothelioma-prognosis-in-formalin-fixed-paraffin-embedded-tissues
#13
Assunta De Rienzo, Robert W Cook, Jeff Wilkinson, Corinne E Gustafson, Waqas Amin, Clare E Johnson, Kristen M Oelschlager, Derek J Maetzold, John F Stone, Michael D Feldman, Michael J Becich, Beow Y Yeap, William G Richards, Raphael Bueno
A molecular test performed using fresh-frozen tissue was proposed for use in the prognosis of patients with pleural mesothelioma. The accuracy of the test and its properties was assessed under Clinical Laboratory Improvement Amendments-approved guidelines using FFPE tissue from an independent multicenter patient cohort. Concordance studies were performed using matched frozen and FFPE mesothelioma samples. The prognostic value of the test was evaluated in an independent validation cohort of 73 mesothelioma patients who underwent surgical resection...
November 15, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27858973/detection-and-genotyping-of-human-papillomaviruses-from-archival-formalin-fixed-tissue-samples
#14
Koenraad Van Doorslaer, Zigui Chen, Alison A McBride
Pathology departments routinely process and store formalin-fixed, paraffin-embedded (FFPE) tissue samples for clinical diagnosis. These collections often contain decades' worth of samples and represent a treasure trove of specimens that can be analyzed for retrospective epidemiological studies, diagnostics, and pathogen discovery. Accurate amplification and sequencing of DNA from these samples is critical for the usability of these FFPE samples. Here we present a collection of protocols that describe extraction of DNA from FFPE tissues, PCR amplification of human papillomavirus DNA, and subsequent genotyping of the infecting virus...
November 18, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27857940/protocol-for-biomarker-ratio-imaging-microscopy-with-specific-application-to-ductal-carcinoma-in-situ-of-the-breast
#15
Andrea J Clark, Howard R Petty
This protocol describes the methods and steps involved in performing biomarker ratio imaging microscopy (BRIM) using formalin fixed paraffin-embedded (FFPE) samples of human breast tissue. The technique is based on the acquisition of two fluorescence images of the same microscopic field using two biomarkers and immunohistochemical tools. The biomarkers are selected such that one biomarker correlates with breast cancer aggressiveness while the second biomarker anti-correlates with aggressiveness. When the former image is divided by the latter image, a computed ratio image is formed that reflects the aggressiveness of tumor cells while increasing contrast and eliminating path-length and other artifacts from the image...
2016: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/27855847/p15-expression-differentiates-nevus-from-melanoma
#16
Laura A Taylor, Conor O'Day, Tzvete Dentchev, Kyle Hood, Emily Y Chu, Todd W Ridky, John T Seykora
Most melanomas are driven by BRAF(V600E)-activating mutations, while nevi harboring the same mutations have growth arrest. Although decreased p16 expression has been associated with melanoma formation, in recent work, p15 represented a primary effector of oncogene-induced senescence in nevomelanocytes that was diminished in melanomas. This study determined whether decreased p15 levels represent a general biomarker for the transition from nevus to melanoma. We performed p15 and p16 IHC analyses on a random series of nevi and melanomas...
December 2016: American Journal of Pathology
https://www.readbyqxmd.com/read/27852699/analysis-of-ror1-protein-expression-in-human-cancer-and-normal-tissues
#17
Ashwini Balakrishnan, Tracy Goodpaster, Julie Randolph-Habecker, Benjamin G Hoffstrom, Florencia G Jalikis, Lisa K Koch, Carolina Berger, Paula L Kosasih, Anusha Rajan, Daniel Sommermeyer, Peggy Porter, Stanley R Riddell
PURPOSE: This study examines cell-surface ROR1 expression in human tumors and normal tissues. ROR1 is considered a promising target for cancer therapy due to putative tumor-specific expression and multiple groups are developing antibodies and/or chimeric antigen receptor-modified T cells to target ROR1. On-target, off-tumor toxicity is a challenge for most non-mutated tumor antigens, however prior studies suggest that ROR1 is absent on most normal tissues. EXPERIMENTAL DESIGN: Our studies show that published antibodies lack sensitivity to detect endogenous levels of cell-surface ROR1 by immunohistochemistry (IHC) in FFPE tissues...
November 16, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27846907/copy-number-analysis-by-low-coverage-whole-genome-sequencing-using-ultra-low-input-dna-from-formalin-fixed-paraffin-embedded-tumor-tissue
#18
Tanjina Kader, David L Goode, Stephen Q Wong, Jacquie Connaughton, Simone M Rowley, Lisa Devereux, David Byrne, Stephen B Fox, Gisela Mir Arnau, Richard W Tothill, Ian G Campbell, Kylie L Gorringe
Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays...
November 15, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27846280/development-and-application-of-a-microfluidics-based-panel-in-the-basal-luminal-transcriptional-characterization-of-archival-bladder-cancers
#19
Doris Kim, YounJeong Choi, James Ireland, Oded Foreman, Rachel N Tam, Rajesh Patel, Erica B Schleifman, Maipelo Motlhabi, Dorothy French, Cheryl V Wong, Eric Peters, Luciana Molinero, Rajiv Raja, Lukas C Amler, Garret M Hampton, Mark R Lackner, Omar Kabbarah
In the age of personalized medicine stratifying tumors into molecularly defined subtypes associated with distinctive clinical behaviors and predictable responses to therapies holds tremendous value. Towards this end, we developed a custom microfluidics-based bladder cancer gene expression panel for characterization of archival clinical samples. In silico analysis indicated that the content of our panel was capable of accurately segregating bladder cancers from several public datasets into the clinically relevant basal and luminal subtypes...
2016: PloS One
https://www.readbyqxmd.com/read/27837339/her2-mrna-transcript-quantitation-in-breast-cancer
#20
K Meehan, B Clynick, B Mirzai, P Maslen, J M Harvey, W N Erber
PURPOSE: The human epidermal growth factor receptor 2 (HER2) status in breast cancer is important for prognostic prediction and the determination of optimal treatment. Current methods rely on protein expression, as determined by immunohistochemistry (IHC), as well as gene amplification as determined by in situ hybridisation (ISH). We explored whether quantitative droplet digital PCR (ddPCR) can be used for the detection and absolute quantitation of HER2 mRNA. METHODS: Digital droplet PCR (ddPCR) was performed for HER2 mRNA on 178 formalin-fixed paraffin-embedded (FFPE) breast cancer specimens...
November 11, 2016: Clinical & Translational Oncology
keyword
keyword
72224
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"