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K R Gedye, M Fremaux, J C Garcia-Ramirez, B D Gartrell
AIM: To describe the Chlamydia psittaci genotypes in samples from native and introduced birds from New Zealand by analysis of the sequence variation of the ompA gene. METHODS: DNA was extracted from samples collected from a non-random sample of birds; either swabs from live asymptomatic birds or birds with clinical signs, or formalin fixed paraffin embedded (FFPE) samples from historical post-mortem cases. The presence of C. psittaci in all samples had been confirmed using a quantitative PCR assay...
February 15, 2018: New Zealand Veterinary Journal
T Gorgani-Firouzjaee, N Kalantrai, S Ghaffari, J Alipour, S Siadati
Echinococcus granulosus is a helminth from the family Taeniidae, which causes cystic echinococcosis (CE) in humans and diverse livestock around the world. The identification of existing genotypes in different regions is a major step towards the prevention and establishment of control programmes for the disease. This study aimed to detect CE genotypes using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the internal transcribed spacer-1 (ITS1) gene and sequencing of the cytochrome c oxidase subunit 1 (Cox1) gene in isolates from the central part of Mazandaran province, northern Iran...
February 15, 2018: Journal of Helminthology
Tracy McMillen, Shauna C Usiak, Liang Hua Chen, Luz Gomez, Peter Ntiamoah, Meera R Hameed, Indre Budvytiene, Niaz Banaei, Mini Kamboj, N Esther Babady
OBJECTIVES In this study, we sought to evaluate the performance of the Xpert MTB/RIF (Cepheid) assay for the detection of Mycobacterium tuberculosis (MTB) complex DNA on fresh and formalin-fixed, paraffin-embedded (FFPE) tissue specimens from oncology patients in an area with a low prevalence of tuberculosis. We also aimed to retrospectively assess the potential impact of Xpert MTB/RIF on the duration of airborne infection isolation (AII). SETTING A 473-bed, tertiary-care cancer center in New York City. DESIGN A total of 203 tissue samples (101 FFPE and 102 fresh) were tested using Xpert MTB/RIF, including 133 pulmonary tissue samples (65...
February 15, 2018: Infection Control and Hospital Epidemiology
Anna Majer, Stephanie A Booth
Brain is a highly heterogeneous organ with numerous layers of specialized cells. Viral infection further adds complexity to downstream analysis because only a subpopulation of the brain is infected. In these instances, molecular changes that occur within infected cells are not truly reflected when whole tissue is used for downstream analysis. Laser capture microdissection (LCM) is a tool that allows for the selection and isolation of cells or regions of interest as determined by microscopic observation. It provides a platform for visually selecting the tissue that truly represents the material one wishes to study, such as viral infected cells...
2018: Methods in Molecular Biology
Aurélie Bruno, Karim Labreche, Maïlys Daniau, Blandine Boisselier, Guillaume Gauchotte, Louis Royer-Perron, Amithys Rahimian, Frédéric Lemoine, Pierre de la Grange, Justine Guégan, Franck Bielle, Marc Polivka, Clovis Adam, David Meyronet, Dominique Figarella-Branger, Chiara Villa, Fabrice Chrétien, Sandrine Eimer, Frédéric Davi, Audrey Rousseau, Caroline Houillier, Carole Soussain, Karima Mokhtari, Khê Hoang-Xuan, Agusti Alentorn
Background: Primary central nervous system lymphoma (PCNSL) represents a particular entity within non-Hodgkin lymphomas and is associated with poor outcome. The present study addresses the potential clinical relevance of chimeric transcripts in PCSNL discovered by using RNA-sequencing (RNA-Seq). Methods: Seventy-two immunocompetent and newly diagnosed PCNSL cases were included in the present study. Among them, six were analyzed by RNA-seq to detect new potential fusion transcripts...
February 8, 2018: Neuro-oncology
Nancy Krieger, Sheida Nabavi, Pamela D Waterman, Ninah S Achacoso, Luana Acton, Stuart J Schnitt, Laurel A Habel
PURPOSE: The purpose of the study was to assess the feasibility of quantifying long-term trends in breast tumor DNA copy number variation (CNV) profiles. METHODS: We evaluated CNV profiles in formalin-fixed paraffin-embedded (FFPE) tumor specimens from 30 randomly selected Kaiser Permanente Northern California health plan women members diagnosed with breast cancer from 1950 to 2010. Assays were conducted for five cases per decade who had available tumor blocks and pathology reports...
February 9, 2018: Cancer Causes & Control: CCC
Kyriaki Papadopoulou, Samuel Murray, Kyriaki Manousou, Ioannis Tikas, Christos Dervenis, Joseph Sgouros, Dimitra Rontogianni, Sotirios Lakis, Mattheos Bobos, Christos Poulios, Stavroula Pervana, Georgios Lazaridis, George Fountzilas, Vassiliki Kotoula
Biliary tract cancer (BTC) represents a heterogeneous disease with dismal outcome. Herein, we examined genotype and angiogenesis features in BTC. We applied genotyping (Sanger, qPCR, 101-gene panel NGS), mRNA relative quantification methods, and β-catenin immunohistochemistry in 84 FFPE BTC (55 gallbladder [GBC], 14 intrahepatic [ICC], 15 extrahepatic [ECC] carcinomas). We identified 541 mutations in 68 (81%) tumors. Top mutated genes were CTNNB1 (36%); PTEN (33%); TP53 (31%); PIK3R1 (29%); PIK3CA (13%); BRCA2 and KRAS (12%); BRCA1 (11%)...
2018: American Journal of Cancer Research
Ashley Di Meo, Rola Saleeb, Samantha J Wala, Heba W Khella, Qiang Ding, Haiyan Zhai, Kalra Krishan, Adriana Krizova, Manal Gabril, Andrew Evans, Fadi Brimo, Maria D Pasic, Antonio Finelli, Eleftherios P Diamandis, George M Yousef
Renal cell carcinoma (RCC) constitutes an array of morphologically and genetically distinct tumors the most prevalent of which are clear cell, papillary, and chromophobe RCC. Accurate distinction between the typically benign-behaving renal oncocytoma and RCC subtypes is a frequent challenge for pathologists. This is critical for clinical decision making. Subtypes also have different survival outcomes and responses to therapy. We extracted RNA from ninety formalin-fixed paraffin-embedded (FFPE) tissues (27 clear cell, 29 papillary, 19 chromophobe, 4 unclassified RCC and 11 oncocytomas)...
January 5, 2018: Oncotarget
Souptik Barua, Penny Fang, Amrish Sharma, Junya Fujimoto, Ignacio Wistuba, Arvind U K Rao, Steven H Lin
OBJECTIVES: To determine the prognostic significance of spatial proximity of lung cancer cells and specific immune cells in the tumor microenvironment. MATERIALS AND METHODS: We probed formalin-fixed, paraffin-embedded (FFPE) tissue microarrays using a novel tyramide signal amplification multiplexing technique labelling CD8, CD4, Foxp3, and CD68+ cells. Each multiplex stained immunohistochemistry slide was digitally processed by Vectra INFORMS software, and an X- and Y-coordinate assigned to each labeled cell type...
February 3, 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
Shiho Asaka, Akihiko Yoshizawa, Rie Nakata, Tatsuya Negishi, Hiroshi Yamamoto, Takayuki Shiina, Shohei Shigeto, Kazuyuki Matsuda, Yukihiro Kobayashi, Takayuki Honda
The detection of epidermal growth factor receptor ( EGFR ) mutations is necessary for the selection of suitable patients with non-small cell lung cancer (NSCLC) for treatment with EGFR tyrosine kinase inhibitors. Cytology specimens are known to be suitable for EGFR mutation detection, although tissue specimens should be prioritized; however, there are limited studies that examine the utility of bronchial lavage fluid (BLF) in mutation detection. The purpose of the present study was to investigate the utility of BLF specimens for the detection of EGFR mutations using a conventional quantitative EGFR polymerase chain reaction (PCR) assay...
February 2018: Oncology Letters
Yue-Ya Liang, Jia-Cheng Huang, Rui-Xue Tang, Wen-Jie Chen, Peng Chen, Wei-Luan Cen, Ke Shi, Li Gao, Xiang Gao, An-Gui Liu, Xiao-Tong Peng, Gang Chen, Su-Ning Huang, Ye-Ying Fang, Yong-Yao Gu
BACKGROUND: To examine the clinical value of miR-198-5p in lung squamous cell carcinoma (LUSC). METHODS: Gene Expression Omnibus (GEO) microarray datasets were used to explore the miR-198-5p expression and its diagnostic value in LUSC. Real-time reverse transcription quantitative polymerase chain reaction was used to evaluate the expression of miR-198-5p in 23 formalin-fixed, paraffin-embedded (FFPE) LUSC tissues and corresponding non-cancerous tissues. The correlation between miR-198-5p expression and clinic pathological features was assessed...
February 2, 2018: World Journal of Surgical Oncology
Jonathan Serrano, Matija Snuderl
In this chapter, we describe the use of Illumina® Infinium® HD Assay in conjunction with Illumina's EPIC Methylation 8-sample array platform to obtain glioblastoma molecular profiles. The procedure spans four days, and can be performed by a single laboratory technician. Starting with as little as 250 ng of DNA input, this method allows the flexibility to begin with DNA derived from either formalin-fixed, paraffin-embedded (FFPE) or fresh tissue and is compatible with an Illumina iScan or HiScan system.
2018: Methods in Molecular Biology
Yuji Eso, Norimitsu Uza, Hiroko Yamagishi, Kazuaki Imada, Yuto Kimura, Toshihiko Masui, Yuzo Kodama, Hiroshi Seno
RATIONALE: It is often challenging to discriminate between intrahepatic cholangiocarcinoma (ICC) and metastatic liver tumors, especially when the hepatic tumor is small and of a mass-forming type. PATIENT CONCERNS: We report a 69-year-old woman presented at our hospital with a small solid tumor in the head of the pancreas that was previously discovered during a medical checkup. DIAGNOSES: The patient was diagnosed with synchronous pancreatic cancer and ICC...
December 2017: Medicine (Baltimore)
Magdalena Bogdanovska Todorovska, Gordana Petrushevska, Vesna Janevska, Liljana Spasevska, Slavica Kostadinova Kunovska
Accurate assessment of human epidermal growth factor receptor 2 (HER-2) is crucial in selecting patients for targeted therapy. Commonly used methods for HER-2 testing are immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Here we presented the implementation, optimization and standardization of two FISH protocols using breast cancer samples and assessed the impact of pre-analytical and analytical factors on HER-2 testing. Formalin fixed paraffin embedded (FFPE) tissue samples from 70 breast cancer patients were tested for HER-2 using PathVysion™ HER-2 DNA Probe Kit and two different paraffin pretreatment kits, Vysis/Abbott Paraffin Pretreatment Reagent Kit (40 samples) and DAKO Histology FISH Accessory Kit (30 samples)...
January 30, 2018: Bosnian Journal of Basic Medical Sciences
Pauline Robbe, Niko Popitsch, Samantha J L Knight, Pavlos Antoniou, Jennifer Becq, Miao He, Alexander Kanapin, Anastasia Samsonova, Dimitrios V Vavoulis, Mark T Ross, Zoya Kingsbury, Maite Cabes, Sara D C Ramos, Suzanne Page, Helene Dreau, Kate Ridout, Louise J Jones, Alice Tuff-Lacey, Shirley Henderson, Joanne Mason, Francesca M Buffa, Clare Verrill, David Maldonado-Perez, Ioannis Roxanis, Elena Collantes, Lisa Browning, Sunanda Dhar, Stephen Damato, Susan Davies, Mark Caulfield, David R Bentley, Jenny C Taylor, Clare Turnbull, Anna Schuh
PurposeFresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS.MethodsWe conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols...
February 1, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Vlastimil Kulda, Martin Svaton, Petr Mukensnabl, Kristyna Hrda, Pavel Dvorak, Zbynek Houdek, Katerina Houfkova, Radana Vrzakova, Vaclav Babuska, Milos Pesek, Martin Pesta
Attributing to their pathophysiological role and stability in biological samples, microRNAs (miRNAs) have the potential to become valuable predictive markers for non-small cell lung cancer (NSCLC). Samples of biopsy tissue constitute suitable material for miRNA profiling with the aim of predicting the effect of palliative chemotherapy. The present study group included 81 patients (74 males, 7 females, all smokers or former smokers) with the squamous cell carcinoma (SCC) histological subtype of NSCLC at a late stage (3B or 4)...
January 2018: Oncology Letters
Xiaolong Liang, Jian Sun, Huanwen Wu, Yufeng Luo, Lili Wang, Junliang Lu, Zhiwen Zhang, Junchao Guo, Zhiyong Liang, Tonghua Liu
BACKGROUND: Programmed death ligand 1 (PD-L1) has shown potential as a therapeutic target in numerous solid tumors. Its prognostic significance has also been established in pancreatic ductal adenocarcinoma (PDAC). The present study aimed to explore PD-L1 expression in PDAC cases in a large Chinese cohort using an in vitro diagnostic (IVD) assay to provide further insight into the potential value of programmed cell death protein 1 (PD-1) as a therapeutic target. METHODS: Three hundred seventy-three PDAC patients were retrospectively recruited in this study...
January 17, 2018: Diagnostic Pathology
B Hirsch, V Endris, S Lassmann, W Weichert, N Pfarr, P Schirmacher, V Kovaleva, M Werner, I Bonzheim, F Fend, J Sperveslage, K Kaulich, A Zacher, G Reifenberger, K Köhrer, S Stepanow, S Lerke, T Mayr, D E Aust, G Baretton, S Weidner, A Jung, T Kirchner, M L Hansmann, L Burbat, E von der Wall, M Dietel, M Hummel
The simultaneous detection of multiple somatic mutations in the context of molecular diagnostics of cancer is frequently performed by means of amplicon-based targeted next-generation sequencing (NGS). However, only few studies are available comparing multicenter testing of different NGS platforms and gene panels. Therefore, seven partner sites of the German Cancer Consortium (DKTK) performed a multicenter interlaboratory trial for targeted NGS using the same formalin-fixed, paraffin-embedded (FFPE) specimen of molecularly pre-characterized tumors (n = 15; each n = 5 cases of Breast, Lung, and Colon carcinoma) and a colorectal cancer cell line DNA dilution series...
January 27, 2018: Virchows Archiv: An International Journal of Pathology
Ali Basi, Flora Khaledi, Mohammad Hadi Karbalaie Niya, Hamid Rezvani, Nasser Rakhshani
Introduction: Lung cancer is the fifth leading tumor in Iran, and while its incidence remains relatively low, it has been increasing steadily. Targeted therapies have brought new hope to patients with non small cell lung cancer (NSCLC). The epidermal growth factor receptor (EGFR) gene is the prototype member of the type I receptor tyrosine kinase (TK) family and plays a pivotal role in cell proliferation and differentiation. Studies from Asian countries have revealed a higher frequency of EGFR mutations than in the West...
January 27, 2018: Asian Pacific Journal of Cancer Prevention: APJCP
Duncan M Chadly, Jennifer Best, Cong Ran, Małgorzata Bruska, Witold Woźniak, Bartosz Kempisty, Mark Schwartz, Bonnie LaFleur, B J Kerns, John A Kessler, Akihiro J Matsuoka
Due to the extreme inaccessibility of fetal human inner ear tissue, defining of the microRNAs (miRNAs) that regulate development of the inner ear has relied on animal tissue. In the present study, we performed the first miRNA sequencing of otic precursors in human specimens. Using HTG miRNA Whole Transcriptome assays, we examined miRNA expression in the cochleovestibular ganglion (CVG), neural crest (NC), and otic vesicle (OV) from paraffin embedded (FFPE) human specimens in the Carnegie developmental stages 13-15...
2018: PloS One
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