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https://www.readbyqxmd.com/read/28822769/somatic-mutation-analysis-in-melanoma-using-targeted-next-generation-sequencing
#1
Allen P Miraflor, Francine B de Abreu, Jason D Peterson, Scott A Turner, Christopher I Amos, Gregory J Tsongalis, Shaofeng Yan
Advanced stage malignant melanoma often responds poorly to therapy with low survival rates. New therapeutic approaches are based upon a growing understanding of the underlying molecular abnormalities. We demonstrate the feasibility of a next generation sequencing (NGS) assay, which targets hotspots in 50 cancer genes, to assess genotypes that may influence therapeutic selection and response. DNA was extracted from formalin fixed paraffin embedded (FFPE) melanoma specimens to create multiplexed libraries which were sequenced...
August 16, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28818508/the-role-of-the-il-8-signaling-pathway-in-the-infiltration-of-granulocytes-into-the-livers-of-patients-with-alcoholic-hepatitis
#2
S W French, A S Mendoza, N Afifiyan, B Tillman, E Vitocruz, B A French
BACKGROUND AND AIM: IL-8 (C-X-L motif chemokine ligase 8) and CXCR2 (C-X-C-motif chemokine receptor 2) are up regulated in alcoholic hepatitis (AH) liver biopsies. One of the consequences is the attraction and chemotactic neutrophilic infiltrate seen at the AH stage of alcoholic liver disease. MATERIALS AND METHODS: Human formalin-fixed, paraffin-embedded (FFPE) liver biopsies from patients who have AH were studied by (2.1) RNA sequencing, (2.2) PCR and (2.3) semi quantitation of specific proteins in biopsy sections using immunohistochemical measurements of antibody fluorescent intensity with morphometric technology...
August 14, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28812131/dna-degrades-during-storage-in-formalin-fixed-and-paraffin-embedded-tissue-blocks
#3
Alice Guyard, Alice Boyez, Anaïs Pujals, Cyrielle Robe, Jeanne Tran Van Nhieu, Yves Allory, Julien Moroch, Odette Georges, Jean-Christophe Fournet, Elie-Serge Zafrani, Karen Leroy
Formalin-fixed paraffin-embedded (FFPE) tissue blocks are widely used to identify clinically actionable molecular alterations or perform retrospective molecular studies. Our goal was to quantify degradation of DNA occurring during mid to long-term storage of samples in usual conditions. We selected 46 FFPE samples of surgically resected carcinomas of lung, colon, and urothelial tract, of which DNA had been previously extracted. We performed a second DNA extraction on the same blocks under identical conditions after a median period of storage of 5...
August 15, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28810295/-utility-and-evaluation-of-immunohistochemical-detection-of-braf-v600e-mutation-in-melanoma
#4
J J Lyu, Y Y Kong, X Cai, X X Shen, Y W Lu, M Ren
Objective: To evaluate the sensitivity, specificity and clinical value of anti-BRAF V600E antibody (clone VE1) in detection of the BRAF V600E mutant in formalin-fixed and paraffin-embedded (FFPE) melanoma specimens by immunohistochemical (IHC) methods. Methods: A total of 50 melanoma samples collected between 2008 and 2016 from 40 patients were analyzed for BRAF mutation (exon 15) by DNA sequencing using FFPE. These tissues were immunostained with VE1 antibody, and the results were analyzed and compared with those by DNA sequencing...
August 8, 2017: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
https://www.readbyqxmd.com/read/28783138/flow-cytometric-sorting-coupled-with-exon-capture-sequencing-identifies-somatic-mutations-in-archival-lymphoma-tissues
#5
Nenggang Jiang, Christopher Chen, Qiang Gong, Kristen Shields, Yuping Li, YuanYuan Chen, Joo Song, Timothy W McKeithan, Wing C Chan
The enormous number of archived formalin-fixed paraffin-embedded (FFPE) tissues available are a valuable resource of material for research. However, the use of such tissues poses many challenges, among which is the difficulty of isolating different cell populations within the tissue. In this study, we used tissue from two types of non-Hodgkin lymphoma as a model to demonstrate a method we have established and optimized to separate FFPE samples into distinct tumor and nonmalignant populations. Using FFPE reactive tonsil sections, various approaches for antigen retrieval and labeling, and the effectiveness of flow cytometric sorting were tested...
August 7, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28767674/versatile-ion-s5xl-sequencer-for-targeted-next-generation-sequencing-of-solid-tumors-in-a-clinical-laboratory
#6
Meenakshi Mehrotra, Dzifa Yawa Duose, Rajesh R Singh, Bedia A Barkoh, Jawad Manekia, Michael A Harmon, Keyur P Patel, Mark J Routbort, L Jeffrey Medeiros, Ignacio I Wistuba, Rajyalakshmi Luthra
BACKGROUND: Next generation sequencing based tumor tissue genotyping involves complex workflow and a relatively longer turnaround time. Semiconductor based next generation platforms varied from low throughput Ion PGM to high throughput Ion Proton and Ion S5XL sequencer. In this study, we compared Ion PGM and Ion Proton, with a new Ion S5XL NGS system for workflow scalability, analytical sensitivity and specificity, turnaround time and sequencing performance in a clinical laboratory. METHODS: Eighteen solid tumor samples positive for various mutations as detected previously by Ion PGM and Ion Proton were selected for study...
2017: PloS One
https://www.readbyqxmd.com/read/28763012/performance-of-a-rt-pcr-assay-in-comparison-to-fish-and-immunohistochemistry-for-the-detection-of-alk-in-non-small-cell-lung-cancer
#7
David R Hout, Brock L Schweitzer, Kasey Lawrence, Stephan W Morris, Tracy Tucker, Rosetta Mazzola, Rachel Skelton, Frank McMahon, John Handshoe, Mary Lesperance, Aly Karsan, David L Saltman
Patients with lung cancers harboring an activating anaplastic lymphoma kinase (ALK) rearrangement respond favorably to ALK inhibitor therapy. Fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) are validated and widely used screening tests for ALK rearrangements but both methods have limitations. The ALK RGQ RT-PCR Kit (RT-PCR) is a single tube quantitative real-time PCR assay for high throughput and automated interpretation of ALK expression. In this study, we performed a direct comparison of formalin-fixed paraffin-embedded (FFPE) lung cancer specimens using all three ALK detection methods...
August 1, 2017: Cancers
https://www.readbyqxmd.com/read/28749631/human-papillomavirus-hpv-genotype-distribution-in-patients-with-recurrent-respiratory-papillomatosis-rrp-in-iran
#8
Negin Sadat Eftekhaar, Mohammad Hadi Karbalaie Niya, Farzad Izadi, Sedigheh Teaghinezhad-S, Hossein Keyvani
Background: Currently, recurrent respiratory papillomatosis (RRP), common laryngeal warts in the upper airway systems of children and adults are on the increase. Human papillomaviruses (HPVs) are suspected as causative agents. This study concerned HPV incidence and genotype distribution in Iranian RRP patients. Methods: Specimens were collected from RRP patients referred to hospitals affiliated with Iran University of Medical Sciences, Tehran, Iran, from Dec 2014 to Feb 2016 in a cross sectional study. After DNA extraction with an QIAamp® DNA FFPE Tissue Kit, conventional PCR was performed and products were sequenced...
July 27, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28748477/chromogenic-in-situ-hybridization-methods-for-microrna-biomarker-monitoring-of-drug-safety-and-efficacy
#9
Barbara R Gould, Tina Damgaard, Boye Schnack Nielsen
Disease research and treatment development have turned to the impact and utility of microRNA. The dynamic and highly specific expression of these molecular regulators can be used to predict and monitor disease progression as well as therapeutic treatment efficacy and safety, thus aiding decisions in patient care. In situ hybridization (ISH) of biopsy material has become a routine clinical pathology procedure for monitoring gene structure, expression, and sample characterization. For ribonucleic acid (RNA), determining cell source and level of expression of these biomarkers gives insight into the cellular function and physiopathology...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28742856/fit-for-genomic-and-proteomic-purposes-sampling-the-fitness-of-nucleic-acid-and-protein-derivatives-from-formalin-fixed-paraffin-embedded-tissue
#10
Anna Yakovleva, Jordan L Plieskatt, Sarah Jensen, Razan Humeida, Jonathan Lang, Guangzhao Li, Paige Bracci, Sylvia Silver, Jeffrey Michael Bethony
The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered "unfit" for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules...
2017: PloS One
https://www.readbyqxmd.com/read/28735303/acid-fast-bacterium-detection-and-identification-from-paraffin-embedded-tissues-using-a-pcr-pyrosequencing-method
#11
Jian R Bao, Richard B Clark, Ronald N Master, Kileen L Shier, Lynn L Eklund
AIMS: Acid-fast bacterium (AFB) identification from formalin-fixed paraffin-embedded (FFPE) tissues is challenging and may not be readily available to the clinical laboratory. A method to detect and identify AFB from FFPE tissues using PCR and pyrosequencing (PCR-Seq) was developed and evaluated. METHODS: The method was validated using spiked cell-clotted paraffin blocks before use with patients' specimens. DNA was extracted from tissue sections, and a 16S rRNA gene fragment was amplified and a signature sequence was produced on a PyroMark ID system...
July 22, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28734863/significant-linkage-evidence-for-interstitial-cystitis-painful-bladder-syndrome-on-chromosome-3
#12
Kristina Allen-Brady, Kerry Rowe, Melissa Cessna, Sara Lenherr, Peggy Norton
PURPOSE: Interstitial cystitis/painful bladder syndrome (IC/PBS) is a chronic pelvic pain condition with unknown etiology. We hypothesized that related IC/PBS cases were more likely to have a genetic etiology. The purpose of this study was to perform a genetic linkage analysis. MATERIALS AND METHODS: IC/PBS cases were identified using diagnostic codes linked to a population-based genealogy resource (Utah Population Database) and electronic medical records. For this analysis, 13 high-risk pedigrees (defined as having a statistical excess number of IC/PBS cases among descendants compared to matched hospital population rates) were used...
July 19, 2017: Journal of Urology
https://www.readbyqxmd.com/read/28732214/crispr-cas9-technology-based-xenograft-tumors-as-candidate-reference-materials-for-multiple-eml4-alk-rearrangements-testing
#13
Rongxue Peng, Rui Zhang, Guigao Lin, Xin Yang, Ziyang Li, Kuo Zhang, Jiawei Zhang, Jinming Li
The echinoderm microtubule-associated protein-like 4 and anaplastic lymphoma kinase (ALK) receptor tyrosine kinase (EML4-ALK) rearrangement is an important biomarker that plays a pivotal role in therapeutic decision making for non-small-cell lung cancer (NSCLC) patients. Ensuring accuracy and reproducibility of EML4-ALK testing by fluorescence in situ hybridization, immunohistochemistry, RT-PCR, and next-generation sequencing requires reliable reference materials for monitoring assay sensitivity and specificity...
July 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28722212/active-human-papillomavirus-involvement-in-barrett-s-dysplasia-and-oesophageal-adenocarcinoma-is-characterized-by-wild-type-p53-and-aberrations-of-the-retinoblastoma-protein-pathway
#14
Shanmugarajah Rajendra, Tao Yang, Wei Xuan, Prateek Sharma, Darren Pavey, Cheong Soon Lee, Son Le, Josephine Collins, Bin Wang
We have previously demonstrated that transcriptionally active high-risk HPV (hr-HPV) is strongly incriminated in Barrett's dysplasia (BD) and oesophageal adenocarcinoma (OAC) using mainly fresh frozen tissue. This study aimed to identify biomarkers of active HPV infection in Barrett's metaplasia, (BM)/BD/OAC by immunohistochemical staining (IHC) of formalin-fixed paraffin embedded (FFPE) tissue for aberrations of p53 and the retinoblastoma (pRb) pathway, which are targets for the viral oncoproteins, E6/E7, respectively...
July 19, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28692984/a-study-of-cell-free-dna-fragmentation-pattern-and-its-application-in-dna-sample-type-classification
#15
Shifu Chen, Ming Liu, Xiaoni Zhang, Renwen Long, Yixing Wang, Yue Han, Shiwei Zhang, Mingyan Xu, Jia Gu
Plasma cell-free DNA (cfDNA) has certain fragmentation patterns, which can bring non-random base content curves of the sequencing data's beginning cycles. We studied the patterns and found that we could determine whether a sample is cfDNA or not by just looking into the first 10 cycles of its base content curves. We analysed 3189 FastQ files, including 1442 cfDNA, 1234 genomic DNA, 507 FFPE tumour DNA and 6 urinary cfDNA. By deep analysing these data, we find the patterns are stable enough to distinguish cfDNA from other kinds of DNA samples...
July 4, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28672021/the-clinical-burden-of-human-cystic-echinococcosis-in-palestine-2010-2015
#16
Amer Al-Jawabreh, Suheir Ereqat, Kamal Dumaidi, Abdelmajeed Nasereddin, Hanan Al-Jawabreh, Kifaya Azmi, Nahed Al-Laham, Moath Nairat, Adriano Casulli, Husni Maqboul, Ziad Abdeen
BACKGROUND: Cystic echinococcosis (CE) is classified by the WHO as a neglected disease inflicting economic losses on the health systems of many countries worldwide. The aim of this case-series study was to investigate the burden of human CE in Palestine during the period between 2010 and 2015. METHODOLOGY/PRINCIPAL FINDINGS: Records of surgically confirmed CE patients from 13 public and private hospitals in the West Bank and Gaza Strip were reviewed. Patients' cysts were collected from surgical wards and formalin-fixed paraffin-embedded (FFPE) blocks were collected from histopathology departments...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28671728/clonality-analysis-of-synchronous-gastroesophageal-junction-carcinoma-and-distal-gastric-cancer-by-whole-exome-sequencing
#17
Xiaofang Xing, Shuqin Jia, Jianmin Wu, Qin Feng, Bin Dong, Bo Li, Yongning Jia, Fei Shan, Ying'ai Li, Yan Zhang, Ying Hu, Xiaodong Wang, Xiangtao Liu, Shiwei Yu, Lianhai Zhang, Zhaode Bu, Aiwen Wu, Ziyu Li, Jiafu Ji
Gastroesophageal junction (GEJ) carcinoma and distal gastric cancer (GC) have distinct epidemiology and clinical features and their relationship is uncertain. Synchronous multiple gastric cancers located mostly at proximal and distal sites provide rare specimens for investigating the comprehensive genomic relationships among these cancers in the context of identical genetic circumstances. Formalin-fixed, paraffin-embedded (FFPE) samples from 12 patients with synchronous GEJ carcinoma and distal GC were collected in this study...
July 3, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28663030/early-experience-with-formalin-fixed-paraffin-embedded-ffpe-based-commercial-clinical-genomic-profiling-of-gliomas-robust-and-informative-with-caveats
#18
Masoud Movassaghi, Maryam Shabihkhani, Seyed A Hojat, Ryan R Williams, Lawrance K Chung, Kyuseok Im, Gregory M Lucey, Bowen Wei, Sergey Mareninov, Michael W Wang, Denise W Ng, Randy S Tashjian, Shino Magaki, Mari Perez-Rosendahl, Isaac Yang, Negar Khanlou, Harry V Vinters, Linda M Liau, Phioanh L Nghiemphu, Albert Lai, Timothy F Cloughesy, William H Yong
BACKGROUND: Commercial targeted genomic profiling with next generation sequencing using formalin-fixed paraffin embedded (FFPE) tissue has recently entered into clinical use for diagnosis and for the guiding of therapy. However, there is limited independent data regarding the accuracy or robustness of commercial genomic profiling in gliomas. METHODS: As part of patient care, FFPE samples of gliomas from 71 patients were submitted for targeted genomic profiling to one commonly used commercial vendor, Foundation Medicine...
June 27, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28642587/systematic-comparison-of-two-whole-genome-amplification-methods-for-targeted-next-generation-sequencing-using-frozen-and-ffpe-normal-and-cancer-tissues
#19
Pedro Mendez, Li Tai Fang, David M Jablons, Il-Jin Kim
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28627450/impact-of-fixation-artifacts-and-threshold-selection-on-high-resolution-melting-analysis-for-kras-mutation-screening
#20
Wendy Pérez-Báez, Ethel A Garcia-Latorre, Hector Aquiles Maldonado-Martinez, Iris Coronado-Martinez, Leonardo Flores-Garcia, Lucía Taja-Chayeb
INTRODUCTION: Treatment in the metastatic colorectal cancer has expanded with monoclonal antibodies targeting Epidermal Growth Factor Receptor, but is restricted to patients with a wild-type (WT) KRAS mutational status. The most sensitive assays for KRAS mutation detection in formalin-fixed paraffin embedded (FFPE) tissues are based on Real-time PCR. Among them, high resolution melting analysis (HRMA), is a simple, fast, highly sensitive, specific and cost-effective method, proposed as adjunct for KRAS mutation detection...
June 13, 2017: Molecular and Cellular Probes
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