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https://www.readbyqxmd.com/read/29238890/real-time-detection-of-braf-v600e-mutation-from-archival-hairy-cell-leukemia-ffpe-tissue-by-nanopore-sequencing
#1
Davide Vacca, Valeria Cancila, Alessandro Gulino, Giosuè Lo Bosco, Beatrice Belmonte, Arianna Di Napoli, Ada Maria Florena, Claudio Tripodo, Walter Arancio
The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixation protocols. In order to investigate the suitability of MinION sequencing on formalin-fixed paraffin-embedded samples, the presence and frequency of BRAF c.1799T > A mutation was investigated in two archival tissue specimens of Hairy cell leukemia and Hairy cell leukemia Variant...
December 13, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/29235112/heat-shock-protein-70-and-tumor-infiltrating-nk-cells-as-prognostic-indicators-for-patients-with-squamous-cell-carcinoma-of-the-head-and-neck-after-radiochemotherapy-a-multicentre-retrospective-study-of-the-german-cancer-consortium-radiation-oncology-group
#2
Stefan Stangl, Nikoletta Tontcheva, Wolfgang Sievert, Maxim Shevtsov, Minli Niu, Thomas E Schmid, Steffi Pigorsch, Stephanie E Combs, Bernhard Haller, Panagiotis Balermpas, Franz Rödel, Claus Rödel, Emmanouil Fokas, Mechthild Krause, Annett Linge, Fabian Lohhaus, Michael Baumann, Inge Tinhofer, Volker Budach, Martin Stuschke, Anca-Ligia Grosu, Amir Abdollahi, Jürgen Debus, Claus Belka, Cornelius Maihöfer, David Mönnich, Daniel Zips, Gabriele Multhoff
Tumor cells frequently overexpress heat shock protein 70 (Hsp70) and present it on their cell surface, where it can be recognized by pre-activated NK cells. In this retrospective study the expression of Hsp70 was determined in relation to tumor-infiltrating CD56+ NK cells in formalin-fixed paraffin embedded (FFPE) tumor specimens of patients with SCCHN (N=145) as potential indicators for survival and disease recurrence. All patients received radical surgery and postoperative cisplatinum-based radiochemotherapy (RCT)...
December 13, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29228314/demodifying-rna-for-transcriptomic-analyses-of-archival-formalin-fixed-paraffin-embedded-samples
#3
Leah C Wehmas, Charles E Wood, Remi Gagne, Andrew Williams, Carole Yauk, Mark M Gosink, Deidre Dalmas, Ruixin Hao, Raegan O'Lone, Susan Hester
Archival formalin-fixed paraffin-embedded (FFPE) tissue samples offer a vast but largely untapped resource for genomic research. The primary technical issues limiting use of FFPE samples are RNA yield and quality. In this study, we evaluated methods to demodify RNA highly fragmented and crosslinked by formalin fixation. Primary endpoints were RNA recovery, RNA-sequencing quality metrics, and transcriptional responses to a reference chemical (phenobarbital, PB). Frozen mouse liver samples from control and PB groups (n = 6/group) were divided and preserved for 3 months as follows: frozen (FR); 70% ethanol (OH); 10% buffered formalin for 18 hours followed by ethanol (18F); or 10% buffered formalin (3F)...
December 7, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29221197/rank-expression-in-ebv-positive-nasopharyngeal-carcinoma-metastasis-a-ready-to-treat-target
#4
Carlo Resteghini, Salvatore Alfieri, Pasquale Quattrone, Francesca Dominoni, Giovanna Garzone, Ester Orlandi, Laura Locati, Cristiana Bergamini, Donata Galbiati, Nicola Alessandro Iacovelli, Carlo Fallai, Lisa Licitra, Paolo Bossi
Epstein Barr Virus (EBV) related Nasopharyngeal Carcinoma (NPC), is an highly chemo- and radiosensitive endemic malignancy in southeast Asia. More than one third of locally advanced cases relapse after curative treatment, especially because of bone, liver and lung metastases. Lymphocyte sub-populations favour EBV-associated carcinogenesis and tumour progression and several strategies aim to reverse this phenomenon. Receptor activator of NF-kB (RANK) and its Ligand (RANKL), key regulator of bone metabolisms, are expressed in several malignancies and tumor-infiltrating Tregs...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29215764/an-evaluation-of-the-challenges-to-developing-tumour-brca1-and-brca2-testing-methodologies-for-clinical-practice
#5
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/29214365/profiling-differential-microrna-expression-between-in-situ-infiltrative-and-lympho-vascular-space-invasive-breast-cancer-a-pilot-study
#6
Patsy S Soon, Pamela J Provan, Edward Kim, Nirmala Pathmanathan, Dinny Graham, Christine L Clarke, Rosemary L Balleine
Ductal carcinoma in situ (DCIS), invasive breast cancer (IBC) and lympho-vascular invasion (LVI) represent distinct stages in breast cancer progression with different clinical implications. Altered microRNA (miRNA) expression may play a role in mediating the progression of DCIS to IBC and LVI. The aim of this pilot study was to investigate whether differential miRNA expression could play a role in breast cancer progression. Cancer cells from DCIS, IBC and LVI were microdissected from formalin fixed paraffin embedded (FFPE) tissue of five breast cancer samples...
December 6, 2017: Clinical & Experimental Metastasis
https://www.readbyqxmd.com/read/29212158/rnascope-in-situ-hybridization-confirms-mrna-integrity-in-formalin-fixed-paraffin-embedded-cancer-tissue-samples
#7
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
#8
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/29209123/prediction-of-early-stage-hepatocellular-carcinoma-using-oncoscan-chromosomal-copy-number-aberration-data
#9
Ming-Chin Yu, Chao-Wei Lee, Yun-Shien Lee, Jang-Hau Lian, Chia-Lung Tsai, Yi-Ping Liu, Chun-Hsing Wu, Chi-Neu Tsai
AIM: To identify chromosomal copy number aberrations (CNAs) in early-stage hepatocellular carcinoma (HCC) and analyze whether they are correlated with patient prognosis. METHODS: One hundred and twenty patients with early-stage HCC were enrolled in our study, with the collection of formalin fixed, paraffin-embedded (FFPE) specimens and clinicopathological data. Tumor areas were marked by certified pathologists on a hematoxylin and eosin-stained slide, and cancer and adjacent non-cancerous tissues underwent extraction of DNA, which was analyzed with the Affymetrix OncoScan platform to assess CNAs and loss of heterozygosity (LOH)...
November 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29207829/evaluation-of-tumour-associated-macrophages-and-angiogenesis-in-ameloblastoma
#10
Akinyele O Adisa, Samuel E Udeabor, Anna Orlowska, Robert A Sader, Shahram Ghanaati
Introduction: Ameloblastoma is a locally invasive odontogenic neoplasm that has a high recurrence rate. The invasion of adjacent tissue is supported by angiogenesis stimulated by Tumour-Associated Macrophages (TAMs). TAMs are macrophages modified in the milieu of the tumour microenvironment and have very weak or no ability to present antigens. Thus, there is collaboration between the tumour and the tumour microenvironment to maintain tumour enlargement. TAMs exist as the classically activated M1 macrophages that possess antitumour activity and the otherwise activated M2 macrophages that support tumour invasion and metastasis...
September 2017: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/29198817/whole-specimen-intraoperative-frozen-section-analysis-experience-with-1082-basal-cell-carcinomas
#11
Muhammed A Kedilioglu, Paul G Bos, Kim De Jong, Niels A Noordzij, Robby E Kibbelaar, Oren Lapid, Chantal M Mouës
BACKGROUND: Basal cell carcinomas (BCCs) excised leaving positive tumour margins, are at a higher risk of recurrence. Accordingly, complete tumour removal with preservation of healthy tissue, aiming for low recurrence rates, is the main goal in treating BCCs. OBJECTIVE: The present study aimed to identify the reliability of the Whole Specimen Intraoperative Frozen Section Analysis (WIFSA) technique by comparing intraoperative WIFSA and postoperative Formalin-Fixed Paraffin-Embedded section analysis (FFPE) results in 1082 basal cell carcinomas and by assessing the recurrence rates during a follow-up period up to 10 years...
November 23, 2017: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29191199/paraffin-immunofluorescence-for-detection-of-immune-complexes-in-renal-biopsies-an-efficient-salvage-technique-for-diagnosis-of-glomerulonephritis-in-dogs
#12
Akira Yabuki, Mariko Sawa, Moeko Kohyama, Takeshi Hamamoto, Osamu Yamato
BACKGROUND: Renal biopsy is an essential tool for the diagnosis of proteinuric kidney diseases in dogs, and evaluation of immune complexes (IC) by immunofluorescence (IF) of frozen sections (IF-F) is required for the diagnosis of IC-mediated glomerulonephritis (ICGN). However, the use of frozen sections from renal biopsies can have limitations. The aim of this study was to develop a reliable IF method using formalin-fixed and paraffin-embedded (FFPE) sections to detect ICs in dog ICGN...
December 1, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/29187510/ercc1-as-predictive-biomarker-to-platinum-based-chemotherapy-in-adrenocortical-carcinomas
#13
Valeria Laufs, Barbara Altieri, Silviu Sbiera, Stefan Kircher, Sonja Steinhauer, Felix Beuschlein, Marcus Quinkler, Holger S Willenberg, Andreas Rosenwald, Martin Fassnacht, Cristina L Ronchi
OBJECTIVE: Platinum-based chemotherapy (PBC) is the most effective cytotoxic treatment for advanced adrenocortical carcinoma (ACC). Excision repair cross complementing group 1 (ERCC1) plays a critical role in the repair of platinum-induced DNA damage. Two studies investigating the role of ERCC1 immunostaining as a predictive marker for the response to PBC in ACC had reported conflicting results. Both studies used the ERCC1-antibody clone 8F1 that later turned out to be not specific. The aim of this study was to evaluate the predictive role of ERCC1 with the new specific antibody in a larger series of ACC...
November 29, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/29186353/prevalence-and-clinical-association-of-gene-mutations-through-multiplex-mutation-testing-in-patients-with-nsclc-results-from-the-etop-lungscape-project
#14
K M Kerr, U Dafni, K Schulze, E Thunnissen, L Bubendorf, H Hager, S Finn, W Biernat, L Vliegen, J H Losa, A Marchetti, R Cheney, A Warth, E-J Speel, F Blackhall, K Monkhorst, E Jantus Lewintre, V Tischler, C Clark, J Bertran-Alamillo, P Meldgaard, K Gately, A Wrona, P Vandenberghe, E Felip, G De Luca, S Savic, T Muley, E F Smit, A-M C Dingemans, L Priest, P Baas, C Camps, W Weder, V Polydoropoulou, T R Geiger, R Kammler, T Sumiyoshi, M A Molina, D S Shames, R A Stahel, S Peters
Background: Reported prevalence of driver gene mutations in non-small cell lung cancer (NSCLC) is highly variable and clinical correlations are emerging. Using NSCLC biomaterial and clinical data from the ETOP Lungscape iBiobank, we explore the epidemiology of mutations and association to clinicopathological features and patient outcome (relapse-free survival, time-to-relapse, overall survival). Methods: Clinically-annotated, resected stage I-III NSCLC FFPE tissue was assessed for gene mutation using a microfluidics-based multiplex PCR platform...
November 23, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29180174/formalin-fixed-paraffin-embedded-sample-conditions-for-deep-next-generation-sequencing
#15
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/29178840/prevalence-of-oncogenic-human-papillomavirus-genotypes-in-patients-diagnosed-with-anogenital-malignancies-in-botswana
#16
Patricia S Rantshabeng, Sikhulile Moyo, Natasha O Moraka, Andrew Ndlovu, Iain J MacLeod, Simani Gaseitsiwe, Ishmael Kasvosve
BACKGROUND: Human papillomavirus (HPV) associated malignancies are the leading cause of cancer death in Botswana. We sought to determine causative HPV types in patients with anogenital malignancies in Botswana to inform vaccine strategy. METHODS: We used formalin-fixed and paraffin-embedded (FFPE) tissue blocks from patients diagnosed with anal, penile and vulvar squamous cell carcinomas between the years, 2014 and 2016. Presence of HPV 16, 18, or other high-risk (HR) types was detected using Abbott m2000 real-time PCR platform...
November 25, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29177668/immunohistochemical-and-flow-cytometric-analysis-of-intracellular-and-membrane-bound-hsp70-as-a-putative-biomarker-of-glioblastoma-multiforme-using-the-cmhsp70-1-monoclonal-antibody
#17
Stefan Stangl, Gemma A Foulds, Helena Fellinger, Geoffrey J Pilkington, A Graham Pockley, Gabriele Multhoff
The major stress-inducible 70 kDa heat shock (stress) protein 70 (Hsp70) is frequently overexpressed in highly aggressive tumor cells and thus might serve as a tumor-specific biomarker of aggressive disease. We have previously shown that, in contrast to normal cells, tumor cells present Hsp70 on their plasma membrane. In order to elucidate the role of intracellular and membrane-bound Hsp70 as a potential tumor biomarker in glioblastoma multiforme, herein, we describe protocols for the staining of cytosolic Hsp70 in tumor formalin fixed paraffin-embedded (FFPE) sections using immunohistochemistry, and for plasma membrane-bound Hsp70 by multi-parametric flow cytometry using the cmHsp70...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29177603/impact-of-multi-gene-mutational-profiling-on-clinical-trial-outcomes-in-metastatic-breast-cancer
#18
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
#19
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/29169801/evaluating-melanocytic-lesions-with-single-nucleotide-polymorphism-snp-chromosomal-microarray
#20
Amin A Hedayat, Konstantinos Linos, Hou-Sung Jung, Laura J Tafe, Shaofeng Yan, Robert E LeBlanc, Joel A Lefferts
Histopathology is the gold standard for diagnosing melanocytic lesions; however, distinguishing benign versus malignant is not always clear histologically. Single nucleotide polymorphism (SNP) microarray analysis may help in making a definitive diagnosis. Here, we share our experience with the Oncoscan FFPE Assay and demonstrate its diagnostic utility in the context of ambiguous melanocytic lesions. Eleven archival melanocytic lesions, including three benign nevi, four melanomas, three BAP1-deficient Spitzoid nevi and one nevoid melanoma were selected for validation...
November 20, 2017: Experimental and Molecular Pathology
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