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https://www.readbyqxmd.com/read/28335433/evaluation-and-adaptation-of-a-laboratory-based-cdna-library-preparation-protocol-for-retrospective-sequencing-of-archived-micrornas-from-up-to-35-year-old-clinical-ffpe-specimens
#1
Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert Greenlee, Deborah Multerer, Stacey Honda, Yihe Daida, Heather Spencer Feigelson, Andrew Glass, Fergus J Couch, Thomas Rohan, Iddo Z Ben-Dov
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28334446/molecular-glycopathology-by-capillary-electrophoresis-analysis-of-the-n-glycome-of-formalin-fixed-paraffin-embedded-mouse-tissue-samples
#2
Boglarka Donczo, Mate Szarka, Jozsef Tovari, Gyorgyi Ostoros, Eszter Csanky, Andras Guttman
Capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection was used to analyze endoglycosidase released and fluorophore-labeled N-glycans from formalin-fixed paraffin-embedded (FFPE) mouse tissue samples of lung, brain, heart, spleen, liver, kidney and intestine. The FFPE samples were first deparaffinized followed by solubilization and glycoprotein retrieval. PNGase F mediated release of the N-linked oligosaccharides was followed by labeling with aminopyrene trisulfonate. After CE-LIF glycoprofiling of the FFPE mouse tissues, the N-glycan pool of the lung specimen was subject to further investigation by exoglycosidase array based carbohydrate sequencing...
March 23, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28330468/tumor-burden-monitoring-using-cell-free-tumor-dna-could-be-limited-by-tumor-heterogeneity-in-advanced-breast-cancer-and-should-be-evaluated-together-with-radiographic-imaging
#3
José Angel García-Saenz, Patricia Ayllón, Marion Laig, Daniel Acosta-Eyzaguirre, Marta García-Esquinas, Myriam Montes, Julián Sanz, Miguel Barquín, Fernando Moreno, Vanesa Garcia-Barberan, Eduardo Díaz-Rubio, Trinidad Caldes, Atocha Romero
BACKGROUND: Accurate measurement of tumor burden in breast cancer disease is essential to improve the clinical management of patients. In this study, we evaluate whether the fluctuations in the fraction of PIK3CA mutant allele correlates with tumor response according to RECIST criteria and tumor markers quantification. METHODS: Eighty six plasma samples were analyzed by digital PCR using Rare Mutation Assays for E542K, E545K and H1047R. Mutant cfDNA and tumor markers CA15-3 and CEA were compared with radiographic imaging...
March 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28323122/exome-analysis-of-the-evolutionary-path-of-hepatocellular-adenoma-carcinoma-transition-vascular-invasion-and-brain-dissemination
#4
Sílvia Vilarinho, Zeynep Erson-Omay, Kisha Mitchell-Richards, Charles Cha, Carol Nelson-Williams, Akdes Serin Harmancı, Katsuhito Yasuno, Murat Günel, Tamar H Taddei
Hepatocellular adenoma (HCA) is a rare benign liver tumor, predominantly seen in young women. Its major complications are malignant transformation, spontaneous hemorrhage, and rupture. We describe a case of a young female with no underlying liver disease who presented with acute abdominal pain and was found to have a 17 cm heterogeneous mass in the left lobe of the liver. She underwent left hepatectomy and pathology revealed a 14 cm moderately differentiated hepatocellular carcinoma (HCC) arising in a shell of a HCA...
March 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28317811/performance-of-the-xpert-mtb-rif-assay-in-the-diagnosis-of-tuberculosis-in-formalin-fixed-paraffin-embedded-tissues
#5
Pascal Polepole, Mwila Kabwe, Mpanga Kasonde, John Tembo, Aaron Shibemba, Justin O'Grady, Nathan Kapata, Alimuddin Zumla, Matthew Bates
OBJECTIVE/BACKGROUND: Extrapulmonary tuberculosis (EPTB), which accounts for 10%-40% of the global burden of TB, with the highest incidence in Sub-Saharan Africa, is strongly associated with human immunodeficiency virus infection. Diagnosing EPTB is challenging, and recently, there has been a concerted effort to evaluate the latest molecular diagnostics for diagnosing TB in a range of specimen types. The Xpert MTB/RIF assay (Cepheid, Sunnyvale, CA, USA) is one such technology, which simultaneously detects Mycobacterium tuberculosis and rifampicin resistance...
January 2017: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28315738/pulmonary-sarcomatoid-carcinomas-commonly-harbor-either-potentially-targetable-genomic-alterations-or-high-tumor-mutational-burden-as-observed-by-comprehensive-genomic-profiling
#6
Alexa B Schrock, Shuyu D Li, Garrett M Frampton, James Suh, Eduardo Braun, Ranee Mehra, Steven Buck, Jose A Bufill, Nir Peled, Nagla Abdel Karim, Cynthia Hsieh, Manuel Doria, James Knost, Rong Chen, Sai-Hong Ignatius Ou, Jeffrey S Ross, Philip J Stephens, Paul Fishkin, Vincent A Miller, Siraj M Ali, Balazs Halmos, Jane J Liu
BACKGROUND: Pulmonary sarcomatoid carcinoma (PSC) is a high-grade non-small cell lung carcinoma (NSCLC) characterized by poor prognosis and resistance to chemotherapy. Development of targeted therapeutic strategies for PSC has been hampered due to limited and inconsistent molecular characterization. METHODS: Hybrid-capture based comprehensive genomic profiling (CGP) was performed on DNA from 15,867 FFPE NSCLCs including 125 PSCs (0.8%). Tumor mutational burden (TMB) was calculated from 1...
March 15, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28315641/development-of-quantitative-real-time-pcr-assays-for-postmortem-detection-of-mycobacterium-spp-common-in-zebrafish-danio-rerio-research-colonies
#7
Danielle M Meritet, Donna M Mulrooney, Michael L Kent, Christiane V Löhr
Mycobacterium spp. infections are common in zebrafish kept in research facilities. These comorbidities can substantially modulate the responses of these fish to external and internal stimuli. Therefore, diagnostic tests to detect Mycobacterium spp. infections in zebrafish colonies prove essential. Here, we outline the development of quantitative simplex real-time PCR assays to detect the 3 Mycobacterium species most commonly identified in laboratory zebrafish. The assays targeted the heatshock protein 65 gene of M...
March 1, 2017: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/28315246/system-wide-profiling-of-protein-amino-termini-from-formalin-fixed-paraffin-embedded-tissue-specimens-for-the-identification-of-novel-substrates
#8
Zon W Lai, Oliver Schilling
Clinical tissues are used for histopathological diagnosis of many diseases including immunostaining and morphology subtyping as well as in molecular research such as for the analyses of DNA, RNA, and proteins. Formalin fixation and paraffin embedment (FFPE) of tissue specimens is routinely used for preserving clinical tissues for long-term storage, allowing histopathological diagnosis of many diseases. As such, FFPE tissues currently represent the most comprehensive collection of all clinical specimens, allowing great source of material for research opportunity, possibly due to the concern of protein integrity from antigen retrieval from fixation process...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28314930/non-reproducible-sequence-artifacts-in-ffpe-tissue-an-experience-report
#9
Richard Ofner, Cathrin Ritter, Selma Ugurel, Lorenzo Cerroni, Mathias Stiller, Thomas Bogenrieder, Flavio Solca, David Schrama, Jürgen C Becker
BACKGROUND: Recent advances in sequencing technologies supported the development of molecularly targeted therapy in cancer patients. Thus, genomic analyses are becoming a routine part in clinical practice and accurate detection of actionable mutations is essential to assist diagnosis and therapy choice. However, this is often challenging due to major problems associated with DNA from formalin-fixed paraffin-embedded tissue which is usually the primary source for genetic testing. OBJECTIVES: Here we want to share our experience regarding major problems associated with FFPE DNA used for PCR-based sequencing as illustrated by the mutational analysis of ERBB4 in melanoma...
March 17, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28301023/optimizing-fixation-protocols-to-improve-molecular-analysis-from-ffpe-tissues
#10
Bruna Jalfim Maraschin, Viviane Palmeira da Silva, Leigha Rock, Huichen Sun, Fernanda Visioli, Pantelis Varvaki Rados, Miriam P Rosin
Most Departments of Pathology around the world have a considerable archive of formalin-fixed paraffin-embedded (FFPE) tissue suitable for molecular assessment. This article points out the potential DNA damage that may occur if basic steps are not followed during processing and storage of these samples. Furthermore, it hopes to establish parameters to optimize quality and quantity of DNA extracted from FFPE tissues.
January 2017: Brazilian Dental Journal
https://www.readbyqxmd.com/read/28291392/new-molecular-assay-for-the-proliferation-signature-in-mantle-cell-lymphoma-applicable-to-formalin-fixed-paraffin-embedded-biopsies
#11
David W Scott, Pau Abrisqueta, George W Wright, Graham W Slack, Anja Mottok, Diego Villa, Pedro Jares, Hilka Rauert-Wunderlich, Cristina Royo, Guillem Clot, Magda Pinyol, Merrill Boyle, Fong Chun Chan, Rita M Braziel, Wing C Chan, Dennis D Weisenburger, James R Cook, Timothy C Greiner, Kai Fu, German Ott, Jan Delabie, Erlend B Smeland, Harald Holte, Elaine S Jaffe, Christian Steidl, Joseph M Connors, Randy D Gascoyne, Andreas Rosenwald, Louis M Staudt, Elias Campo, Lisa M Rimsza
Purpose Mantle cell lymphoma is an aggressive B-cell neoplasm that displays heterogeneous outcomes after treatment. In 2003, the Lymphoma/Leukemia Molecular Profiling Project described a powerful biomarker-the proliferation signature-using gene expression in fresh frozen material. Herein, we describe the training and validation of a new assay that measures the proliferation signature in RNA derived from routinely available formalin-fixed paraffin-embedded (FFPE) biopsies. Methods Forty-seven FFPE biopsies were used to train an assay on the NanoString platform, using microarray gene expression data of matched fresh frozen biopsies as a gold standard...
March 14, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28274670/detection-of-copy-number-variations-in-melanocytic-lesions-utilising-array-based-comparative-genomic-hybridisation
#12
Nima Mesbah Ardakani, Carla Thomas, Cleo Robinson, Kym Mina, Nathan Tobias Harvey, Benhur Amanuel, Benjamin Andrew Wood
Distinction between melanocytic naevi and melanoma occasionally poses a diagnostic challenge in ambiguous cases showing overlapping histological features. Melanomas are characterised by the presence of multiple genomic copy number variants (CNVs), while this is not a feature of naevi. We assessed the feasibility and utility of array-based comparative genomic hybridisation (aCGH) to assess CNVs in melanocytic lesions. DNA was extracted from formalin fixed, paraffin embedded (FFPE) sections of unambiguous naevi (n=19) and melanomas (n=19)...
March 5, 2017: Pathology
https://www.readbyqxmd.com/read/28274512/practical-use-and-utility-of-fluorescence-in-situ-hybridization-in-the-pathological-diagnosis-of-soft-tissue-and-bone-tumors
#13
Shintaro Sugita, Tadashi Hasegawa
During routine pathological examination, fluorescence in situ hybridization (FISH) plays a significant role in the genetic analysis of samples. FISH can detect genetic abnormalities such as chromosomal translocations, gene amplifications, and deletions in formalin-fixed, paraffin-embedded (FFPE) specimens. Due to its practical advantages, FISH is already used in many pathology laboratories. It is especially useful for the diagnosis of translocation-related sarcomas (TRSs), which comprise about 25% of soft tissue sarcomas...
March 5, 2017: Journal of Orthopaedic Science: Official Journal of the Japanese Orthopaedic Association
https://www.readbyqxmd.com/read/28274481/no-detection-of-varicella-zoster-virus-in-temporal-arteries-of-patients-with-giant-cell-arteritis
#14
Francesco Muratore, Stefania Croci, Ione Tamagnini, Alessandro Zerbini, Salvatore Bellafiore, Lucia Belloni, Luigi Boiardi, Alessandra Bisagni, Nicolò Pipitone, Maria Parmeggiani, Alberto Cavazza, Carlo Salvarani
OBJECTIVE: Data on the presence of varicella-zoster virus (VZV) in temporal arteries of patients with giant cell arteritis (GCA) are controversial. We analyzed VZV infection in temporal arteries from Italian patients with temporal artery biopsy (TAB)-positive GCA, TAB-negative GCA, and controls. METHODS: A total of 79 formalin-fixed, paraffin-embedded (FFPE) TABs performed between 2009 and 2012 at a single institution from 34 TAB-positive GCA patients, 15 TAB-negative GCA patients, and 30 controls were retrieved...
February 10, 2017: Seminars in Arthritis and Rheumatism
https://www.readbyqxmd.com/read/28271569/n-glycan-matrix-assisted-laser-desorption-ionization-mass-spectrometry-imaging-protocol-for-formalin-fixed-paraffin-embedded-tissues
#15
Matthew T Briggs, Yin Ying Ho, Gurjeet Kaur, Martin K Oehler, Arun V Everest-Dass, Nicolle H Packer, Peter Hoffmann
RATIONALE: Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) of the proteome of a tissue has been an established technique for the past decade. In the last few years, MALDI-MSI of the N-glycome has emerged as a novel MALDI-MSI technique. To assess the accuracy and clinical significance of the N-linked glycan spatial distribution, we have developed a method that utilises MALDI-MSI followed by liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS) in order to assign glycan structures to the differentiating MALDI-MSI glycan masses released from the tissue glycoproteins...
March 8, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28269754/evaluation-of-pik3ca-mutations-as-a-biomarker-in-chinese-breast-carcinomas-from-western-china
#16
Jingliang Cheng, Shangyi Fu, Chunli Wei, Mousumi Tania, Asaduzzaman Khan, Saber Imani, Baixu Zhou, Hanchun Chen, Xiuli Xiao, Jingbo Wu, Junjiang Fu
BACKGROUND: PIK3CA gene encodes the p110 α catalytic subunit of the oncoprotein phosphatidylinositol 3-kinase (PI3 K) which regulates many biological processes such as cell proliferation, differentiation, migration and survival through the activation of various signaling pathways. OBJECTIVE: In this study, we have investigated the possible somatic mutations in PIK3CA gene in invasive ductal breast carcinomas of Chinese women from Western China. METHODS: Genomic DNA was extracted from the formalin-fixed paraffin-embedded (FFPE) tissue samples...
February 27, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28264878/assessment-of-alk-gene-rearrangement-in-lung-cancer-using-a-new-rapid-automated-surefish-dako-omnis-assay
#17
Maiko Takeda, Takahiko Kasai, Shigeki Shimizu, Masanori Kitaichi, Kensuke Kojima, Akihiro Nagoya, Akio Hayashi, Tomoki Utsumi, Hyung-Eun Yoon, Akihide Matsumura, Shinji Atagi
The ALK fluorescence in situ hybridisation (FISH) method is the examination essential for pathological diagnosis and choice of molecular-targeted therapy in ALK-rearranged lung cancer. Here, for detection of ALK gene rearrangement in patients with lung cancer, we evaluated the rapid FISH technology (ALK SureFISH), a newly developed assay for the automated staining platform Dako Omnis, using 21 formalin-fixed paraffin-embedded (FFPE) samples. All cases could be evaluated with the SureFISH method. SureFISH provided excellent quality signals without any background staining...
March 6, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28258387/-brca-diagnostics-of-ovarian-cancer-molecular-tumor-testing-since-the-introduction-of-parp-inhibitor-therapy
#18
H Löser, C Heydt, R Büttner, B Markiefka
Approximately 9000 women are diagnosed with ovarian cancer in Germany each year. The most common subtype is high-grade serous ovarian cancer. A relevant proportion of these tumors are associated with mutations in the breast and ovarian cancer susceptibility genes (BRCA1 and BRCA2) representing highly penetrant tumor suppressor genes with autosomal inheritance and play a crucial role in DNA repair mechanisms. These patients have predominantly germline mutations and less frequently have somatic BRCA mutations...
March 3, 2017: Der Pathologe
https://www.readbyqxmd.com/read/28250362/technical-aspects-and-applications-for-developing-in-situ-hybridization-procedures-for-formalin-fixed-and-paraffin-embedded-ffpe-tissues-for-diagnosis-of-fungal-infections
#19
Minoru Shinozaki, Naobumi Tochigi, Sota Sadamoto, Somay Yamagata Murayama, Megumi Wakayama, Tetsuo Nemoto, Kazutoshi Shibuya
Although histopathology is required for definitive diagnosis of fungal infections, conclusive identification and discrimination of fungi in tissue sections and cytological preparations remain technically difficult. Therefore, new diagnostic tools are needed for the routine diagnosis of pathogenic fungi. In situ hybridization (ISH) is a non-culture based procedure that has many advantages over traditional diagnostics for identification of pathogenic fungi in histological specimens. This review highlights the basic ISH technique, with particular emphasis on using pretreatment of tissue sections prior to hybridization to solve problems associated with formalin fixation...
2017: Medical Mycology Journal
https://www.readbyqxmd.com/read/28249711/comparison-of-ffpe-histological-versus-lbp-cytological-samples-for-hpv-detection-and-typing-in-cervical-cancer
#20
Geehyuk Kim, Hyemi Cho, Dongsup Lee, Sunyoung Park, Jiyoung Lee, Hye-Young Wang, Sunghyun Kim, Kwang Hwa Park, Hyeyoung Lee
Human papillomavirus (HPV) infection is closely associated with cervical cancer. This study analyzed HPV genotype prevalence in 75 cases of formalin-fixed paraffin embedded (FFPE) tissue samples from patients diagnosed with cervical cancer. Genotype prevalence was assessed using Reverse Blot Assay (REBA) and quantitative polymerase chain reaction (qPCR), which target the HPV L1 and HPV E6/E7 genes, respectively. HPV DNA chip tests were also performed using liquid based preparation (LBP) cytological samples from the same patients who provided the FFPE histological samples...
February 27, 2017: Experimental and Molecular Pathology
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