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https://www.readbyqxmd.com/read/29447087/a-preliminary-survey-of-chlamydia-psittaci-genotypes-from-native-and-introduced-birds-in-new-zealand
#1
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
https://www.readbyqxmd.com/read/29446344/genotype-characterization-of-livestock-and-human-cystic-echinococcosis-in-mazandaran-province-iran
#2
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
https://www.readbyqxmd.com/read/29432597/identification-of-novel-recurrent-etv6-igh-fusions-in-primary-central-nervous-system-lymphoma
#3
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
https://www.readbyqxmd.com/read/29388947/clinical-whole-genome-sequencing-from-routine-formalin-fixed-paraffin-embedded-specimens-pilot-study-for-the-100-000-genomes-project
#4
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
https://www.readbyqxmd.com/read/29374318/multicenter-validation-of-cancer-gene-panel-based-next-generation-sequencing-for-translational-research-and-molecular-diagnostics
#5
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
https://www.readbyqxmd.com/read/29373900/epidermal-growth-factor-receptor-mutations-in-lung-adenocarcinomas-a-single-center-study-from-iran
#6
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
https://www.readbyqxmd.com/read/29373586/developmental-profiling-of-micrornas-in-the-human-embryonic-inner-ear
#7
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
https://www.readbyqxmd.com/read/29364576/simultaneous-detection-of-single-nucleotide-variant-deletion-insertion-and-fusion-in-lung-and-thyroid-carcinoma-using-cytology-specimen-and-an-rna-based-next-generation-sequencing-assay
#8
Natalya V Guseva, Omar Jaber, Aaron A Stence, Krishnaveni Sompallae, Amani Bashir, Ramakrishna Sompallae, Aaron D Bossler, Chris S Jensen, Deqin Ma
BACKGROUND: Molecular testing for epidermal growth factor receptor (EGFR) mutation and anaplastic lymphoma kinase (ALK) and ROS proto-oncogene 1, receptor tyrosine kinase (ROS1) fusion is routinely performed in patients with stage IV lung adenocarcinoma to assess their eligibility for targeted therapy. Fine-needle aspiration (FNA)-derived material frequently is the only pathologic material available. The identification of genomic aberrations in thyroid nodules from FNA smears may help stratify cancer risk and spare patients from a second surgery...
January 24, 2018: Cancer Cytopathology
https://www.readbyqxmd.com/read/29354287/a-robust-targeted-sequencing-approach-for-low-input-and-variable-quality-dna-from-clinical-samples
#9
Austin P So, Anna Vilborg, Yosr Bouhlal, Ryan T Koehler, Susan M Grimes, Yannick Pouliot, Daniel Mendoza, Janet Ziegle, Jason Stein, Federico Goodsaid, Michael Y Lucero, Francisco M De La Vega, Hanlee P Ji
Next-generation deep sequencing of gene panels is being adopted as a diagnostic test to identify actionable mutations in cancer patient samples. However, clinical samples, such as formalin-fixed, paraffin-embedded specimens, frequently provide low quantities of degraded, poor quality DNA. To overcome these issues, many sequencing assays rely on extensive PCR amplification leading to an accumulation of bias and artifacts. Thus, there is a need for a targeted sequencing assay that performs well with DNA of low quality and quantity without relying on extensive PCR amplification...
2018: NPJ Genomic Medicine
https://www.readbyqxmd.com/read/29344856/next-generation-sequencing-analysis-of-laser-microdissected-formalin-fixed-and-paraffin-embedded-ffpe-tissue-specimens
#10
Lavinia Mägel, Stephan Bartels, Ulrich Lehmann
In recent years, next-generation sequencing (NGS) became widely used in molecular pathology. Comprehensive mutational profiling improved diagnosis and prognosis, as well as the identification of therapeutically relevant genetic alterations. However, the vast majority of studies analyzing tissue samples use DNA extracted from bulk tissue or only manually microdissected specimens. Laser-assisted microdissection offers the possibility of isolating morphologically defined small tissue compartments (like individual glands) or even of single cells for further molecular analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29341374/validation-of-the-digital-pcr-system-in-tyrosine-kinase-inhibitor-resistant-egfr-mutant-non-small-cell-lung-cancer
#11
Katsuhiro Masago, Shiro Fujita, Akito Hata, Chiyuki Okuda, Yuko Yoshizumi, Reiko Kaji, Nobuyuki Katakami, Yukio Hirata, Yasushi Yatabe
The aim of this study was to compare the accuracy of the QuantStudio 3D Digital polymerase chain reaction (dPCR) system and a PCR-based next generation sequencing (NGS) system for detecting a secondary mutation in the epidermal growth factor receptor (EGFR) gene T790M in non-small cell lung cancer (NSCLC) patients previously diagnosed with EGFR-activating mutations. Twenty-five patients with NSCLC previously treated with EGFR-TKIs were examined. The patients were treated daily with either erlotinib or gefitinib...
January 17, 2018: Pathology International
https://www.readbyqxmd.com/read/29340109/development-of-a-targeted-sequencing-approach-to-identify-prognostic-predictive-and-diagnostic-markers-in-paediatric-solid-tumours
#12
Elisa Izquierdo, Lina Yuan, Sally George, Michael Hubank, Chris Jones, Paula Proszek, Janet Shipley, Susanne A Gatz, Caedyn Stinson, Andrew S Moore, Steven C Clifford, Debbie Hicks, Janet C Lindsey, Rebecca M Hill, Thomas S Jacques, Jane Chalker, Khin Thway, Simon O'Connor, Lynley Marshall, Lucas Moreno, Andrew Pearson, Louis Chesler, Brian A Walker, David Gonzalez De Castro
The implementation of personalised medicine in childhood cancers has been limited by a lack of clinically validated multi-target sequencing approaches specific for paediatric solid tumours. In order to support innovative clinical trials in high-risk patients with unmet need, we have developed a clinically relevant targeted sequencing panel spanning 311 kb and comprising 78 genes involved in childhood cancers. A total of 132 samples were used for the validation of the panel, including Horizon Discovery cell blends (n=4), cell lines (n=15), formalin-fixed paraffin embedded (FFPE, n=83) and fresh frozen tissue (FF, n=30) patient samples...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29329546/whole-genome-sequencing-of-genotype-vi-newcastle-disease-viruses-from-formalin-fixed-paraffin-embedded-tissues-from-wild-pigeons-reveals-continuous-evolution-and-previously-unrecognized-genetic-diversity-in-the-u-s
#13
Ying He, Tonya L Taylor, Kiril M Dimitrov, Salman L Butt, James B Stanton, Iryna V Goraichuk, Heather Fenton, Rebecca Poulson, Jian Zhang, Corrie C Brown, Hon S Ip, Marcos Isidoro-Ayza, Claudio L Afonso
BACKGROUND: Newcastle disease viruses (NDV) are highly contagious and cause disease in both wild birds and poultry. A pigeon-adapted variant of genotype VI NDV, often termed pigeon paramyxovirus 1, is commonly isolated from columbids in the United States and worldwide. Complete genomic characterization of these genotype VI viruses circulating in wild columbids in the United States is limited, and due to the genetic variability of the virus, failure of rapid diagnostic detection has been reported...
January 12, 2018: Virology Journal
https://www.readbyqxmd.com/read/29298688/enhanced-response-rate-to-pegylated-liposomal-doxorubicin-in-high-grade-serous-ovarian-carcinomas-harbouring-brca1-and-brca2-aberrations
#14
Robert L Hollis, Alison M Meynert, Michael Churchman, Tzyvia Rye, Melanie Mackean, Fiona Nussey, Mark J Arends, Andrew H Sims, Colin A Semple, C Simon Herrington, Charlie Gourley
BACKGROUND: Approximately 10-15% of ovarian carcinomas (OC) are attributed to inherited susceptibility, the majority of which are due to mutations in BRCA1 or BRCA2 (BRCA1/2). These patients display superior clinical outcome, including enhanced sensitivity to platinum-based chemotherapy. Here, we seek to investigate whether BRCA1/2 status influences the response rate to single-agent pegylated liposomal doxorubicin (PLD) in high grade serous (HGS) OC. METHODS: One hundred and forty-eight patients treated with single-agent PLD were identified retrospectively from the Edinburgh Ovarian Cancer Database...
January 3, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29286417/building-up-a-high-throughput-screening-platform-to-assess-the-heterogeneity-of-her2-gene-amplification-in-breast-cancers
#15
Giulia Ercoli, Gianluca Lopez, Camilla Ciapponi, Chiara Corti, Luca Despini, Donatella Gambini, Letterio Runza, Concetta Blundo, Amedeo Sciarra, Nicola Fusco
Targeted therapies against the human epidermal growth factor receptor 2 (HER2) have radically changed the outcome of patients with HER2-positive breast cancers. However, a minority of cases displays a heterogeneous distribution of HER2-positive cells, which generates major clinical challenges. To date, no reliable and standardized protocols for the characterization and quantification of HER2 heterogeneous gene amplification in large cohorts have been proposed. Here, we present a high-throughput methodology to simultaneously assess the HER2 status across different topographic areas of multiple breast cancers...
December 5, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29285045/optimization-of-rna-extraction-from-formalin-fixed-paraffin-embedded-blocks-for-targeted-next-generation-sequencing
#16
Yoojin Choi, Aeree Kim, Jinkyoung Kim, Jinhwan Lee, Soo Yeon Lee, Chungyeul Kim
Purpose: Breast cancer has a high prevalence in Korea. To achieve personalized therapy for breast cancer, long-term follow-up specimens are needed for next-generation sequencing (NGS) and multigene analysis. Formalin-fixed paraffin-embedded (FFPE) samples are easier to store than fresh frozen (FF) samples. The objective of this study was to optimize RNA extraction from FFPE blocks for NGS. Methods: RNA quality from FF and FFPE tissues (n=5), expected RNA amount per unit area, the relationship between archiving time and quantity/quality of FFPE-extracted RNA (n=14), differences in quantitative real-time polymerase chain reaction (qRT-PCR) and NGS results, and comparisons of both techniques with tissue processing at different institutions (n=96) were determined in this study...
December 2017: Journal of Breast Cancer
https://www.readbyqxmd.com/read/29238890/real-time-detection-of-braf-v600e-mutation-from-archival-hairy-cell-leukemia-ffpe-tissue-by-nanopore-sequencing
#17
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/29228314/demodifying-rna-for-transcriptomic-analyses-of-archival-formalin-fixed-paraffin-embedded-samples
#18
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/29215764/an-evaluation-of-the-challenges-to-developing-tumour-brca1-and-brca2-testing-methodologies-for-clinical-practice
#19
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/29212158/rnascope-in-situ-hybridization-confirms-mrna-integrity-in-formalin-fixed-paraffin-embedded-cancer-tissue-samples
#20
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
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