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https://www.readbyqxmd.com/read/27818284/cardiac-angiosarcoma-histopathologic-immunohistochemical-and-cytogenetic-analysis-of-10-cases
#1
Charles Leduc, Sarah M Jenkins, William R Sukov, Jeannette G Rustin, Joseph J Maleszewski
Angiosarcoma (AS) is the most common cardiac sarcoma with differentiation, and is poorly characterized from a molecular genetic standpoint. Prognosis remains poor, owing to several factors including aggressive tumor biology, poor response to adjuvant therapy, and lack of targeted therapy. The clinical, pathologic and molecular cytogenetic features were studied in ten cardiac AS surgically resected at Mayo Clinic (1994-2015) using a whole genome single nucleotide polymorphism based platform (OncoScan). Mean patient age was 47...
November 3, 2016: Human Pathology
https://www.readbyqxmd.com/read/27716627/precise-erbb2-copy-number-assessment-in-breast-cancer-by-means-of-molecular-inversion-probe-array-analysis
#2
Matthias Christgen, Jana L van Luttikhuizen, Mieke Raap, Peter Braubach, Lars Schmidt, Danny Jonigk, Friedrich Feuerhake, Ulrich Lehmann, Brigitte Schlegelberger, Hans H Kreipe, Doris Steinemann
HER2/ERBB2 amplification/overexpression determines the eligibility of breast cancer patients to HER2-targeted therapy. This study evaluates the agreement between ERBB2 copy number assessment by fluorescence in situ hybridization, a standard method recommended by the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP), and newly available DNA extraction-based methods. A series of n=29 formalin-fixed paraffin-embedded breast cancers were subjected to ERBB2 copy number assessment by fluorescence in situ hybridization (FISH, Vysis, Abbott)...
October 3, 2016: Oncotarget
https://www.readbyqxmd.com/read/27683181/patient-derived-xenograft-establishment-from-human-malignant-pleural-mesothelioma
#3
Ming-Sound Tsao, Licun Wu, Ghassan Allo, Thomas John, Ming Li, Tetsuzo Tagawa, Isabelle Opitz, Masaki Anraku, Zhihong Yun, Melania Pintilie, Geoffrey Liu, Bethany Pitcher, Ron Feld, Michael R Johnston, Marc de Perrot
PURPOSE: Malignant pleural mesothelioma (MPM) is a rare but aggressive disease with few therapeutic options. The tumor stromal interface is important in MPM, but this is lost in cell lines, the main model used for preclinical studies. We sought to characterise MPM patient derived xenografts (PDX) to determine their suitability as pre-clinical models and whether tumors that engraft reflect a more aggressive biological phenotype. EXPERIMENTAL DESIGN: Fresh tumors were harvested from extrapleural pneumonectomy (EPP), decortication or biopsy samples of 50 MPM patients, and implanted subcutaneously into immunodeficient mice and serially passaged for up to five generations...
September 28, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27626691/tumornext-a-comprehensive-tumor-profiling-assay-that-incorporates-high-resolution-copy-number-analysis-and-germline-status-to-improve-testing-accuracy
#4
Phillip N Gray, Huy Vuong, Pei Tsai, Hsaio-Mei Lu, Wenbo Mu, Vickie Hsuan, Jayne Hoo, Swati Shah, Lisa Uyeda, Susanne Fox, Harshil Patel, Mike Janicek, Sandra Brown, Lavinia Dobrea, Lawrence Wagman, Elizabeth Plimack, Ranee Mehra, Erica A Golemis, Marijo Bilusic, Matthew Zibelman, Aaron Elliott
The development of targeted therapies for both germline and somatic DNA mutations has increased the need for molecular profiling assays to determine the mutational status of specific genes. Moreover, the potential of off-label prescription of targeted therapies favors classifying tumors based on DNA alterations rather than traditional tissue pathology. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext, which can detect single nucleotide variants, small insertions and deletions in 142 genes that are frequently mutated in somatic and/or germline cancers...
September 8, 2016: Oncotarget
https://www.readbyqxmd.com/read/27582547/detection-of-ccne1-uri-19q12-amplification-by-in-situ-hybridisation-is-common-in-high-grade-and-type-ii-endometrial-cancer
#5
Aurelia Noske, Simone Brandt, Nadejda Valtcheva, Ulrich Wagner, Qing Zhong, Elisa Bellini, Daniel Fink, Ellen C Obermann, Holger Moch, Peter J Wild
One TCGA subgroup of endometrial cancer (EC) is characterised by extensive genomic DNA copy number alterations. CCNE1 located at 19q12 is frequently amplified in EC and a target for anti-cancer therapy. The relevance of URI, also located at 19q12, is unknown. To evaluate the prevalence of 19q12 (CCNE1/URI) in EC, we investigated different histologic types by in situ hybridisation (ISH) and copy number assay. We applied a previously established 19q12 ISH for the detection of CCNE1/URI copy numbers in EC (n = 270) using conventional bright field microscopy...
August 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27566563/copy-number-gain-of-chromosome-3q-is-a-recurrent-event-in-patients-with-intraductal-papillary-mucinous-neoplasm-ipmn-associated-with-disease-progression
#6
Sandra Durante, Silvia Vecchiarelli, Annalisa Astolfi, Elisa Grassi, Riccardo Casadei, Donatella Santini, Riccardo Panzacchi, Claudio Ricci, Salvatore Serravalle, Giuseppe Tarantino, Mirella Falconi, Gabriella Teti, Valentina Indio, Andrea Pession, Francesco Minni, Guido Biasco, Mariacristina Di Marco
BACKGROUND: Intraductal papillary mucinous neoplasm (IPMN) is the most common cystic preneoplastic lesion of pancreatic cancer. We used an approach coupling high resolution cytogenetic analysis (Affymetrix Oncoscan FFPE Array) with clinically-oriented bioinformatic interpretation of data to understand the most relevant alterations of precursor lesions at different stages to identify new diagnostic markers. RESULTS: We identified multiple copy number alterations, particularly in lesions with severe dysplasia, with 7 IPMN with low-intermediate dysplasia carrying a nearly normal karyotype and 13 IPMN with complex Karyotype (> 4 alterations), showing high grade dysplasia...
August 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/27499911/the-molecular-landscape-of-extraskeletal-osteosarcoma-a-clinicopathological-and-molecular-biomarker-study
#7
George Jour, Lu Wang, Sumit Middha, Ahmet Zehir, Wen Chen, Justyna Sadowska, John Healey, Narasimhan P Agaram, Lisa Choi, Khedoudja Nafa, Meera Hameed
Extraskeletal osteosarcoma (ESOSA) is a rare soft tissue neoplasm representing <5% of osteosarcomas and <1% of all soft-tissue sarcomas. Herein, we investigate the clinicopathological and molecular features of ESOSA and explore potential parameters that may affect outcome. Thirty-two cases were retrieved and histomorphology was reviewed. Clinical history and follow-up were obtained through electronic record review. DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted and processed from 27 cases...
January 2016: Journal of Pathology. Clinical Research
https://www.readbyqxmd.com/read/27440268/genomic-copy-number-profiling-using-circulating-free-tumor-dna-highlights-heterogeneity-in-neuroblastoma
#8
Mathieu Chicard, Sandrine Boyault, Leo Colmet Daage, Wilfrid Richer, David Gentien, Gaelle Pierron, Eve Lapouble, Angela Bellini, Nathalie Clement, Isabelle Iacono, Stéphanie Bréjon, Marjorie Carrere, Cécile Reyes, Toby Hocking, Virginie Bernard, Michel Peuchmaur, Nadège Corradini, Cécile Faure-Conter, Carole Coze, Dominique Plantaz, Anne Sophie Defachelles, Estelle Thebaud, Marion Gambart, Frédéric Millot, Dominique Valteau-Couanet, Jean Michon, Alain Puisieux, Olivier Delattre, Valérie Combaret, Gudrun Schleiermacher
PURPOSE: The tumor genomic copy number profile is of prognostic significance in neuroblastoma patients. We have studied the genomic copy number profile of cell-free DNA (cfDNA) and compared this with primary tumor arrayCGH (aCGH) at diagnosis. EXPERIMENTAL DESIGN: In 70 patients, cfDNA genomic copy number profiling was performed using the OncoScan platform. The profiles were classified according to the overall pattern, including numerical chromosome alterations (NCA), segmental chromosome alterations (SCA), and MYCN amplification (MNA)...
July 20, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27248473/recurrent-truncating-sox9-mutations-are-associated-with-sox9-overexpression-kras-mutation-and-tp53-wild-type-status-in-colorectal-carcinoma
#9
Breanna M Javier, Rona Yaeger, Lu Wang, Francisco Sanchez-Vega, Ahmet Zehir, Sumit Middha, Justyna Sadowska, Efsevia Vakiani, Jinru Shia, David Klimstra, Marc Ladanyi, Christine A Iacobuzio-Donahue, Jaclyn F Hechtman
PURPOSE: The extent to which the developmental transcription factor SOX9 functions as an oncogene or tumor suppressor in colorectal carcinoma (CRC) is debatable. We aimed to clarify the effect of SOX9 mutations on SOX9 protein expression and their association with known molecular subtypes and clinical characteristics in advanced CRC. EXPERIMENTAL DESIGN: Next generation sequencing data (MSK-IMPACT) from CRC patients was used to interrogate SOX9, KRAS, NRAS, BRAF, TP53, APC, and PIK3CA...
May 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27173781/unclassified-renal-cell-carcinoma-with-tubulopapillary-architecture-clear-cell-phenotype-and-chromosome-8-monosomy-a-new-kid-on-the-block
#10
Thanh T H Lan, Jennifer Keller-Ramey, Carrie Fitzpatrick, Sabah Kadri, Jerome B Taxy, Jeremy P Segal, Larissa V Furtado, Tatjana Antic
Accurate subtyping of renal cell carcinomas (RCCs) has become clinically important for therapy and prognostication. RCC subtypes are defined by distinct morphologic and immunohistochemical profiles, and in some instances recurrent cytogenetic and molecular properties. However, some tumors exhibit overlapping morphologic and immunophenotypic features, frequent enough to pose diagnostic dilemmas. This report concerns six histologically unusual RCCs that showed tubulopapillary architecture, clear cell phenotype, and non-diagnostic immunohistochemical profiles...
July 2016: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/26925973/clinical-application-of-genomic-profiling-to-find-druggable-targets-for-adolescent-and-young-adult-aya-cancer-patients-with-metastasis
#11
Soojin Cha, Jeongeun Lee, Jong-Yeon Shin, Ji-Yeon Kim, Sung Hoon Sim, Bhumsuk Keam, Tae Min Kim, Dong-Wan Kim, Dae Seog Heo, Se-Hoon Lee, Jong-Il Kim
BACKGROUND: Although adolescent and young adult (AYA) cancers are characterized by biological features and clinical outcomes distinct from those of other age groups, the molecular profile of AYA cancers has not been well defined. In this study, we analyzed cancer genomes from rare types of metastatic AYA cancers to identify driving and/or druggable genetic alterations. METHODS: Prospectively collected AYA tumor samples from seven different patients were analyzed using three different genomics platforms (whole-exome sequencing, whole-transcriptome sequencing or OncoScan™)...
2016: BMC Cancer
https://www.readbyqxmd.com/read/26864375/segmental-chromosomal-aberrations-in-localized-neuroblastoma-can-be-detected-in-formalin-fixed-paraffin-embedded-tissue-samples-and-are-associated-with-recurrence
#12
Navin Pinto, Jodi R Mayfield, Gordana Raca, Mark A Applebaum, Alexandre Chlenski, Madina Sukhanova, Rochelle Bagatell, Meredith S Irwin, Anthony Little, Jawhar Rawwas, Yasmin Gosiengfiao, Olivier Delattre, Isabelle Janoueix-Lerosey, Eve Lapouble, Gudrun Schleiermacher, Susan L Cohn
BACKGROUND: Array comparative genomic hybridization (CGH) analyses of frozen tumors have shown strong associations between the pattern of chromosomal aberrations and outcome in patients with advanced-stage neuroblastoma. New platforms for analyzing chromosomal aberrations using formalin-fixed paraffin-embedded (FFPE) tissue have recently been developed. We sought to determine whether chromosomal microarray analysis (CMA) using FFPE tumors is feasible and if segmental chromosomal aberrations were prognostic of recurrence in localized neuroblastoma...
June 2016: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/26852708/extensive-therapies-for-extraneural-metastases-from-glioblastoma-as-confirmed-with-the-oncoscan-assay
#13
Ming Xu, Ying Wang, Jian Xu, Yu Yao, Wei-Xing Yu, Ping Zhong
BACKGROUND: The diagnosis of extraneural metastasis from glioblastoma is usually based on the histopathology and immunohistochemical staining of a tumor specimen. Information regarding the molecular features of glioblastoma and optimal treatment strategies for extraneural metastasis is limited. CASE DESCRIPTION: A 58-year-old woman with a glioblastoma located in the left temporal lobe underwent resection followed by radiotherapy plus concomitant and adjuvant temozolomide...
June 2016: World Neurosurgery
https://www.readbyqxmd.com/read/26743478/genomic-copy-number-analysis-of-a-spectrum-of-blue-nevi-identifies-recurrent-aberrations-of-entire-chromosomal-arms-in-melanoma-ex-blue-nevus
#14
May P Chan, Aleodor A Andea, Paul W Harms, Alison B Durham, Rajiv M Patel, Min Wang, Patrick Robichaud, Gary J Fisher, Timothy M Johnson, Douglas R Fullen
Blue nevi may display significant atypia or undergo malignant transformation. Morphologic diagnosis of this spectrum of lesions is notoriously difficult, and molecular tools are increasingly used to improve diagnostic accuracy. We studied copy number aberrations in a cohort of cellular blue nevi, atypical cellular blue nevi, and melanomas ex blue nevi using Affymetrix's OncoScan platform. Cases with sufficient DNA were analyzed for GNAQ, GNA11, and HRAS mutations. Copy number aberrations were detected in 0 of 5 (0%) cellular blue nevi, 3 of 12 (25%) atypical cellular blue nevi, and 6 of 9 (67%) melanomas ex blue nevi...
March 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/26568296/intra-tumor-genetic-heterogeneity-in-rectal-cancer
#15
Karin M Hardiman, Peter J Ulintz, Rork D Kuick, Daniel H Hovelson, Christopher M Gates, Ashwini Bhasi, Ana Rodrigues Grant, Jianhua Liu, Andi K Cani, Joel K Greenson, Scott A Tomlins, Eric R Fearon
Colorectal cancer arises in part from the cumulative effects of multiple gene lesions. Recent studies in selected cancer types have revealed significant intra-tumor genetic heterogeneity and highlighted its potential role in disease progression and resistance to therapy. We hypothesized the existence of significant intra-tumor genetic heterogeneity in rectal cancers involving variations in localized somatic mutations and copy number abnormalities. Two or three spatially disparate regions from each of six rectal tumors were dissected and subjected to the next-generation whole-exome DNA sequencing, Oncoscan SNP arrays, and targeted confirmatory sequencing and analysis...
January 2016: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/26546618/combined-tumor-suppressor-defects-characterize-clinically-defined-aggressive-variant-prostate-cancers
#16
Ana M Aparicio, Li Shen, Elsa Li Ning Tapia, Jing-Fang Lu, Hsiang-Chun Chen, Jiexin Zhang, Guanglin Wu, Xuemei Wang, Patricia Troncoso, Paul Corn, Timothy C Thompson, Bradley Broom, Keith Baggerly, Sankar N Maity, Christopher J Logothetis
PURPOSE: Morphologically heterogeneous prostate cancers that behave clinically like small-cell prostate cancers (SCPC) share their chemotherapy responsiveness. We asked whether these clinically defined, morphologically diverse, "aggressive variant prostate cancer (AVPC)" also share molecular features with SCPC. EXPERIMENTAL DESIGN: Fifty-nine prostate cancer samples from 40 clinical trial participants meeting AVPC criteria, and 8 patient-tumor derived xenografts (PDX) from 6 of them, were stained for markers aberrantly expressed in SCPC...
March 15, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/26456192/multiomics-approach-showing-genome-wide-copy-number-alterations-and-differential-gene-expression-in-different-types-of-north-indian-pediatric-brain-tumors
#17
Neetu Singh, Dinesh Kumar Sahu, Archana Mishra, Preeti Agarwal, Madhu Mati Goel, Anil Chandra, Sunil Kumar Singh, Chhitij Srivastava, Bal Krishna Ojha, Devendra Kumar Gupta, Ravi Kant
PURPOSE: Based on copy number alterations and transcriptional profiles, the posterior fossa tumors (medulloblastoma (MB), ependymoma and pilocytic astrocytoma) have been classified into various subgroups. The study design was aimed to identify and catalog genome-wide copy number alterations and differential gene expression in different types of North-Indian pediatric posterior fossa tumors and matched control tissue through Molecular Inversion Probe (MIP) Based and Human Transcriptome Array...
February 1, 2016: Gene
https://www.readbyqxmd.com/read/26415226/next-generation-sequencing-in-synovial-sarcoma-reveals-novel-gene-mutations
#18
Myrella Vlenterie, Melissa H S Hillebrandt-Roeffen, Uta E Flucke, Patricia J T A Groenen, Bastiaan B J Tops, Eveline J Kamping, Rolph Pfundt, Diederik R H de Bruijn, Ad H M Geurts van Kessel, Han J H J M van Krieken, Winette T A van der Graaf, Yvonne M H Versleijen-Jonkers
Over 95% of all synovial sarcomas (SS) share a unique translocation, t(X;18), however, they show heterogeneous clinical behavior. We analyzed multiple SS to reveal additional genetic alterations besides the translocation. Twenty-six SS from 22 patients were sequenced for 409 cancer-related genes using the Comprehensive Cancer Panel (Life Technologies, USA) on an Ion Torrent platform. The detected variants were verified by Sanger sequencing and compared to matched normal DNAs. Copy number variation was assessed in six tumors using the Oncoscan array (Affymetrix, USA)...
October 27, 2015: Oncotarget
https://www.readbyqxmd.com/read/26321097/copy-number-analysis-of-ductal-carcinoma-in-situ-with-and-without-recurrence
#19
Kylie L Gorringe, Sally M Hunter, Jia-Min Pang, Ken Opeskin, Prue Hill, Simone M Rowley, David Y H Choong, Ella R Thompson, Alexander Dobrovic, Stephen B Fox, G Bruce Mann, Ian G Campbell
Ductal carcinoma in situ (DCIS) is a non-obligate precursor of invasive breast cancer and a frequent mammographic finding requiring treatment. Up to 25% of DCIS can recur and half of recurrences are invasive, but there are no reliable biomarkers for recurrence. We hypothesised that copy number aberrations could predict likelihood of recurrence. We analysed a cohort of pure DCIS cases treated only with wide local excision for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan MIP arrays...
September 2015: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/26214323/streamlining-the-oncoscan%C3%A2-array-procedure-for-use-in-a-clinical-laboratory
#20
Christian N Paxton, Leslie R Rowe, Sarah T South
Microarray analysis has found tremendous utility in the clinical laboratory testing for detection of copy number changes (CNCs) and loss of heterozygosity (LOH). Recently the OncoScan® array was introduced as a tool for identification of CNCs and LOH in formalin-fixed paraffin-embedded oncology samples. The objective of this study was to identify steps in the OncoScan procedure that could be modified to make the process more efficient and technician-friendly in the clinical laboratory setting. Eighteen samples previously processed according to the manufacturer-recommended protocol were reprocessed using a modified protocol...
2015: Journal of the Association of Genetic Technologists
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