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Joshua Smith, Aditi Kulkarni, Andrew C Birkeland, Jonathan B McHugh, J Chad Brenner
Objective The pathogenetic underpinnings of extrapulmonary small cell carcinomas (EPSCCs) of the head and neck are poorly understood. We sought to describe the clinical case and whole-exome DNA sequencing data of a patient with sinonasal Schneiderian carcinoma in situ whose tumor progressed to small cell carcinoma (SCC). Study Design Case report and whole-exome sequencing of tumor DNA. Setting Academic medical center. Subjects and Methods A 52-year-old man with sinonasal Schneiderian carcinoma in situ whose tumor progressed to small cell carcinoma...
May 1, 2018: Otolaryngology—Head and Neck Surgery
Nancy Krieger, Sheida Nabavi, Pamela D Waterman, Ninah S Achacoso, Luana Acton, Stuart J Schnitt, Laurel A Habel
PURPOSE: The purpose of the study was to assess the feasibility of quantifying long-term trends in breast tumor DNA copy number variation (CNV) profiles. METHODS: We evaluated CNV profiles in formalin-fixed paraffin-embedded (FFPE) tumor specimens from 30 randomly selected Kaiser Permanente Northern California health plan women members diagnosed with breast cancer from 1950 to 2010. Assays were conducted for five cases per decade who had available tumor blocks and pathology reports...
March 2018: Cancer Causes & Control: CCC
Vanessa Y Ruiz, Corinne E Praska, Georgina Armstrong, Thomas M Kollmeyer, Seiji Yamada, Paul A Decker, Matthew L Kosel, Jeanette E Eckel-Passow, The Gliogene Consortium, Daniel H Lachance, Matthew N Bainbridge, Beatrice S Melin, Melissa L Bondy, Robert B Jenkins
BACKGROUND: Single-gene mutation syndromes account for some familial glioma (FG); however, they make up only a small fraction of glioma families. Gliomas can be classified into 3 major molecular subtypes based on IDH mutation and 1p/19q co-deletion. We hypothesized that the prevalence of molecular subtypes might differ in familial versus sporadic gliomas, and that tumors in the same family should have the same molecular subtype. METHODS: Participants in the FG study (Gliogene) provided samples for germline DNA analysis...
October 10, 2017: Neuro-oncology
Tae Jun Kil, Hyun Sil Kim, Hyung Jun Kim, Woong Nam, In-Ho Cha
BACKGROUND: The cancer progression of oral leukoplakia is an important watchpoint in the follow-up observation of the patients. However, potential malignancies of oral leukoplakia cannot be estimated by histopathologic assessment alone. We evaluated genetic abnormalities at the level of copy number variation (CNV) to investigate the risk for developing cancer in oral leukoplakias. MATERIALS AND METHODS: The current study used 27 oral leukoplakias with histological evidence of dysplasia...
2016: Asian Pacific Journal of Cancer Prevention: APJCP
Nicole Pfarr, Roland Penzel, Frederick Klauschen, Daniel Heim, Regine Brandt, Daniel Kazdal, Moritz Jesinghaus, Esther Herpel, Peter Schirmacher, Arne Warth, Wilko Weichert, Volker Endris, Albrecht Stenzinger
Targeted deep massive parallel sequencing has been implemented in routine molecular diagnostics for high-throughput genetic profiling of formalin-fixed paraffin-embedded (FFPE) cancer samples. This approach is widely used to interrogate simple somatic mutations but experience with the analysis of copy number variations (CNV) is limited. Here, we retrospectively analyzed CNV in 822 cancer cases (135 melanoma, 468 non-small cell lung cancers (NSCLC), 219 colorectal cancers (CRC)). We observed a decreasing frequency of CNV in clinically actionable genes from melanoma to NSCLC to CRC...
November 2016: Genes, Chromosomes & Cancer
Soomin Ahn, Mineui Hong, Michael Van Vrancken, You Jeong Lyou, Seung Tae Kim, Se Hoon Park, Won Ki Kang, Young Suk Park, Sin-Ho Jung, Minah Woo, Jeeyun Lee, Kyoung-Mee Kim
AIM: Screening amplified genes for targeted therapy with high-throughput technology is very important. The NanoString nCounter system allows multiplexed digital quantification of target molecules through the use of color-coded barcodes with the great advantage that formalin-fixed, paraffin-embedded (FFPE) tissue can be utilized. METHODS: We tested nCounter custom copy number variation (CNV) panels in 220 gastric cancer samples and evaluated the utility of this method as a screening tool for the detection of CNV using HER2...
August 2016: Molecular Diagnosis & Therapy
Chantal E Hargreaves, Chisako Iriyama, Matthew J J Rose-Zerilli, Sietse Q Nagelkerke, Khiyam Hussain, Rosalind Ganderton, Charlotte Lee, Lee R Machado, Edward J Hollox, Helen Parker, Kate V Latham, Taco W Kuijpers, Kathleen N Potter, Sarah E Coupland, Andrew Davies, Michael Stackpole, Melanie Oates, Andrew R Pettitt, Martin J Glennie, Mark S Cragg, Jonathan C Strefford
Cancer immunotherapy has been revolutionised by the use monoclonal antibodies (mAb) that function through their interaction with Fc gamma receptors (FcγRs). The low-affinity FcγR genes are highly homologous, map to a complex locus at 1p23 and harbour single nucleotide polymorphisms (SNPs) and copy number variation (CNV) that can impact on receptor function and response to therapeutic mAbs. This complexity can hinder accurate characterisation of the locus. We therefore evaluated and optimised a suite of assays for the genomic analysis of the FcγR locus amenable to peripheral blood mononuclear cells and formalin-fixed paraffin-embedded (FFPE) material that can be employed in a high-throughput manner...
2015: PloS One
L M Ernst, C M Rand, R Bao, J Andrade, R L Linn, L Minturn, C Zhang, W Kang, D E Weese-Mayer
INTRODUCTION: Stillbirth remains a devastating health issue with 26,000 stillbirths occurring annually in the United States. Formalin-fixed, paraffin-embedded (FFPE) umbilical cord samples are available for many stillbirths. Our aim was to validate the use of these samples in identifying genetic variations in stillbirth through microarray analysis. METHODS: This is a retrospective case-control study from a single institution of stillbirths ≥ 23 weeks gestational age and control liveborn infants...
August 2015: Placenta
Joaquim Bellmunt, Lillian Werner, Jeffrey J Leow, Stephanie A Mullane, André P Fay, Markus Riester, Paul Van Hummelen, Mary-Ellen Taplin, Toni K Choueiri, Eliezer Van Allen, Jonathan Rosenberg
BACKGROUND: An integrative analysis was conducted to identify genomic alterations at a pathway level that could predict overall survival (OS) in patients with advanced urothelial carcinoma (UC) treated with platinum-based chemotherapy. PATIENTS AND METHODS: DNA and RNA were extracted from 103 formalin-fixed paraffin embedded (FFPE) invasive high-grade UC samples and were screened for mutations, copy number variation (CNV) and gene expression analysis. Clinical data were available from 85 cases...
2015: PloS One
Neetu Singh, Dinesh K Sahu, Madhumati Goel, Ravi Kant, Devendra K Gupta
In this report, retrospectively, we analyzed fifteen histo-pathologically characterized FFPE based Wilms' Tumor (WT) samples following an integrative approach of copy number (CN) and loss of heterozygosity (LOH) imbalances. The isolated-DNA was tested on CN and somatic-mutation related Molecular-Inversion-Probe based-Oncoscan Array™ and was analyzed through Nexus-Express OncoScan-3.0 and 7.0 software. We identified gain of 3p13.0-q29, 4p16.3-14.0, 7, 12p13.33-q24.33, and losses of 1p36.11-q44, 11p15.5-q25, 21q 22...
July 10, 2015: Gene
Yan P Yu, Amantha Michalopoulos, Ying Ding, George Tseng, Jian-Hua Luo
Detection of human genome copy number variation (CNV) is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE) tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis...
2014: PloS One
J P Johnson, J Waterson, C Schwanke, J Schoof
Individuals with mosaic paternal uniparental disomy (UPD) of apparently all chromosomes have recently been described. They show a 46,XX karyotype, but with a mixture of normal biparental cells and cells entirely of paternal isodisomic origin. We describe an infant who primarily showed signs of Beckwith-Wiedemann syndrome (BWS), but also had other severe and eventually lethal medical problems, notably refractory hypoglycemia. We performed methylation studies for BWS, but incidentally for Angelman syndrome (AS) on leukocytes and in a skin FFPE sample...
March 2014: Clinical Genetics
Holly N Cukier, Margaret A Pericak-Vance, John R Gilbert, Dale J Hedges
The recent implication of genomic copy number variations (CNVs) in multiple human genetic disorders has led to increased interest in CNV discovery technologies. There is a growing consensus that, in addition to the method used for detection, at least one additional technology should be employed for validation. Real-time quantitative polymerase chain reaction (qPCR) analysis, incorporating a normal (2N) copy number standard, is commonly used as a means of validating CNVs. Whereas it has previously been reported that formalin-fixed paraffin-embedded (FFPE) DNA samples can yield spurious CNV calls in real-time qPCR assays, here we report that sample degradation under standard laboratory storage conditions generates a significant increase in false-positive CNV results...
March 15, 2009: Analytical Biochemistry
Marianne Tuefferd, An De Bondt, Ilse Van Den Wyngaert, Willem Talloen, Tobias Verbeke, Benilton Carvalho, Djork-Arne Clevert, Marco Alifano, Nandini Raghavan, Dhammika Amaratunga, Hinrich Göhlmann, Philippe Broët, Sophie Camilleri-Broët
SNP arrays offer the opportunity to get a genome-wide view on copy number alterations and are increasingly used in oncology. DNA from formalin-fixed paraffin-embedded material (FFPE) is partially degraded which limits the application of those technologies for retrospective studies. We present the use of Affymetrix GeneChip SNP6.0 for identification of copy number alterations in fresh frozen (FF) and matched FFPE samples. Fifteen pairs of adenocarcinomas with both frozen and FFPE embedded material were analyzed...
November 2008: Genes, Chromosomes & Cancer
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