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copy number variation AND cancer

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https://www.readbyqxmd.com/read/29152119/a-genome-wide-comprehensively-analyses-of-long-noncoding-rna-profiling-and-metastasis-associated-lncrnas-in-renal-cell-carcinoma
#1
Xue Xu, Yongcan Xu, Chuanqin Shi, Baoyu Wang, Xiang Yu, Yanfen Zou, Tao Hu
Recently, a growing number of studies have indicated that long noncoding RNAs (lncRNAs) are emerging as new critical regulators of tumorigenesis and prognostic markers in multiple cancers. However, the expression pattern of lncRNAs and their contributions in renal cell carcinoma (RCC) remains poorly understood. In this study, we performed a genome-wide comprehensively analysis of lncRNAs profiling and clinical relevance to provide valuable lncRNA candidates for the further study in RCC. RCC and non-tumor tissues RNA sequencing data, and microarray data were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), then, these data were annotated and analyzed to find dysregulated lncRNAs in RCC...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29152113/the-prognostic-significance-of-mcl1-copy-number-gain-in-esophageal-squamous-cell-carcinoma
#2
Chen Xu, Yalan Liu, Jie Huang, Hao Wang, Lijie Tan, Yifan Xu, Zhengzeng Jiang, Xin Wang, Yingyong Hou, Dongxian Jiang, Qun Wang
Background: MCL1 copy number variations have been reported to be associated with cancer prognosis in several cancers. However, the role of MCL1 gain has not yet been determined in esophageal squamous cell carcinomas (ESCC). Methods: Fluorescence in situ hybridization (FISH) for MCL1 was performed on 262 ESCC samples using tissue microarray (TMA). Results: The median age of ESCC patients was 62 years (range 37-83), with frequencies between women (16...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29147009/mitochondrial-uqcrb-as-a-new-molecular-prognostic-biomarker-of-human-colorectal-cancer
#3
Hyun-Chul Kim, Junghwa Chang, Hannah S Lee, Ho Jeong Kwon
Ubiquinol cytochrome c reductase binding protein (UQCRB) is important for mitochondrial complex III stability, electron transport, cellular oxygen sensing and angiogenesis. However, its potential as a prognostic marker in colorectal cancer (CRC) remains unclear. The aim of this study was to determine whether UQCRB can be used as a diagnostic molecular marker for CRC. The correlation between the expression of three genes (UQCRB, UQCRFS1 and MT-CYB) in the mitochondrial respiratory chain complex III and clinico-pathological features was determined...
November 17, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29144792/effect-of-blood-collection-tube-type-and-time-to-processing-on-the-enumeration-and-high-content-characterization-of-circulating-tumor-cells-using-the-high-definition-single-cell-assay
#4
Mariam Rodríguez-Lee, Anand Kolatkar, Madelyn McCormick, Angel D Dago, Jude Kendall, Nils Anders Carlsson, Kelly Bethel, Emily J Greenspan, Shelley E Hwang, Kathryn R Waitman, Jorge J Nieva, James Hicks, Peter Kuhn
CONTEXT: - As circulating tumor cell (CTC) assays gain clinical relevance, it is essential to address preanalytic variability and to develop standard operating procedures for sample handling in order to successfully implement genomically informed, precision health care. OBJECTIVE: - To evaluate the effects of blood collection tube (BCT) type and time-to-assay (TTA) on the enumeration and high-content characterization of CTCs by using the high-definition single-cell assay (HD-SCA)...
November 16, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29141226/a-pan-cancer-analysis-of-the-expression-and-clinical-relevance-of-small-nucleolar-rnas-in-human-cancer
#5
Jing Gong, Yajuan Li, Chun-Jie Liu, Yu Xiang, Chunlai Li, Youqiong Ye, Zhao Zhang, David H Hawke, Peter K Park, Lixia Diao, John A Putkey, Liuqing Yang, An-Yuan Guo, Chunru Lin, Leng Han
Increasing evidence has demonstrated that small nucleolar RNAs (snoRNAs) play important roles in tumorigenesis. We systematically investigated the expression landscape and clinical relevance of snoRNAs in >10,000 samples across 31 cancer types from The Cancer Genome Atlas. We observed overall elevated expression of snoRNAs and their ribonucleoproteins in multiple cancer types. We showed complex regulation of snoRNA expression by their host genes, copy number variation, and DNA methylation. Unsupervised clustering revealed that the snoRNA expression subtype is highly concordant with other molecular/clinical subtypes...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29135520/epithelial-myoepithelial-carcinoma-frequent-morphologic-and-molecular-evidence-of-preexisting-pleomorphic-adenoma-common-hras-mutations-in-plag1-intact-and-hmga2-intact-cases-and-occasional-tp53-fbxw7-and-smarcb1-alterations-in-high-grade-cases
#6
Soufiane El Hallani, Aaron M Udager, Diana Bell, Isabel Fonseca, Lester D R Thompson, Adel Assaad, Abbas Agaimy, Alyssa M Luvison, Caitlyn Miller, Raja R Seethala, Simion Chiosea
We hypothesized that there is a relationship between the preexisting pleomorphic adenoma [PA]), histologic grade of epithelial-myoepithelial carcinomas (EMCAs), and genetic alterations. EMCAs (n=39) were analyzed for morphologic and molecular evidence of preexisting PA (PLAG1, HMGA2 status by fluorescence in situ hybridization, FISH, and FGFR1-PLAG1 fusion by next-generation sequencing, NGS). Twenty-three EMCAs were further analyzed by NGS for mutations and copy number variation in 50 cancer-related genes. On the basis of combined morphologic and molecular evidence of PA, the following subsets of EMCA emerged: (a) EMCAs with morphologic evidence of preexisting PA, but intact PLAG1 and HMGA2 (12/39, 31%), (b) Carcinomas with PLAG1 alterations (9/39, 23%), or (c) HMGA2 alterations (10/39, 26%), and (d) de novo carcinomas, without morphologic or molecular evidence of PA (8/39, 21%)...
November 9, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29134670/altered-mitochondrial-genome-content-signals-worse-pathology-and-prognosis-in-prostate-cancer
#7
Anton M F Kalsbeek, Eva K F Chan, Judith Grogan, Desiree C Petersen, Weerachai Jaratlerdsiri, Ruta Gupta, Ruth J Lyons, Anne-Maree Haynes, Lisa G Horvath, James G Kench, Phillip D Stricker, Vanessa M Hayes
BACKGROUND: Mitochondrial genome (mtDNA) content is depleted in many cancers. In prostate cancer, there is intra-glandular as well as inter-patient mtDNA copy number variation. In this study, we determine if mtDNA content can be used as a predictor for prostate cancer staging and outcomes. METHODS: Fresh prostate cancer biopsies from 115 patients were obtained at time of surgery. All cores underwent pathological review, followed by isolation of cancer and normal tissue...
November 14, 2017: Prostate
https://www.readbyqxmd.com/read/29116104/germline-copy-number-variations-are-associated-with-breast-cancer-risk-and-prognosis
#8
Mahalakshmi Kumaran, Carol E Cass, Kathryn Graham, John R Mackey, Roland Hubaux, Wan Lam, Yutaka Yasui, Sambasivarao Damaraju
Breast cancer is one of the most common cancers among women, and susceptibility is explained by genetic, lifestyle and environmental components. Copy Number Variants (CNVs) are structural DNA variations that contribute to diverse phenotypes via gene-dosage effects or cis-regulation. In this study, we aimed to identify germline CNVs associated with breast cancer susceptibility and their relevance to prognosis. We performed whole genome CNV genotyping in 422 cases and 348 controls using Human Affymetrix SNP 6 array...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29113949/dysregulated-expression-of-the-microrna-mir-137-and-its-target-yb-1-contribute-to-the-invasive-characteristics-of-malignant-pleural-mesothelioma
#9
Thomas G Johnson, Karin Schelch, Yuen Y Cheng, Marissa Williams, Kadir H Sarun, Michaela B Kirschner, Steven Kao, Anthony Linton, Sonja Klebe, Brian C McCaughan, Ruby Cy Lin, Christine Pirker, Walter Berger, Annette Lasham, Nico van Zandwijk, Glen Reid
BACKGROUND: Malignant pleural mesothelioma (MPM) is an aggressive malignancy linked to asbestos exposure. On a genomic level, MPM is characterised by frequent chromosomal deletions of tumour suppressors, including microRNAs. MiR-137 plays a tumour suppressor role in other cancers, so the aim of this study was to characterise it and its target Y-box binding protein-1 (YB-1) in MPM. BASIC PROCEDURES: Expression, methylation and copy number status of miR-137 and its host gene MIR137HG were assessed by PCR...
November 4, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/29108259/copy-number-variations-and-expression-of-mpdz-are-prognostic-biomarkers-for-clear-cell-renal-cell-carcinoma
#10
Yong-Sheng Huang, Wen-Bin Liu, Fei Han, Jun-Tang Yang, Xiang-Lin Hao, Hong-Qiang Chen, Xiao Jiang, Li Yin, Lin Ao, Zhi-Hong Cui, Jia Cao, Jin-Yi Liu
The vital copy number variation (CNV) plays a crucial role in clear cell renal cell carcinoma (ccRCC). MPDZ inhibit cell polarity associate with osmotic pressure response and cancer-related biological processes. In order to clarify the role of the CNV of MPDZ in the progression of ccRCC, we analyzed the CNV and expression of MPDZ and prognosis in ccRCC patients from The Cancer Genome Atlas data portal. Notably, we found that the deletion of MPDZ was the common CNV, which was present in 28.65% of ccRCC patients...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29105743/whole-exome-sequencing-reveals-intertumor-heterogeneity-and-distinct-genetic-origins-of-sporadic-synchronous-colorectal-cancer
#11
Jiabo Di, Hong Yang, Beihai Jiang, Zaozao Wang, Jiafu Ji, Xiangqian Su
Sporadic synchronous colorectal cancer (CRC) refers to more than one primary tumor detected in a single patient at the time of the first diagnosis without predisposition of cancer development. Given the same genetic and microenvironment they raise, sporadic synchronous CRC is a unique model to study CRC tumorigenesis. We performed whole exome sequencing in 32 fresh frozen tumor lesions from 15 patients with sporadic synchronous CRC to compare their genetic alterations. This approach identified ubiquitously mutated genes in the range from 0...
November 6, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29072129/cell-free-mitochondrial-dna-copy-number-variation-in-head-and-neck-squamous-cell-carcinoma-a-study-of-non-invasive-biomarker-from-northeast-india
#12
Manish Kumar, Shilpee Srivastava, Seram Anil Singh, Anup Kumar Das, Ganesh Chandra Das, Bishal Dhar, Sankar Kumar Ghosh, Rosy Mondal
Head and neck squamous cell carcinoma is the most commonly diagnosed cancer worldwide. The lifestyle, food habits, and customary practices manifest the Northeast Indian population toward higher susceptibility to develop head and neck squamous cell carcinoma. Here, we have investigated the association of smoke and smokeless tobacco, and alcohol with copy number variation of cell-free mitochondrial DNA and cell-free nuclear DNA in cases and controls. Cell-free DNA from plasma was isolated from 50 head and neck squamous cell carcinoma cases and 50 controls with informed written consent using QIAamp Circulating Nucleic Acid Kit...
October 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29069713/selective-dna-methylation-in-cancers-controls-collateral-damage-induced-by-large-structural-variations
#13
Vakul Mohanty, Ogulsheker Akmamedova, Kakajan Komurov
Chromosomal instability is a hallmark of human cancers, and is characterized by large structural variations in the genome. Such large structural variations are expected to create intrinsic collateral stress due to gene dosage changes in many genes that are co-deleted or co-amplified in large chromosomal segments (onco-passenger genes). We show that the tumor-toxic effects of gene dosage changes of onco-passenger genes are compensated by the uncoupling of their copy number variations from their expression by means of selective DNA methylation...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29066617/a-novel-approach-for-data-integration-and-disease-subtyping
#14
Tin Nguyen, Rebecca Tagett, Diana Diaz, Sorin Draghici
Advances in high-throughput technologies allow for measurements of many types of omics data, yet the meaningful integration of several different data types remains a significant challenge. Another important and difficult problem is the discovery of molecular disease subtypes characterized by relevant clinical differences, such as survival. Here we present a novel approach, called Perturbation clustering for data INtegration and disease Subtyping (PINS), which is able to address both challenges. The framework has been validated on thousands of cancer samples, using gene expression, DNA methylation, non-coding microRNA, and copy number variation data available from the Gene Expression Omnibus, the Broad Institute, The Cancer Genome Atlas (TCGA), and the European Genome-Phenome Archive...
October 24, 2017: Genome Research
https://www.readbyqxmd.com/read/29059177/automated-deconvolution-of-structured-mixtures-from-heterogeneous-tumor-genomic-data
#15
COMPARATIVE STUDY
Theodore Roman, Lu Xie, Russell Schwartz
With increasing appreciation for the extent and importance of intratumor heterogeneity, much attention in cancer research has focused on profiling heterogeneity on a single patient level. Although true single-cell genomic technologies are rapidly improving, they remain too noisy and costly at present for population-level studies. Bulk sequencing remains the standard for population-scale tumor genomics, creating a need for computational tools to separate contributions of multiple tumor clones and assorted stromal and infiltrating cell populations to pooled genomic data...
October 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29054765/characterization-of-germline-mutations-in-familial-lung-cancer-from-the-chinese-population
#16
Madiha Kanwal, Xiao-Jie Ding, Zhans-Han Ma, Lian-Wei Li, Ping Wang, Ying Chen, Yun-Chao Huang, Yi Cao
Compared with numerous studies of somatic mutations using sporadic lung cancer, the research into germline mutations using familial lung cancer (FLC) is limited. In the present study, we used FLC samples obtained from the Chinese population in highly air-polluted regions to screen for novel germline mutations in lung cancer. Through a whole genome sequencing (WGS) analysis of the nine subjects (four lung cancer patients and five normal family members of FLC), we obtained a whole genome dataset of DNA alterations in FLC samples...
October 17, 2017: Gene
https://www.readbyqxmd.com/read/29050365/mitochondrial-genome-variation-and-prostate-cancer-a-review-of-the-mutational-landscape-and-application-to-clinical-management
#17
REVIEW
Anton M F Kalsbeek, Eva K F Chan, Niall M Corcoran, Christopher M Hovens, Vanessa M Hayes
Prostate cancer is a genetic disease. While next generation sequencing has allowed for the emergence of molecular taxonomy, classification is restricted to the nuclear genome. Mutations within the maternally inherited mitochondrial genome are known to impact cancer pathogenesis, as a result of disturbances in energy metabolism and apoptosis. With a higher mutation rate, limited repair and increased copy number compared to the nuclear genome, the clinical relevance of mitochondrial DNA (mtDNA) variation requires deeper exploration...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29048467/identification-of-copy-number-variations-and-translocations-in-cancer-cells-from-hi-c-data
#18
Abhijit Chakraborty, Ferhat Ay
Motivation: Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities (e.g., copy number variations (CNVs) and translocations) altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e...
October 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29047230/a-comprehensive-genome-wide-analysis-of-long-noncoding-rna-expression-profile-in-hepatocellular-carcinoma
#19
Hongxia Cui, Yunxing Zhang, Qiujie Zhang, Wenming Chen, Haibo Zhao, Jun Liang
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, especially in East Asia and China. Long noncoding RNAs (lncRNAs) are emerging as critical regulators that may be involved in the development and progression of cancers in humans. However, the contributions of lncRNAs to HCC development, metastasis, and recurrence remain largely unknown. In this study, we comprehensively investigated lncRNA expression profile in HCC and normal tissues using TCGA RNA sequencing data, one RNA sequencing dataset, and two microarray datasets from GEO...
October 18, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/29039585/identification-of-genome-variations-in-patients-with-lung-adenocarcinoma-using-whole-genome-re%C3%A2-sequencing
#20
Guiyuan Li, Yunqing Mei, Fan Yang, Shengming Yi, Lemin Wang
Lung adenocarcinoma is one of the types of non‑small cell lung carcinoma, which tends to be treated with surgical therapy rather than radiation therapy. It occurs in smokers and non‑smokers, and is the most common form of lung cancer among non‑smokers and women. Gene rearrangements, including ALK, ROS1 and RET, and gene mutations, including epidermal growth factor receptor (EGFR), HER2, Kristen rat sarcoma viral oncogene homolog, BRAF, phosphoinositide‑3‑kinase, catalytic, α polypeptide and MET, have been identified in lung adenocarcinoma, which enable targeted therapy in lung adenocarcinoma, for example erlotinib, gefitinib and afatinib, which are EGFR inhibitors...
December 2017: Molecular Medicine Reports
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