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copy number variation AND cancer

Kelly Kyker-Snowman, Bracha Erlanger Avigdor, Mansoor Nasim, Ashley Cimino-Mathews, Sarah J Wheelan, Pedram Argani, Ben Ho Park
BACKGROUND/PURPOSE: Tumor heterogeneity is a now well-recognized phenomenon that can affect the classification, prognosis and treatment of human cancers. Heterogeneity is often described in primary breast cancers based upon histologic subtypes, hormone- and HER2-receptor status, and immunolabeling for various markers, which can be seen within a single tumor as mixed cellular populations, or as separate discrete foci. EXPERIMENTAL DESIGN/METHODS: Here, we present a case report of a patient's primary breast cancer that had two separate but adjacent histologic components, one that was estrogen receptor (ER) positive, and the other ER negative...
March 15, 2018: Breast Cancer Research and Treatment
Chen Su, Daojiang Li, Nanpeng Li, Yuheng Du, Chunxing Yang, Yang Bai, Changwei Lin, Xiaorong Li, Yi Zhang
Pleomorphic adenoma gene like-2 (PLAGL2) is a zinc finger protein transcription factor, which is upregulated and serves an oncogenic function in multiple human malignancies, including colorectal cancer (CRC). First, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression levels of PLAGL2 in CRC tissues and normal tissues. Then, bioinformatics analysis, RT-qPCR, western blotting, luciferase reporter assays and RNA-binding protein immunoprecipitation assays were performed to explore whether the underlying mechanisms, including copy number variation (CNV), microRNAs (miRNAs/miRs) and RNA-binding proteins (RBPs) led to the abnormal expression of PLAGL2...
March 6, 2018: International Journal of Oncology
Renu Verma, Prakash C Sharma
Gastric cancer (GC) is one of the leading causes of cancer related mortality in the world. Being asymptomatic in nature till advanced stage, diagnosis of gastric cancer becomes difficult in early stages of the disease. The onset and progression of gastric cancer has been attributed to multiple factors including genetic alterations, epigenetic modifications, Helicobacter pylori and Epstein-Barr Virus (EBV) infection, and dietary habits. Next Generation Sequencing (NGS) based approaches viz . Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), RNA-Seq, and targeted sequencing have expanded the knowledge base of molecular pathogenesis of gastric cancer...
2018: American Journal of Cancer Research
Bruna R S Correa, Joanna Hu, Luiz O F Penalva, Richard Schlegel, David L Rimm, Pedro A F Galante, Seema Agarwal
Preclinical in vitro models provide an essential tool to study cancer cell biology as well as aid in translational research, including drug target identification and drug discovery efforts. For any model to be clinically relevant, it needs to recapitulate the biology and cell heterogeneity of the primary tumor. We recently developed and described a conditional reprogramming (CR) cell technology that addresses many of these needs and avoids the deficiencies of most current cancer cell lines, which are usually clonal in origin...
March 6, 2018: Scientific Reports
A M Rose, A Krishan, C F Chakarova, L Moya, S Chambers, M Hollands, J C Illingworth, S M G Williams, H E James, A Z Shah, C N A Palmer, A Chakravarti, J N Berg, J Batra, S S Bhattacharya
Background: MSR1 repeats are a 36-38bp minisatellite element that have recently been implicated in the regulation of gene expression, through copy number variation (CNV). Patients and methods: Bioinformatic and experimental methods were used to assess the distribution of MSR1 across the genome, evaluate the regulatory potential of such elements and explore the role of MSR1 elements in cancer, particularly non-familial breast cancer and prostate cancer. Results: MSR1s are predominately located at chromosome 19 and are functionally enriched in regulatory regions of the genome, particularly regions implicated in short-range regulatory activities (H3K27ac, H3K4me1, and H3K4me3)...
March 2, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Inyoung Kim, Saemi Choi, Sun Kim
BACKGROUND: Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcriptome data with pathway based interpretation. Over the years, the amount of omics data has become huge, e.g., TCGA, and the data types to be analyzed have come in many varieties, including mutations, copy number variations, and transcriptome. We also need to consider a complex relationship with regulators of genes, particularly Transcription Factors(TF)...
February 19, 2018: BMC Bioinformatics
Yuzhuo Wang, Cheng Wang, Jiahui Zhang, Meng Zhu, Xu Zhang, Zhihua Li, Juncheng Dai, Hongxia Ma, Zhibin Hu, Guangfu Jin, Hongbing Shen
Emerging evidence indicates that germline variations may interact with somatic events in carcinogenesis. However, the germline-somatic interaction in lung cancer remains largely unknown. We investigated whether lung cancer driver genes (CDGs) were more likely to locate within cancer susceptibility regions. Pathway analysis was performed to identify common pathways underlying CDGs and cancer susceptibility genes (CSGs). Next, we analyzed the associations between lung cancer risk SNPs and somatic alterations, including mutations and copy number alterations, in the level of genes, pathways, and overall burden of alterations...
March 1, 2018: International Journal of Cancer. Journal International du Cancer
Maria Cristina Sini, Valentina Doneddu, Panagiotis Paliogiannis, Milena Casula, Maria Colombino, Antonella Manca, Gerardo Botti, Paolo A Ascierto, Amelia Lissia, Antonio Cossu, Giuseppe Palmieri
Cutaneous melanoma is a common and aggressive human skin cancers. Much is actually known about the molecular mechanisms underlying melanoma pathogenesis. The aim of the study was to evaluate any possible correlation between mutations in main growth-controlling genes ( BRAF, NRAS, CDKN2A ) and copy number variations in frequently amplified candidate genes ( MITF, EGFR, CCND1, cMET, and cKIT ) during melanoma initiation and progression. A large series of primary and secondary melanoma tissue samples ( N = 274) from 232 consecutively-collected patients of Italian origin as well as 32 tumor cell lines derived from primary and metastatic melanomas underwent mutation screening and fluorescence in situ hybridization (FISH) analysis...
February 2, 2018: Oncotarget
Amélie Osio, Shuo Xu, Morad El Bouchtaoui, Christophe Leboeuf, Guillaume Gapihan, Christine Lemaignan, Guilhem Bousquet, Céleste Lebbé, Anne Janin, Maxime Battistella
Dermatofibrosarcoma protuberans (DFSP), amounting to 6% of all soft tissue sarcomas, has a slow growth rate, contrasting with a likelihood for local recurrence and a 10-20% evolution to higher-grade sarcoma, or "transformed DFSP" (DFSP-T). At molecular level, the characteristic COL1A1-PDGFB rearrangement, leading to sustained PDGFR signaling, is not linked to the evolutive potential. Here, we studied EGFR, another tyrosine kinase receptor, using laser-microdissection to select the different histologic components of DFSP (DFSP center, DFSP infiltrative periphery, DFSP-T higher-grade sarcoma), in 22 patients followed over 3 to 156 months...
February 2, 2018: Oncotarget
Xiaotu Ma, Yu Liu, Yanling Liu, Ludmil B Alexandrov, Michael N Edmonson, Charles Gawad, Xin Zhou, Yongjin Li, Michael C Rusch, John Easton, Robert Huether, Veronica Gonzalez-Pena, Mark R Wilkinson, Leandro C Hermida, Sean Davis, Edgar Sioson, Stanley Pounds, Xueyuan Cao, Rhonda E Ries, Zhaoming Wang, Xiang Chen, Li Dong, Sharon J Diskin, Malcolm A Smith, Jaime M Guidry Auvil, Paul S Meltzer, Ching C Lau, Elizabeth J Perlman, John M Maris, Soheil Meshinchi, Stephen P Hunger, Daniela S Gerhard, Jinghui Zhang
Analysis of molecular aberrations across multiple cancer types, known as pan-cancer analysis, identifies commonalities and differences in key biological processes that are dysregulated in cancer cells from diverse lineages. Pan-cancer analyses have been performed for adult but not paediatric cancers, which commonly occur in developing mesodermic rather than adult epithelial tissues. Here we present a pan-cancer study of somatic alterations, including single nucleotide variants, small insertions or deletions, structural variations, copy number alterations, gene fusions and internal tandem duplications in 1,699 paediatric leukaemias and solid tumours across six histotypes, with whole-genome, whole-exome and transcriptome sequencing data processed under a uniform analytical framework...
February 28, 2018: Nature
Mitra Mehrad, Somak Roy, William A LaFramboise, Patti Petrosko, Caitlyn Miller, Pimpin Incharoen, Sanja Dacic
Pulmonary Sarcomatoid Carcinoma (PSC) is a poorly-differentiated non-small cell lung carcinoma (NSCLC) with aggressive behavior. This study aimed to evaluate the prognostic clinicopathologic and genetic characteristics of PSCs. Fifty-three cases of surgically treated PSCs were selected, of which 23 were subjected to mutation and copy number variation analysis using 50-gene Ion AmpliSeq Cancer Panel. Majority of the patients were male (32/53, 60.3%) and smoker (51/53, 96.2%). Overall, 25 (47.1%) patients died within 2 to 105 months (mean 22...
February 28, 2018: Histopathology
Liming Wang, Hui Shen, Da Zhu, Bei Feng, Lan Yu, Xun Tian, Ci Ren, Chun Gao, Xiaomin Li, Ding Ma, Zheng Hu, Hui Wang
Integration of the high risk human papillomavirus (HR-HPV) genome into host chromatin is an important step in cervical carcinogenesis. We identified HR-HPV integration sites within the human genome through detection of integrated papillomavirus sequences-PCR and assessed the role of high mobility group A 2 (HMGA2) in cervical carcinogenesis in clinical samples and cell lines. HPV integration sites were analyzed in 40 cervical cancer samples, while copy number variation and protein expression were assessed in 19 normal cervixes, 49 cervical intraepithelial neoplasia (CIN), and 52 cervical cancer samples...
January 30, 2018: Oncotarget
Ling Tan, Yerong Hu, Yongguang Tao, Bin Wang, Jun Xiao, Zhenjie Tang, Ting Lu, Hao Tang
BACKGROUND: To identify whether RET is a potential target for NSCLC treatment, we examined the status of the RET gene in 631 early and mid stage NSCLC cases from south central China. METHODS: RET expression was identified by Western blot. RET-positive expression samples were verified by immunohistochemistry. RET gene mutation, copy number variation, and rearrangement were analyzed by DNA Sanger sequencing, TaqMan copy number assays, and reverse transcription-PCR...
February 23, 2018: Thoracic Cancer
Akishi Ooi, Takeru Oyama
The CCND1 locus is located in 11q13 and encodes the G1-S regulatory protein, cyclin D1. Cyclin D1 is frequently amplified in various types of cancers, and is an attractive potential therapeutic target. Multiplex ligation-dependent probe amplification (MLPA) is a new, high-resolution method for the detection of amplification of numerous genes including CCND1 in small amounts of DNA fragments derived from formalin-fixed, paraffin-embedded material in a single reaction. This approach is, however, based on PCR and averages many different cells, so validation by morphological methods such as fluorescence in situ hybridization (FISH) is theoretically mandatory...
2018: Methods in Molecular Biology
Julie Johnson, Darrell C Bessette, Jodi M Saunus, Chanel E Smart, Sarah Song, Rebecca L Johnston, Sibylle Cocciardi, Esdy N Rozali, Cameron N Johnstone, Ana Christina Vargas, Stephen H Kazakoff, Victorian Cancer BioBank, Kum Kum Khanna, Sunil R Lakhani, Georgia Chenevix-Trench, Peter T Simpson, Katia Nones, Nicola Waddell, Fares Al-Ejeh
PURPOSE: We aimed to generate and characterize a novel cell line from a breast cancer bone metastasis to better study the progression of the disease. METHODS: The cell line, P7731, was derived from a metastatic bone lesion of a breast cancer patient and assessed for marker expression. P7731 was analyzed for DNA copy number variation, somatic mutations, and gene expression and was compared with the primary tumor. RESULTS: P7731 cells are negative for estrogen receptor alpha (ERα), progesterone receptor (PR), and HER2 (triple-negative); strongly express vimentin (100% of cells positive) and also express cytokeratins 8/18 and 19 but at lower frequencies...
February 21, 2018: Breast Cancer Research and Treatment
Minsoo Kim, Brooke R Druliner, Nikolaos Vasmatzis, Taejeong Bae, Nicholas Chia, Alexej Abyzov, Lisa A Boardman
Besides the classical evolutionary model of colorectal cancer (CRC) defined by the stepwise accumulation of mutations in which normal epithelium transforms through an intermediary polyp stage to cancer, a few studies have proposed alternative modes of evolution (MOE): early eruptive subclonal expansion, branching of the subclones in parallel evolution, and neutral evolution. However, frequencies of MOEs and their connection to mutational characteristics of cancer remain elusive. In this study, we analyzed patterns of somatic single nucleotide variations (SNVs) and copy number aberrations (CNAs) in CRC with residual polyp of origin from 13 patients in order to determine this relationship...
January 23, 2018: Oncotarget
Jun-Feng Xu, Qian Kang, Xing-Yong Ma, Yuan-Ming Pan, Lang Yang, Peng Jin, Xin Wang, Chen-Guang Li, Xiao-Chen Chen, Chao Wu, Shao-Zhuo Jiao, Jian-Qiu Sheng
BACKGROUND/AIMS: Colonoscopy screening has been accepted broadly to evaluate the risk and incidence of colorectal cancer (CRC) during health examination in outpatients. However, the intrusiveness, complexity and discomfort of colonoscopy may limit its application and the compliance of patients. Thus, more reliable and convenient diagnostic methods are necessary for CRC screening. Genome instability, especially copy-number variation (CNV), is a hallmark of cancer and has been proved to have potential in clinical application...
February 16, 2018: Cellular Physiology and Biochemistry
YongKiat Wee, Yining Liu, Jiachun Lu, Xiaoyan Li, Min Zhao
Prognosis identifies the seriousness and the chances of survival of a cancer patient. However, it remains a challenge to identify the key cancer genes in prognostic studies. In this study, we collected 2064 genes that were related to prognostic studies by using gene expression measurements curated from published literatures. Among them, 1820 genes were associated with copy number variations (CNVs). The further functional enrichment on 889 genes with frequent copy number gains (CNGs) revealed that these genes were significantly associated with cancer pathways including regulation of cell cycle, cell differentiation and mitogen-activated protein kinase (MAPK) cascade...
February 19, 2018: Scientific Reports
Paola Concolino, Roberta Rizza, Flavio Mignone, Alessandra Costella, Donatella Guarino, Ilaria Carboni, Ettore Capoluongo, Concetta Santonocito, Andrea Urbani, Angelo Minucci
No abstract text is available yet for this article.
February 16, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
Paulina Cybulska, Jocelyn M Stewart, Azin Sayad, Carl Virtanen, Patricia A Shaw, Blaise Clarke, Natalie Stickle, Marcus Q Bernardini, Benjamin G Neel
High-grade serous ovarian cancer (HGSC) is the leading cause of morbidity and mortality from gynecologic malignancy. Overall survival remains low, due to the nearly ubiquitous emergence of platinum-resistance and the paucity of effective next-line treatments. Current cell culture-based models show limited similarity to HGSC and are therefore unreliable predictive models for pre-clinical evaluation of investigational drugs. This deficiency could help explain the low overall rate of successful drug development and the decades of largely unchanged approaches to HGSC treatment...
February 16, 2018: American Journal of Pathology
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