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copy number variation AND cancer

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https://www.readbyqxmd.com/read/28930282/esophageal-cancer-genomic-and-molecular-characterization-stem-cell-compartment-and-clonal-evolution
#1
REVIEW
Ugo Testa, Germana Castelli, Elvira Pelosi
Esophageal cancer (EC) is the eighth most common cancer and is the sixth leading cause of death worldwide. The incidence of histologic subtypes of EC, esophageal adenocarcinoma (EAC) and esophageal squamous carcinoma (ESCC), display considerable geographic variation. EAC arises from metaplastic Barrett's esophagus (BE) in the context of chronic inflammation secondary to exposure to acid and bile. The main risk factors for developing ESCC are cigarette smoking and alcohol consumption. The main somatic genetic abnormalities showed a different genetic landscape in EAC compared to ESCC...
September 14, 2017: Medicines (Basel, Switzerland)
https://www.readbyqxmd.com/read/28927463/towards-precision-medicine-discovering-novel-gynecological-cancer-biomarkers-and-pathways-using-linked-data
#2
Alokkumar Jha, Yasar Khan, Muntazir Mehdi, Md Rezaul Karim, Qaiser Mehmood, Achille Zappa, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
BACKGROUND: Next Generation Sequencing (NGS) is playing a key role in therapeutic decision making for the cancer prognosis and treatment. The NGS technologies are producing a massive amount of sequencing datasets. Often, these datasets are published from the isolated and different sequencing facilities. Consequently, the process of sharing and aggregating multisite sequencing datasets are thwarted by issues such as the need to discover relevant data from different sources, built scalable repositories, the automation of data linkage, the volume of the data, efficient querying mechanism, and information rich intuitive visualisation...
September 19, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28926134/early-genetic-aberrations-in-patients-with-sporadic-colorectal-cancer
#3
Brooke R Druliner, Xiaoyang Ruan, Hugues Sicotte, Daniel O'Brien, Hongfang Liu, Jean-Pierre A Kocher, Lisa Boardman
Chromosome instability (CIN) is widely observed in both sporadic and hereditary colorectal cancer (CRC). Defects in APC and WNT signaling are primarily associated with CIN in hereditary CRC, but the genetic causes for CIN in sporadic CRC remain elusive. Using high-density SNP array and exome data from The Cancer Genome Atlas, we characterized loss of heterozygosity (LOH) and copy number variation (CNV) in the peripheral blood, normal colon and corresponding tumor tissue in 15 CRC patients with proficient mismatch repair (MMR) and 24 CRC patients with deficient MMR...
September 19, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28917518/genome-stability-of-programmed-stem-cell-products
#4
REVIEW
Ulrich Martin
Inherited and acquired genomic abnormalities are known to cause genetic diseases and contribute to cancer formation. Recent studies demonstrated a substantial mutational load in mouse and human embryonic and induced pluripotent stem cells (ESCs and iPSCs). Single nucleotide variants, copy number variations, and larger chromosomal abnormalities may influence the differentiation capacity of pluripotent stem cells and the functionality of their derivatives in disease modelling and drug screening, and are considered a serious risk for cellular therapies based on ESC or iPSC derivatives...
September 13, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/28915599/copy-number-variations-of-circulating-cell-free-dna-in-urothelial-carcinoma-of-the-bladder-patients-treated-with-radical-cystectomy-a-prospective-study
#5
Armin Soave, Felix K-H Chun, Timo Hillebrand, Michael Rink, Lars Weisbach, Bettina Steinbach, Margit Fisch, Klaus Pantel, Heidi Schwarzenbach
The aim of the present study was to establish a rapid profiling method using multiplex ligation-dependent probe amplification (MLPA) and characterize copy number variations (CNV) in circulating, cell-free DNA (cfDNA) in 85 urothelial carcinoma of the bladder (UCB) patients treated with radical cystectomy (RC). MLPA was tested for the use of cfDNA extracted from serum and plasma by various commercial extraction kits. Eighteen probes served as reference to control denaturation, ligation and amplification efficiency...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28913947/extreme-chromosome-17-copy-number-instability-is-a-prognostic-factor-in-patients-with-gastroesophageal-adenocarcinoma-a-retrospective-cohort-study
#6
Jacqueline E Birkness, Neal G Spada, Caitlyn Miller, James D Luketich, Katie S Nason, Weijing Sun, Jon M Davison
Gastric and esophageal cancers frequently show genomic instability and aneuploidy. Chromosomal copy number instability (CIN) is a form of genomic instability that exerts pleiotropic effects on cellular biology and is a source of genetic heterogeneity in a population of cells. CIN results in cell-to-cell variation in chromosome copy number which can be detected and quantified by fluorescence in situ hybridization (FISH). CIN is a biomarker associated with differential response to a number of chemotherapy compounds...
September 14, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28911002/intratumor-heterogeneity-predicts-metastasis-of-triple-negative-breast-cancer
#7
Fang Yang, Yucai Wang, Quan Li, Lulu Cao, Zijia Sun, Juan Jin, Hehui Fang, Aiyu Zhu, Yan Li, Wenwen Zhang, Yanru Wang, Hui Xie, Jan-Åke Gustafsson, Shui Wang, Xiaoxiang Guan
Even with the identical clinicopathological features, the ability for metastasis is vastly different among triple-negative breast cancer (TNBC) patients. Intratumor heterogeneity (ITH), which is common in breast cancer, may be a key mechanism leading to the tumor progression. In this study, we studied whether a quantitative genetic definition of ITH can predict clinical outcomes in patients with TNBC. We quantified ITH by calculating Shannon index, a measure of diversity in a population, based on Myc, epidermal growth factor receptor/centromeric probe 7 (EGFR/CEP7) and cyclin D1/centromeric probe 11 (CCND1/CEP11) copy number variations (CNVs) in 300 cells at three different locations of a tumor...
September 1, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28910969/polymorphisms-of-immunoglobulin-receptors-and-the-effects-on-clinical-outcome-in-cancer-immunotherapy-and-other-immune-diseases-a-general-review
#8
Tomonori Kaifu, Akira Nakamura
Receptors for the Fc domain of immunoglobulins [Fc receptors (FcRs)] are essential for the maintenance of antibody-mediated immune responses. FcRs consist of activating- and inhibitory-type receptors that regulate adequate thresholds for various immune cells. In particular, polymorphisms and/or gene copy-number variations of FcRs for IgG (FcγRs) are closely associated with the development of inflammatory disorders, including autoimmune diseases. Recent evidence has implicated polymorphisms of FcRs in the efficacy of monoclonal antibody (mAb)-mediated therapy...
July 1, 2017: International Immunology
https://www.readbyqxmd.com/read/28910957/-effects-of-cell-cycle-regulatory-genes-on-breast-cancer-neo-adjuvant-chemotherapy-by-m-fish
#9
C Y Li, W Su, S Zhang, Y H Hu, J J Liu, J Zhang
Objective: The dysregulation of cell cycle could influence cell proliferation, differentiation and response to medicine. The purpose of this study is to explore the correlation between cell cycle regulatory genes and breast cancer neo-adjuvant chemotherapy (NAC) in patients with local advanced breast cancer, and thus to find some predictors of NAC to provide guidance for clinical treatment. Methods: Ninety five cases of local advanced breast cancer were collected, which were treated with NAC of TAC (Taxanes/Anthracycline/Cyclophosphamide) regimen...
September 12, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/28904201/heterogeneity-of-the-epstein-barr-virus-major-internal-repeat-reveals-evolutionary-mechanisms-of-ebv-and-a-functional-defect-in-the-prototype-ebv-strain-b95-8
#10
Mohammed Ba Abdullah, Richard Palermo, Anne Palser, Nicholas E Grayson, Paul Kellam, Samantha Correia, Agnieszka Szymula, Rob White
Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified both through co-evolution with its host, and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging, because of the large number and length of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat of EBV (IR1 or BamW repeats) from over 70 strains...
September 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28901451/genomic-profile-of-oral-squamous-cell-carcinomas-with-an-adjacent-leukoplakia-or-with-an-erythroleukoplakia-that-evolved-after-the-treatment-of-primary-tumor-a-report-of-two-cases
#11
Ilda P Ribeiro, Francisco Marques, Leonor Barroso, Joana Rodrigues, Francisco Caramelo, Joana B Melo, Isabel M Carreira
Oral leukoplakia and erythroleukoplakia are common oral potentially malignant disorders diagnosed in the oral cavity. The specific outcome of these lesions remains to be elucidated, as their malignant transformation rate exhibits great variation. The ability to predict which of those potentially malignant lesions are likely to progress to cancer would be vital to guide their future clinical management. The present study reported two patients with tongue squamous cell carcinoma: Case study 1 was diagnosed with a simultaneous leukoplakia and case study 2 developed an erythroleukoplakia following the primary tumor treatment...
September 5, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28888996/mutations-of-rna-splicing-factors-in-hematological-malignancies
#12
Girish C Shukla, Jagjit Singh
Systematic large-scale cancer genomic studies have produced numerous significant findings. These studies have not only revealed new cancer-promoting genes, but they also have identified cancer-promoting functions of previously known "housekeeping" genes. These studies have identified numerous mutations in genes which play a fundamental role in nuclear precursor mRNA splicing. Somatic mutations and copy number variation in many of the splicing factors which participate in the formation of multiple spliceosomal complexes appear to play a role in many cancers and in particular in myelodysplastic syndromes (MDS)...
September 6, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28882566/genetic-variations-in-ugt2b28-ugt2b17-ugt2b15-genes-and-the-risk-of-prostate-cancer-a-case-control-study
#13
Mohsen Habibi, Reza Mirfakhraie, Maryam Khani, Azadeh Rakhshan, Eznollah Azargashb, Farkhondeh Pouresmaeili
Glucuronidation is a major pathway for elimination of exogenous and endogenous compounds such as environmental carcinogens and androgens from the body. This biochemical pathway is mediated by enzymes called uridine diphosphoglucuronosyltransferases (UGTs). Null (del/del) genes polymorphisms in UGT2B17, and UGT2B28 and D85Y single-nucleotide polymorphism (SNP) of UGT2B15 have been reported to increase the risk of prostate cancer. The goal of this study was to determine the association of mentioned genetic variants with the risk of prostate cancer...
September 4, 2017: Gene
https://www.readbyqxmd.com/read/28882180/high-performance-of-targeted-next-generation-sequencing-on-variance-detection-in-clinical-tumor-specimens-in-comparison-with-current-conventional-methods
#14
Dan Su, Dadong Zhang, Kaiyan Chen, Jing Lu, Junzhou Wu, Xinkai Cao, Lisha Ying, Qihuang Jin, Yizhou Ye, Zhenghua Xie, Lei Xiong, Weimin Mao, Fugen Li
BACKGROUND: Next generation sequencing (NGS) is being increasingly applied for assisting cancer molecular diagnosis. However, it is still needed to validate NGS accuracy on detection of DNA alternations based on a large number of clinical samples, especially for DNA rearrangements and copy number variations (CNVs). This study is to set up basic parameters of targeted NGS for clinical diagnosis and to understand advantage of targeted NGS in comparison with the conventional methods of molecular diagnosis...
September 7, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28880866/ribosomal-dna-copy-number-amplification-and-loss-in-human-cancers-is-linked-to-tumor-genetic-context-nucleolus-activity-and-proliferation
#15
Meng Wang, Bernardo Lemos
Ribosomal RNAs (rRNAs) are transcribed from two multicopy DNA arrays: the 5S ribosomal DNA (rDNA) array residing in a single human autosome and the 45S rDNA array residing in five human autosomes. The arrays are among the most variable segments of the genome, exhibit concerted copy number variation (cCNV), encode essential components of the ribosome, and modulate global gene expression. Here we combined whole genome data from >700 tumors and paired normal tissues to provide a portrait of rDNA variation in human tissues and cancers of diverse mutational signatures, including stomach and lung adenocarcinomas, ovarian cancers, and others of the TCGA panel...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28879097/signatures-derived-from-increase-in-sharpin-gene-copy-number-are-associated-with-poor-prognosis-in-patients-with-breast-cancer
#16
Diane Ojo, Maryam Seliman, Damu Tang
We report three signatures produced from SHARPIN gene copy number increase (GCN-Increase) and their effects on patients with breast cancer (BC). In the Metabric dataset (n = 2059, cBioPortal), SHARPIN GCN-Increase occurs preferentially or mutual exclusively with mutations in TP53, PIK3CA, and CDH1. These genomic alterations constitute a signature (SigMut) that significantly correlates with reductions in overall survival (OS) in BC patients (n = 1980; p = 1.081e - 6). Additionally, SHARPIN GCN-Increase is associated with 4220 differentially expressed genes (DEGs)...
December 2017: BBA Clinical
https://www.readbyqxmd.com/read/28875717/sult1a1-copy-number-variation-ethnic-distribution-analysis-in-indian-population
#17
Suhani Almal, Harish Padh
Cytosolic sulfotransferases (SULTs) are phase II detoxification enzymes involved in metabolism of numerous xenobiotics, drugs, and endogenous compounds. Interindividual variation in sulfonation capacity is important for determining an individual's response to xenobiotics. SNPs in SULTs, mainly SULT1A1 have been associated with cancer risk and also with response to therapeutic agents. Copy number variation (CNVs) in SULT1A1 is found to be correlated with altered enzyme activity. This short report primarily focuses on CNV in SULT1A1 and its distribution among different ethnic populations around the globe...
September 6, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28874807/integrated-analysis-of-copy-number-variations-and-gene-expression-profiling-in-hepatocellular-carcinoma
#18
Chenhao Zhou, Wentao Zhang, Wanyong Chen, Yirui Yin, Manar Atyah, Shuang Liu, Lei Guo, Yi Shi, Qinghai Ye, Qiongzhu Dong, Ning Ren
Hepatocellular carcinoma (HCC) is one of the top three cancer killers worldwide. To identify CNV-driven differentially expressed genes (DEGs) in HBV related HCC, this study integrated analysis of copy number variations (CNVs) and gene expression profiling. Significant genes in regions of CNVs were overlapped with those obtained from the expression profiling. 93 CNV-driven genes exhibiting increased expression in the duplicated regions and 45 showing decreased expression in the deleted regions were obtained, which duplications and deletions were mainly documented at chromosome 1 and 4...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28862264/sox2-silenced-squamous-cell-carcinoma-a-highly-malignant-form-of-esophageal-cancer-with-sox2-promoter-hypermethylation
#19
Ritsuko Maehara, Kohei Fujikura, Kengo Takeuchi, Masayuki Akita, Shiho Abe-Suzuki, Jana Karbanová, Denis Corbeil, Tomoo Itoh, Yoshihiro Kakeji, Yoh Zen
This study originally aimed to investigate whether the overexpression of SOX2 is associated with the poor prognosis of patients with squamous cell carcinoma of the esophagus. However, we unexpectedly found that esophageal squamous cell carcinomas completely lacking SOX2 expression showed distinct pathologic features and highly aggressive clinical courses. The study cohort consisted of 113 consecutive patients with esophageal squamous cell carcinoma who underwent surgical resection without neoadjuvant therapy...
September 1, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28857495/identification-of-dysregulated-lncrnas-profiling-and-metastasis-associated-lncrnas-in-colorectal-cancer-by-genome-wide-analysis
#20
Yan Chen, Xiang Yu, Yongcan Xu, Hua Shen
The colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide, but the pathogenesis of CRC remains not well-known. Increasing studies have highlighted the critical roles of long noncoding RNAs (lncRNAs) in tumorigenesis and cancer cells metastasis, however, the expression pattern, biological roles of lncRNAs, and the mechanisms responsible for their function in CRC remain elusive. In this study, we performed a genome-wide comprehensive analysis of lncRNAs profiling and clinical relevance to identify novel lncRNAs for the further study in CRC...
August 31, 2017: Cancer Medicine
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