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copy number variation AND cancer

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https://www.readbyqxmd.com/read/29776329/convaq-a-web-tool-for-copy-number-variation-based-association-studies
#1
Simon Jonas Larsen, Luisa Matos do Canto, Silvia Regina Rogatto, Jan Baumbach
BACKGROUND: Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. RESULTS: We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29767721/bhd-associated-kidney-cancer-exhibits-unique-molecular-characteristics-and-a-wide-variety-of-variants-in-chromatin-remodeling-genes
#2
Hisashi Hasumi, Mitsuko Furuya, Kenji Tatsuno, Shogo Yamamoto, Masaya Baba, Yukiko Hasumi, Yasuhiro Isono, Kae Suzuki, Ryosuke Jikuya, Shinji Otake, Kentaro Muraoka, Kimito Osaka, Narihiko Hayashi, Kazuhide Makiyama, Yasuhide Miyoshi, Keiichi Kondo, Noboru Nakaigawa, Takashi Kawahara, Koji Izumi, Junichi Teranishi, Yasushi Yumura, Hiroji Uemura, Yoji Nagashima, Adam R Metwalli, Laura S Schmidt, Hiroyuki Aburatani, W Marston Linehan, Masahiro Yao
Birt-Hogg-Dubé (BHD) syndrome is a hereditary kidney cancer syndrome, which predisposes patients to develop kidney cancer, cutaneous fibrofolliculomas and pulmonary cysts. The responsible gene FLCN is a tumor suppressor for kidney cancer which plays an important role in energy homeostasis through the regulation of mitochondrial oxidative metabolism. However, the process by which FLCN-deficiency leads to renal tumorigenesis is unclear. In order to clarify molecular pathogenesis of BHD-associated kidney cancer, we conducted whole-exome sequencing analysis using next-generation sequencing technology as well as metabolite analysis using LC/MS and GC/MS...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29760470/breast-cancer-associated-germline-structural-variants-harboring-small-noncoding-rnas-impact-post-transcriptional-gene-regulation
#3
Mahalakshmi Kumaran, Preethi Krishnan, Carol E Cass, Roland Hubaux, Wan Lam, Yutaka Yasui, Sambasivarao Damaraju
Copy Number Variants (CNVs) are a class of structural variations of DNA. Germline CNVs are known to confer disease susceptibility, but their role in breast cancer warrants further investigations. We hypothesized that breast cancer associated germline CNVs contribute to disease risk through gene dosage or other post-transcriptional regulatory mechanisms, possibly through tissue specific expression of CNV-embedded small-noncoding RNAs (CNV-sncRNAs). Our objectives are to identify breast cancer associated CNVs using a genome wide association study (GWAS), identify sncRNA genes embedded within CNVs, confirm breast tissue (tumor and normal) expression of the sncRNAs, correlate their expression with germline copy status and identify pathways influenced by the genes regulated by sncRNAs...
May 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29760279/histone-h3k27-methylation-is-required-for-nhej-and-genome-stability-by-modulating-the-dynamics-of-fancd2-on-chromatin
#4
Ye Zhang, Jian-Feng Chang, Jin Sun, Lu Chen, Xiao-Mei Yang, Huan-Yin Tang, Yuan-Ya Jing, Xuan Kang, Zhi-Min He, Jun-Yu Wu, Hui-Min Wei, Da-Liang Wang, Rong-Gang Xu, Rui-Bao Zhu, Ying Shen, Shi-Yang Zeng, Chen Wang, Kui-Nan Liu, Yong Zhang, Zhi-Ying Mao, Ci-Zhong Jiang, Fang-Lin Sun
Dysregulation of homeostatic balance in di- and tri-methyl H3K27 levels or that caused by mis-sense mutations of histone H3 (H3K27M) was reported to be associated with various types of cancers. In this study, we found that reduction in H3K27me2/3 caused by H3.1K27M, a mutation of H3 variants found in DIPG patients, dramatically attenuated the presence of 53BP1 foci and NHEJ repair capability in HDF cells. H3.1K27M cells showed increased rates of genomic insertions/deletions (In/Dels) and copy number variations (CNVs), as well as augmented p53-dependent apoptotic cells...
May 14, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29754608/multiplex-polymerase-chain-reaction-in-combination-with-gel-electrophoresis-inductively-coupled-plasma-mass-spectrometry-a-powerful-tool-for-the-determination-of-gene-copy-number-variations-and-gene-expression-changes
#5
A Fernández Asensio, T Iglesias, A Cotarelo, M Espina, E Blanco-González, L M Sierra, M Montes-Bayón
During the last few years multiplex real-time or quantitative polymerase chain reaction PCR (qPCR) has become the method of choice for multiplex gene expression changes and gene copy number variations (CNVs) analysis. However, such determinations require the use of different fluorescent labels for the different amplified sequences, which increases significantly the costs of the analysis and limits the applicability of the technique for simultaneous amplification of many targets of interest in a single reaction...
September 6, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29751042/next-generation-sequencing-analysis-for-gastric-adenocarcinoma-with-enteroblastic-differentiation-emphasis-on-the-relationship-with-hepatoid-adenocarcinoma
#6
Yoichi Akazawa, Tsuyoshi Saito, Takuo Hayashi, Yuka Yanai, Sho Tsuyama, Keisuke Akaike, Yoshiyuki Suehara, Fumiyuki Takahashi, Kazuya Takamochi, Hiroya Ueyama, Takashi Murakami, Sumio Watanabe, Akihito Nagahara, Takashi Yao
Histologically tubulo-papillary structures with glycogen-rich clear cytoplasm in gastric adenocarcinoma with enteroblastic differentiation (GAED) are well-known, but a solid growth pattern can also be observed as a minor component. In contrast, hepatoid adenocarcinoma (HAC) of the stomach shows many overlapping features, including solid pattern and alpha-fetoprotein expression. In this study, we employed next-generation sequencing (NGS) to establish a molecular/clinicopathological concept of GAED and clarify whether these two tumors should be grouped together in one category...
May 8, 2018: Human Pathology
https://www.readbyqxmd.com/read/29748005/genomic-alterations-of-plasma-cell-free-dnas-in-small-cell-lung-cancer-and-their-clinical-relevance
#7
Meijun Du, Jonathan Thompson, Hannah Fisher, Peng Zhang, Chiang-Ching Huang, Liang Wang
OBJECTIVES: To identify genomic variations in cell-free DNA (cfDNA) and evaluate their clinical utility in small cell lung cancer (SCLC). MATERIALS AND METHODS: We performed whole genome sequencing using plasma cfDNAs derived from 24 SCLC patients for copy number variation (CNV) analysis, and targeted sequencing using 17 pairs of plasma cfDNA and their matched gDNA for mutation analysis. We defined somatic mutations by comparing cfDNA to its matched gDNA with 5% variant alleles as the cutoff for mutation calls...
June 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29743853/mitochondrial-dna-copy-number-instability-in-erbb2-amplified-breast-cancer-tumors
#8
Elmira Ebrahimi, Amir Almasi-Hashiani, Kimia Ghaffari, Reza Shirkoohi
Increase in the copy number of ERBB2 , a Tyrosine Kinase Receptor (TKR) leads to the overexpression of oncogene product and consequently uncontrolled cell proliferation which has been reported in different aggressive cancers with mitochondrial malfunctions. Although, amplification of ERBB2 has been reported in different studies; however, the association between changes in mitochondrial DNA content and the ERBB2 gene copy number is poorly understood. The relative mitochondrial DNA content of breast cancer tumor tissues of 70 patients who were referred to Imam Khomeini Hospital Complex was determined using quantitative Real-time PCR...
2018: EXCLI Journal
https://www.readbyqxmd.com/read/29743053/pdxliver-a-database-of-liver-cancer-patient-derived-xenograft-mouse-models
#9
Sheng He, Bo Hu, Chao Li, Ping Lin, Wei-Guo Tang, Yun-Fan Sun, Fang-You-Min Feng, Wei Guo, Jia Li, Yang Xu, Qian-Lan Yao, Xin Zhang, Shuang-Jian Qiu, Jian Zhou, Jia Fan, Yi-Xue Li, Hong Li, Xin-Rong Yang
BACKGROUND: Liver cancer is the second leading cause of cancer-related deaths and characterized by heterogeneity and drug resistance. Patient-derived xenograft (PDX) models have been widely used in cancer research because they reproduce the characteristics of original tumors. However, the current studies of liver cancer PDX mice are scattered and the number of available PDX models are too small to represent the heterogeneity of liver cancer patients. To improve this situation and to complement available PDX models related resources, here we constructed a comprehensive database, PDXliver, to integrate and analyze liver cancer PDX models...
May 9, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29740534/genomic-dna-methylation-derived-algorithm-enables-accurate-detection-of-malignant-prostate-tissues
#10
Erfan Aref-Eshghi, Laila C Schenkel, Peter Ainsworth, Hanxin Lin, David I Rodenhiser, Jean-Claude Cutz, Bekim Sadikovic
Introduction: The current methodology involving diagnosis of prostate cancer (PCa) relies on the pathology examination of prostate needle biopsies, a method with high false negative rates partly due to temporospatial, molecular, and morphological heterogeneity of prostate adenocarcinoma. It is postulated that molecular markers have a potential to assign diagnosis to a considerable portion of undetected prostate tumors. This study examines the genome-wide DNA methylation changes in PCa in search of genomic markers for the development of a diagnostic algorithm for PCa screening...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29736010/mps1-inhibitors-synergise-with-low-doses-of-taxanes-in-promoting-tumour-cell-death-by-enhancement-of-errors-in-cell-division
#11
Ana Rita R Maia, Simon Linder, Ji-Ying Song, Chantal Vaarting, Ute Boon, Colin E J Pritchard, Arno Velds, Ivo J Huijbers, Olaf van Tellingen, Jos Jonkers, René H Medema
BACKGROUND: Chromosomal instability (CIN) is a common trait of cancer characterised by the continuous gain and loss of chromosomes during mitosis. Excessive levels of CIN can suppress tumour growth, providing a possible therapeutic strategy. The Mps1/TTK kinase has been one of the prime targets to explore this concept, and indeed Mps1 inhibitors synergise with the spindle poison docetaxel in inhibiting the growth of tumours in mice. METHODS: To investigate how the combination of docetaxel and a Mps1 inhibitor (Cpd-5) promote tumour cell death, we treated mice transplanted with BRCA1-/- ;TP53-/- mammary tumours with docetaxel and/or Cpd-5...
May 8, 2018: British Journal of Cancer
https://www.readbyqxmd.com/read/29735413/dna-methylation-patterns-in-normal-tissue-correlate-more-strongly-with-breast-cancer-status-than-copy-number-variants
#12
Yang Gao, Martin Widschwendter, Andrew E Teschendorff
Normal tissue at risk of neoplastic transformation is characterized by somatic mutations, copy-number variation and DNA methylation changes. It is unclear however, which type of alteration may be more informative of cancer risk. We analyzed genome-wide DNA methylation and copy-number calls from the same DNA assay in a cohort of healthy breast samples and age-matched normal samples collected adjacent to breast cancer. Using statistical methods to adjust for cell type heterogeneity, we show that DNA methylation changes can discriminate normal-adjacent from normal samples better than somatic copy-number variants...
May 4, 2018: EBioMedicine
https://www.readbyqxmd.com/read/29726617/copy-number-variant-analysis-using-genome-wide-mate-pair-sequencing
#13
James B Smadbeck, Sarah H Johnson, Stephanie A Smoley, Athanasios Gaitatzes, Travis M Drucker, Roman M Zenka, Farhad Kosari, Stephen J Murphy, Nicole Hoppman, Umut Aypar, William R Sukov, Robert B Jenkins, Hutton M Kearney, Andrew L Feldman, George Vasmatzis
Copy number variation (CNV) is a common form of structural variation detected in human genomes, occurring as both constitutional and somatic events. Cytogenetic techniques like chromosomal microarray (CMA) are widely used in analyzing CNVs. However, CMA techniques cannot resolve the full nature of these structural variations (i.e. the orientation and location of associated breakpoint junctions) and must be combined with other cytogenetic techniques, such as karyotyping or FISH, to do so. This makes the development of a next-generation sequencing (NGS) approach capable of resolving both CNVs and breakpoint junctions desirable...
May 4, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29725535/defects-in-homologous-recombination-repair-genes-are-associated-with-good-prognosis-and-clinical-sensitivity-to-dna-damaging-agents-in-pancreatic-cancer-a-case-report
#14
Amir Sonnenblick, Aviad Zick, Myriam Maoz, Sherri Cohen, Luna Kadouri, Tamar Peretz, Ayala Hubert
Tumor genome sequencing is important for increasing our understanding of the development of cancer, which may be affected by different therapies. In the present study, genomic evolution was investigated in a patient with stage IV pancreatic cancer bearing a germline breast cancer 2 ( BRCA2 ) mutation. The patient received cisplatin, a DNA cross-linking agent, which led to a long-lasting complete response. Eventually the patient developed brain metastasis, suggesting the acquisition of resistance to cisplatin...
May 2018: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/29724815/biomarker-assessment-of-hr-deficiency-tumor-brca1-2-mutations-and-ccne1-copy-number-in-ovarian-cancer-associations-with-clinical-outcome-following-platinum-monotherapy
#15
Euan A Stronach, James Paul, Kirsten M Timms, Elisha Hughes, Krystal Brown, Chris Neff, Michael Perry, Alexander Gutin, Mona El-Bahrawy, Jennifer H Steel, Xinxue Liu, Liz-Anne Lewsley, Nadeem Siddiqui, Hani Gabra, Jerry S Lanchbury, Robert Brown
The current study evaluated three biomarkers [homologous recombination deficiency (HRD), tumor BRCA1/2 (tBRCA) mutations, and CCNE1 copy number variation (CNV)] in ovarian tumors from patients enrolled on the SCOTROC4 clinical trial for associations with outcome following carboplatinum monotherapy. Ovarian tumors (n=250), with high-grade serous (HGSOC) subgroup analysis (n=179), were classified as HRD positive (HRD score ≥42 or tBRCA mutation) and as CCNE1 amplification positive (CCNE1 CNV score >2.4)...
May 3, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29720381/whole-exome-and-transcriptome-analyses-integrated-with-microenvironmental-immune-signatures-of-lung-squamous-cell-carcinoma
#16
Jeong-Sun Seo, Ji Won Lee, Ahreum Kim, Jong-Yeon Shin, Yoo Jin Jung, Sae Bom Lee, Yoon Ho Kim, Samina Park, Hyun Joo Lee, In-Kyu Park, Chang Hyun Kang, Ji-Young Yun, Jihye Kim, Young T Kim
The immune microenvironment in lung squamous cell carcinoma (LUSC) is not well understood, with interactions between the host immune system and the tumor, as well as the molecular pathogenesis of LUSC, awaiting better characterization. To date, no molecularly targeted agents have been developed for LUSC treatment. Identification of predictive and prognostic biomarkers for LUSC could help optimize therapy decisions. We sequenced whole exomes and RNA from 101 tumors and matched noncancer control Korean samples...
May 2, 2018: Cancer Immunology Research
https://www.readbyqxmd.com/read/29717442/analyzing-copy-number-variation-with-droplet-digital-pcr
#17
Avery Davis Bell, Christina L Usher, Steven A McCarroll
Many genomic segments vary in copy number among individuals of the same species, or between cancer and normal cells within the same person. Correctly measuring this copy number variation is critical for studying its genetic properties, its distribution in populations and its relationship to phenotypes. Droplet digital PCR (ddPCR) enables accurate measurement of copy number by partitioning a PCR reaction into thousands of nanoliter-scale droplets, so that a genomic sequence of interest-whose presence or absence in a droplet is determined by end-point fluorescence-can be digitally counted...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29704571/detection-of-egfr-variants-in-plasma-a-multilaboratory-comparison-of-the-cobas-egfr-mutation-test-v2-in-europe
#18
Cleo Keppens, John F Palma, Partha M Das, Sidney Scudder, Wei Wen, Nicola Normanno, J Han Van Krieken, Alessandra Sacco, Francesca Fenizia, David Gonzalez de Castro, Selma Hönigschnabl, Izidor Kern, Fernando Lopez-Rios, Maria D Lozano, Antonio Marchetti, Philippe Halfon, Ed Schuuring, Ulrike Setinek, Boe Sorensen, Phillipe Taniere, Markus Tiemann, Hana Vosmikova, Elisabeth M C Dequeker
Molecular testing of EGFR is required to predict the response likelihood to targeted therapy in non-small-cell lung cancer. Analysis of circulating tumor DNA in plasma may complement limitations of tumor tissue. This study evaluated the interlaboratory performance and reproducibility of the cobas EGFR Mutation Test v2 to detect EGFR variants in plasma. Fourteen laboratories received two identical panels of 27 single-blinded plasma samples. Samples were wild-type or spiked with plasmid DNA to contain seven common EGFR variants at six predefined concentrations from 50 to 5000 copies per mL...
April 25, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29692413/structural-variation-in-the-3d-genome
#19
REVIEW
Malte Spielmann, Darío G Lupiáñez, Stefan Mundlos
Structural and quantitative chromosomal rearrangements, collectively referred to as structural variation (SV), contribute to a large extent to the genetic diversity of the human genome and thus are of high relevance for cancer genetics, rare diseases and evolutionary genetics. Recent studies have shown that SVs can not only affect gene dosage but also modulate basic mechanisms of gene regulation. SVs can alter the copy number of regulatory elements or modify the 3D genome by disrupting higher-order chromatin organization such as topologically associating domains...
April 24, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29673117/mitochondrial-dna-copy-number-is-associated-with-risk-of-head-and-neck-squamous-cell-carcinoma-in-chinese-population
#20
Lihua Wang, Hong Lv, Pei Ji, Xun Zhu, Hua Yuan, Guangfu Jin, Juncheng Dai, Zhibin Hu, Yuxiong Su, Hongxia Ma
Mitochondria show the special role in cellular bioenergy and many essential physiological activities. Previous researches have suggested that variations of mitochondrial DNA copy number contribute to development of different types of carcinomas. However, the relationship of mtDNA copy number in peripheral blood leukocytes (PBLs) with the risk of head and neck squamous cell carcinoma (HNSCC) is still inconclusive. We investigated the association of mtDNA with HNSCC risk through a case-control study including 570 HNSCC cases and 597 cancer-free controls...
April 19, 2018: Cancer Medicine
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