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copy number variation AND cancer

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https://www.readbyqxmd.com/read/28104681/copy-number-variations-of-e2f1-a-new-genetic-risk-factor-for-testicular-cancer
#1
Maria Santa Rocca, Andrea Di Nisio, Arianna Marchiori, Marco Ghezzi, Giuseppe Opocher, Carlo Foresta, Alberto Ferlin
Testicular germ cell tumor (TGCT) is one of the most heritable forms of cancer. In last years many evidence suggested that constitutional genetic factors, mainly single nucleotide polymorphisms, can increase its risk. However, the possible contribution of copy-number variations (CNVs) in TGCT susceptibility has not been substantially addressed. Indeed, an increasing number of studies have focused on the effect of CNVs on gene expression and on the role of these structural genetic variations as risk factors for different forms of cancer...
January 19, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28104311/comprehensive-profiling-of-the-androgen-receptor-in-liquid-biopsies-from-castration-resistant-prostate-cancer-reveals-novel-intra-ar-structural-variation-and-splice-variant-expression-patterns
#2
Bram De Laere, Pieter-Jan van Dam, Tom Whitington, Markus Mayrhofer, Emanuela Henao Diaz, Gert Van den Eynden, Jean Vandebroek, Jurgen Del-Favero, Steven Van Laere, Luc Dirix, Henrik Grönberg, Johan Lindberg
BACKGROUND: Expression of the androgen receptor splice variant 7 (AR-V7) is associated with poor response to second-line endocrine therapy in castration-resistant prostate cancer (CRPC). However, a large fraction of nonresponding patients are AR-V7-negative. OBJECTIVE: To investigate if a comprehensive liquid biopsy-based AR profile may improve patient stratification in the context of second-line endocrine therapy. DESIGN, SETTING, AND PARTICIPANTS: Peripheral blood was collected from patients with CRPC (n=30) before initiation of a new line of systemic therapy...
January 16, 2017: European Urology
https://www.readbyqxmd.com/read/28097046/molecular-classification-of-tissue-from-a-transformed-non-hogkin-s-lymphoma-case-with-unexpected-long-time-remission
#3
Julie Støve Bødker, Marianne Tang Severinsen, Tarec Christoffer El-Galaly, Rasmus Froberg Brøndum, Maria Bach Laursen, Steffen Falgreen, Mette Nyegaard, Alexander Schmitz, Lasse Hjort Jakobsen, Anna Amanda Schönherz, Hanne Due, Linn Reinholdt, Martin Bøgsted, Karen Dybkær, Hans Erik Johnsen
BACKGROUND: The concept of precision medicine in cancer includes individual molecular studies to predict clinical outcomes. In the present N = 1 case we retrospectively have analysed lymphoma tissue by exome sequencing and global gene expression in a patient with unexpected long-term remission following relaps. The goals were to phenotype the diagnostic and relapsed lymphoma tissue and evaluate its pattern. Furthermore, to identify mutations available for targeted therapy and expression of genes to predict specific drug effects by resistance gene signatures (REGS) for R-CHOP as described at http://www...
2017: Experimental Hematology & Oncology
https://www.readbyqxmd.com/read/28093616/rare-germline-alterations-in-cancer-related-genes-associated-with-the-risk-of-multiple-primary-tumor-development
#4
Rolando A R Villacis, Tatiane R Basso, Luisa M Canto, Maísa Pinheiro, Karina M Santiago, Juliana Giacomazzi, Cláudia A A de Paula, Dirce M Carraro, Patrícia Ashton-Prolla, Maria I Achatz, Silvia R Rogatto
: Multiple primary tumors (MPT) have been described in carriers of inherited cancer predisposition genes. However, the genetic etiology of a large proportion of MPT cases remains unclear. We reviewed 267 patients with hereditary cancer predisposition syndromes (HCPS) that underwent genetic counseling and selected 22 patients with MPT to perform genomic analysis (CytoScan HD Array, Affymetrix) aiming to identify new alterations related to a high risk of developing MPT. Twenty patients had a positive family history of cancer and 11 met phenotypic criteria for HCPS...
January 16, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28068329/the-primacy-of-nf1-loss-as-the-driver-of-tumorigenesis-in-neurofibromatosis-type-1-associated-plexiform-neurofibromas
#5
A Pemov, H Li, R Patidar, N F Hansen, S Sindiri, S W Hartley, J S Wei, A Elkahloun, S C Chandrasekharappa, J F Boland, S Bass, J C Mullikin, J Khan, B C Widemann, M R Wallace, D R Stewart
Neurofibromatosis type 1 (NF1) is a common tumor-predisposition disorder due to germline mutations in the tumor suppressor gene NF1. A virtually pathognomonic finding of NF1 is the plexiform neurofibroma (PN), a benign, likely congenital tumor that arises from bi-allelic inactivation of NF1. PN can undergo transformation to a malignant peripheral nerve sheath tumor, an aggressive soft-tissue sarcoma. To better understand the non-NF1 genetic contributions to PN pathogenesis, we performed whole-exome sequencing, RNASeq profiling and genome-wide copy-number determination for 23 low-passage Schwann cell cultures established from surgical PN material with matching germline DNA...
January 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28067383/the-functional-consequences-and-prognostic-value-of-dosage-sensitivity-in-ovarian-cancer
#6
Zichuang Yan, Yongjing Liu, Yunzhen Wei, Ning Zhao, Qiang Zhang, Cheng Wu, Zhiqiang Chang, Yan Xu
Copy number alteration (CNA) represents an important class of genetic variations that may contribute to tumorigenesis, tumor growth and metastatic spread. CNA can directly affect the expression of genes within the CNA regions; however, genes within the CNA regions exhibit heterogeneity in gene dosage sensitivity. In this study, a computational framework was built to identify 1170 dosage-sensitive genes (DSGs) and 1215 dosage-resistant genes (DRGs) that were related to ovarian serous cystadenocarcinoma (OV) through the association between CNA and gene expression...
January 9, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28059585/initiation-of-aberrant-dna-methylation-patterns-and-heterogeneity-in-precancerous-lesions-of-human-hepatocellular-cancer
#7
Ryan A Hlady, Dan Zhou, William Puszyk, Lewis R Roberts, Chen Liu, Keith D Robertson
While intratumor heterogeneity contributes to disease progression, metastasis, and resistance to chemotherapy, it also provides a route to understanding the evolution and drivers of disease. Defects in epigenetic landscapes are intimately linked to pathogenesis of a variety of human diseases, with epigenetic deregulation promoting tumorigenesis. Understanding epigenetic heterogeneity is crucial in hepatocellular carcinoma (HCC), where epigenetic alterations are frequent, early, and pathogenic events. We determined genome-wide DNA methylation and copy number variation leveraging the Infinium 450 K in a series of regenerative nodules from within single patient livers...
January 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28056863/growth-progression-and-chromosome-instability-of-neuroblastoma-a-new-scenario-of-tumorigenesis
#8
Gian Paolo Tonini
BACKGROUND: Neuroblastoma is a pediatric cancer with a low survival rate of patients with metastatic stage 4 disease. Tumor aggressiveness and progression have been associated with structural copy number variations (CNVs) that are observed in malignant cells. In contrast, localized Neuroblastomas, which are associated with a low number of structural CNVs but frequent numerical CNVs, are less aggressive, and patients have good outcomes. Finally, whole-genome and whole-exome sequencing of Neuroblastoma tissues have shown few damaging mutations in these tumors...
January 5, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28053124/hmcan-diff-a-method-to-detect-changes-in-histone-modifications-in-cells-with-different-genetic-characteristics
#9
Haitham Ashoor, Caroline Louis-Brennetot, Isabelle Janoueix-Lerosey, Vladimir B Bajic, Valentina Boeva
Comparing histone modification profiles between cancer and normal states, or across different tumor samples, can provide insights into understanding cancer initiation, progression and response to therapy. ChIP-seq histone modification data of cancer samples are distorted by copy number variation innate to any cancer cell. We present HMCan-diff, the first method designed to analyze ChIP-seq data to detect changes in histone modifications between two cancer samples of different genetic backgrounds, or between a cancer sample and a normal control...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28052041/non-malignant-respiratory-epithelial-cells-preferentially-proliferate-from-resected-non-small-cell-lung-cancer-specimens-cultured-under-conditionally-reprogrammed-conditions
#10
Boning Gao, Chunxian Huang, Kemp Kernstine, Vasiliki Pelekanou, Yuval Kluger, Tingting Jiang, Jennifer R Peters-Hall, Melissa Coquelin, Luc Girard, Wei Zhang, Kenneth Huffman, Dwight Oliver, Fumi Kinose, Eric Haura, Jamie K Teer, Uwe Rix, Anh T Le, Dara L Aisner, Marileila Varella-Garcia, Robert C Doebele, Kyle R Covington, Oliver A Hampton, Harsha V Doddapaneni, Joy C Jayaseelan, Jianhong Hu, David A Wheeler, Jerry W Shay, David L Rimm, Adi Gazdar, John D Minna
The "conditionally reprogrammed cells" (CRC) method, using a Rho kinase inhibitor and irradiated mouse fibroblast cells has been described for the efficient growth of cells from malignant and non-malignant samples from primary tumor and non-malignant sites. Using the CRC method, four institutions independently cultured tumor tissues from 48 non-small cell lung cancers (NSCLC, mostly from primary resected tumors) and 22 non-malignant lungs. We found that epithelial cells could be cultured from tumor and non-malignant lung...
December 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/28049410/tcga2bed-extracting-extending-integrating-and-querying-the-cancer-genome-atlas
#11
Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, Emanuel Weitschek
BACKGROUND: Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of high-throughout experiments, mainly Next Generation Sequencing, for more than 30 cancer types. RESULTS: We propose TCGA2BED a software tool to search and retrieve TCGA data, and convert them in the structured BED format for their seamless use and integration...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28048759/tu-a-207b-00-imaging-genomics-associations-and-biological-correlates-of-radiomics
#12
Yitan Zhu
With the growth of quantitative imaging and quantitative image analysis, image-based biomarkers (i.e. image-based phenotypes) are becoming potential descriptors in personalized medicine as well as in cancer discovery research. Genomic study measures molecular cancer status and provides abundant information about cancer development mechanism. There is a need to understand the relationship between the image-based cancer phenotypes (from radiomics) and the underlying molecular and genomic system. Imaging scientists and genomic scientists need to be able to speak the same language in this common era of Big Data...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047278/tu-a-207b-01-imaging-genomics-associations-and-biological-correlates-of-radiomics
#13
Y Zhu
With the growth of quantitative imaging and quantitative image analysis, image-based biomarkers (i.e. image-based phenotypes) are becoming potential descriptors in personalized medicine as well as in cancer discovery research. Genomic study measures molecular cancer status and provides abundant information about cancer development mechanism. There is a need to understand the relationship between the image-based cancer phenotypes (from radiomics) and the underlying molecular and genomic system. Imaging scientists and genomic scientists need to be able to speak the same language in this common era of Big Data...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28040546/whole-genome-sequencing-reveals-the-mutational-landscape-of-metastatic-small-cell-gallbladder-neuroendocrine-carcinoma-gb-scnec
#14
Maolan Li, Fatao Liu, Yijian Zhang, Xiangsong Wu, Wenguang Wu, Xu-An Wang, Shuai Zhao, Shibo Liu, Haibin Liang, Fei Zhang, Qiang Ma, Shanshan Xiang, Huaifeng Li, Lin Jiang, Yunping Hu, Wei Gong, Yun Zhang, Tieliang Ma, Kai Zhang, Yun Liu, Yingbin Liu
Small-cell gallbladder neuroendocrine carcinoma (GB-SCNEC) is a relatively rare histological type of gallbladder cancer, and the genomic landscape of GB-SCNEC is rarely considered in treatment decisions. We performed whole-genome sequencing on an advanced case of GB-SCNEC. We identified approximately 900 high-quality somatic single nucleotide variants (SNVs) and small insertions and deletions (INDELs), 109 of which were shared by both the primary and metastatic tumor tissues. Somatic non-synonymous coding variations with damaging impact in HMCN1 and CDH10 were observed in both the primary and metastatic tissue specimens...
December 29, 2016: Cancer Letters
https://www.readbyqxmd.com/read/28035070/elucidation-of-the-genetic-and-epigenetic-landscape-alterations-in-rna-binding-proteins-in-glioblastoma
#15
Shruti Bhargava, Vikas Patil, Kulandaivelu Mahalingam, Kumaravel Somasundaram
RNA binding proteins (RBPs) have been implicated in cancer development. An integrated bioinformatics analysis of RBPs (n = 1756) in various datasets (n = 11) revealed several genetic and epigenetically altered events among RBPs in glioblastoma (GBM). We identified 13 mutated and 472 differentially regulated RBPs in GBM samples. Mutations in AHNAK predicted poor prognosis. Copy number variation (CNV), DNA methylation and miRNA targeting contributed to RBP differential regulation. Two sets of differentially regulated RBPs that may be implicated in initial astrocytic transformation and glioma progression were identified...
December 27, 2016: Oncotarget
https://www.readbyqxmd.com/read/28031973/life-as-an-early-career-researcher-interview-with-heloisa-helena-milioli
#16
Heloisa Helena Milioli
Heloisa Helena Milioli speaks to Francesca Lake, Managing Editor: Heloisa received a BSc degree in Biological Sciences (2008) from the Universidade Federal de Santa Catarina (Brazil) and obtained a MSc degree in Genetics (2011) from Universidade Federal do Paraná (Brazil). In 2011 and 2012, she worked as a lecturer and tutor in the Department of Cell Biology, Embryology and Genetics (Universidade Federal de Santa Catarina). She moved to Australia in 2012 to obtain her PhD in Biological Sciences, with emphasis on Bioinformatics, from The University of Newcastle...
June 2016: Future Science OA
https://www.readbyqxmd.com/read/28027312/the-subclonal-architecture-of-metastatic-breast-cancer-results-from-a-prospective-community-based-rapid-autopsy-program-cascade
#17
Peter Savas, Zhi Ling Teo, Christophe Lefevre, Christoffer Flensburg, Franco Caramia, Kathryn Alsop, Mariam Mansour, Prudence A Francis, Heather A Thorne, Maria Joao Silva, Nnennaya Kanu, Michelle Dietzen, Andrew Rowan, Maik Kschischo, Stephen Fox, David D Bowtell, Sarah-Jane Dawson, Terence P Speed, Charles Swanton, Sherene Loi
BACKGROUND: Understanding the cancer genome is seen as a key step in improving outcomes for cancer patients. Genomic assays are emerging as a possible avenue to personalised medicine in breast cancer. However, evolution of the cancer genome during the natural history of breast cancer is largely unknown, as is the profile of disease at death. We sought to study in detail these aspects of advanced breast cancers that have resulted in lethal disease. METHODS AND FINDINGS: Three patients with oestrogen-receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative breast cancer and one patient with triple negative breast cancer underwent rapid autopsy as part of an institutional prospective community-based rapid autopsy program (CASCADE)...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/28013532/aurora-kinase-a-is-a-prognostic-marker-in-colorectal-adenocarcinoma
#18
Hyun Min Koh, Bo Geun Jang, Chang Lim Hyun, Young Sill Kim, Jin Won Hyun, Weon Young Chang, Young Hee Maeng
BACKGROUND: Aurora kinase A (AURKA), or STK15/BTAK, is a member of the serine/threonine kinase family and plays important roles in mitosis and chromosome stability. This study investigated the clinical significance of AURKA expression in colorectal cancer patients in Korea. METHODS: AURKA protein expression was evaluated by immunohistochemistry in 151 patients with colorectal adenocarcinoma using tissue microarray blocks. We analyzed the relationship between clinicopathological characteristics and AURKA expression...
January 2017: Journal of Pathology and Translational Medicine
https://www.readbyqxmd.com/read/28009604/renal-cell-carcinoma-with-chromosome-6p-amplification-including-the-tfeb-gene-a-novel-mechanism-of-tumor-pathogenesis
#19
Sean R Williamson, David J Grignon, Liang Cheng, Laura Favazza, Dibson D Gondim, Shannon Carskadon, Nilesh S Gupta, Dhananjay A Chitale, Shanker Kalyana-Sundaram, Nallasivam Palanisamy
Amplification of chromosome 6p has been implicated in aggressive behavior in several cancers, but has not been characterized in renal cell carcinoma (RCC). We identified 9 renal tumors with amplification of chromosome 6p including the TFEB gene, 3 by fluorescence in situ hybridization, and 6 from the Cancer Genome Atlas (TCGA) databases. Patients' ages were 28 to 78 years (median, 61 y). Most tumors were high stage (7/9 pT3a, 2/9 pN1). Using immunohistochemistry, 2/4 were positive for melanocytic markers and cathepsin K...
December 22, 2016: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28008139/identifying-the-clonal-origin-of-synchronous-multifocal-tumors-in-the-hepatobiliary-and-pancreatic-system-using-multi-omic-platforms
#20
Weiqin Jiang, Yongfeng Ding, Yifei Shen, Longjiang Fan, Linfu Zhou, Zhi Li, Yi Zheng, Peng Zhao, Lulu Liu, Zhou Tong, Weijia Fang, Weilin Wang
Synchronous multifocal tumors often pose a diagnostic challenge for oncologists. The purpose of this study was to determine the clonal origin and metastatic relationship of synchronous multifocal tumors in the hepatobiliary and pancreatic system using multi-omic platforms. DNA samples were extracted from three masses harvested from a 50-year-old Han Chinese male patient who suffered from synchronous multifocal tumors in the pancreatic tail, upper biliary duct, and omentum at the time of diagnosis. The clonal origin of these samples was tested using two platforms: next-generation sequencing (NGS) of 390 key genes harboring cancer-relevant actionable mutations and whole-genome copy number variation (CNV) chip analysis...
December 19, 2016: Oncotarget
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