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copy number variation AND cancer

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https://www.readbyqxmd.com/read/28194035/recurrently-deregulated-lncrnas-in-hepatocellular-carcinoma
#1
Yang Yang, Lei Chen, Jin Gu, Hanshuo Zhang, Jiapei Yuan, Qiuyu Lian, Guishuai Lv, Siqi Wang, Yang Wu, Yu-Cheng T Yang, Dongfang Wang, Yang Liu, Jing Tang, Guijuan Luo, Yang Li, Long Hu, Xinbao Sun, Dong Wang, Mingzhou Guo, Qiaoran Xi, Jianzhong Xi, Hongyang Wang, Michael Q Zhang, Zhi John Lu
Hepatocellular carcinoma (HCC) cells often invade the portal venous system and subsequently develop into portal vein tumour thrombosis (PVTT). Long noncoding RNAs (lncRNAs) have been associated with HCC, but a comprehensive analysis of their specific association with HCC metastasis has not been conducted. Here, by analysing 60 clinical samples' RNA-seq data from 20 HCC patients, we have identified and characterized 8,603 candidate lncRNAs. The expression patterns of 917 recurrently deregulated lncRNAs are correlated with clinical data in a TCGA cohort and published liver cancer data...
February 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28191267/single-cell-digital-polymerase-chain-reaction-on-self-priming-compartmentalization-chip
#2
Qiangyuan Zhu, Lin Qiu, Yanan Xu, Guang Li, Ying Mu
Single cell analysis provides a new framework for understanding biology and disease, however, an absolute quantification of single cell gene expression still faces many challenges. Microfluidic digital polymerase chain reaction (PCR) provides a unique method to absolutely quantify the single cell gene expression, but only limited devices are developed to analyze a single cell with detection variation. This paper describes a self-priming compartmentalization (SPC) microfluidic digital polymerase chain reaction chip being capable of performing single molecule amplification from single cell...
January 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/28184012/chromosome-20q-amplification-defines-a-subtype-of-microsatellite-stable-left-sided-colon-cancers-with-wild-type-ras-raf-and-better-overall-survival
#3
Ryan N Ptashkin, Carlos Pagan, Rona Yaeger, Sumit Middha, Jinru Shia, Kevin P O'Rourke, Michael F Berger, Lu Wang, Robert Cimera, Jiajing Wang, David S Klimstra, Leonard Saltz, Marc Ladanyi, Ahmet Zehir, Jaclyn F Hechtman
: Here comprehensive analysis was performed on the molecular and clinical features of colorectal carcinoma (CRC) harboring chromosome 20q amplification. Tumor and normal DNA from patients with advanced CRC underwent next generation sequencing (NGS) via MSK-IMPACT and a subset of case samples were subjected to high resolution microarray (Oncoscan). Relationships between genomic copy number and transcript expression were assessed with The Cancer Genome Atlas (TCGA) CRC data. Of the CRC patients sequenced (n=401) with MSK-IMPACT, 148 (37%) had 20q gain, and 30 (7%) had 20q amplification...
February 9, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28165479/whole-genome-single-cell-copy-number-profiling-from-formalin-fixed-paraffin-embedded-samples
#4
Luciano G Martelotto, Timour Baslan, Jude Kendall, Felipe C Geyer, Kathleen A Burke, Lee Spraggon, Salvatore Piscuoglio, Kalyani Chadalavada, Gouri Nanjangud, Charlotte K Y Ng, Pamela Moody, Sean D'Italia, Linda Rodgers, Hilary Cox, Arnaud da Cruz Paula, Asya Stepansky, Michail Schizas, Hannah Y Wen, Tari A King, Larry Norton, Britta Weigelt, James B Hicks, Jorge S Reis-Filho
A substantial proportion of tumors consist of genotypically distinct subpopulations of cancer cells. This intratumor genetic heterogeneity poses a substantial challenge for the implementation of precision medicine. Single-cell genomics constitutes a powerful approach to resolve complex mixtures of cancer cells by tracing cell lineages and discovering cryptic genetic variations that would otherwise be obscured in tumor bulk analyses. Because of the chemical alterations that result from formalin fixation, single-cell genomic approaches have largely remained limited to fresh or rapidly frozen specimens...
February 6, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28161563/single-center-experience-with-a-targeted-next-generation-sequencing-assay-for-assessment-of-relevant-somatic-alterations-in-solid-tumors
#5
Aino Paasinen-Sohns, Viktor H Koelzer, Angela Frank, Julian Schafroth, Aline Gisler, Melanie Sachs, Anne Graber, Sacha I Rothschild, Andreas Wicki, Gieri Cathomas, Kirsten D Mertz
Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material...
February 2, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28147217/ccg-an-integrative-resource-of-cancer-protein-coding-genes-and-long-noncoding-rnas
#6
Mengrong Liu, Yu-Cheng T Yang, Gang Xu, Chang Tan, Zhi John Lu
The identification of cancer genes remains a main aim of cancer research. With the advances of high-throughput sequencing technologies, thousands of novel cancer genes were identified through recurrent mutation analyses and differential expression analyses between normal tissues and tumors in large populations. Many databases were developed to document the cancer genes. However, no public database providing both cancer protein-coding genes and cancer lncRNAs is available presently. Here, we present the Catalogue of Cancer Genes (CCG) database (http://ccg...
December 2016: Discovery Medicine
https://www.readbyqxmd.com/read/28144969/high-levels-of-the-ar-v7-splice-variant-and-co-amplification-of-the-golgi-protein-coding-yipf6-in-ar-amplified-prostate-cancer-bone-metastases
#7
Erik Djusberg, Emma Jernberg, Elin Thysell, Irina Golovleva, Pia Lundberg, Sead Crnalic, Anders Widmark, Anders Bergh, Maria Brattsand, Pernilla Wikström
BACKGROUND: The relation between androgen receptor (AR) gene amplification and other mechanisms behind castration-resistant prostate cancer (CRPC), such as expression of constitutively active AR variants and steroid-converting enzymes has been poorly examined. Specific aim was to examine AR amplification in PC bone metastases and to explore molecular and functional consequences of this, with the long-term goal of identifying novel molecular targets for treatment. METHODS: Gene amplification was assessed by fluorescence in situ hybridization in cryo-sections of clinical PC bone metastases (n = 40) and by PCR-based copy number variation analysis...
February 1, 2017: Prostate
https://www.readbyqxmd.com/read/28123515/genetic-alterations-and-epigenetic-alterations-of-cancer-associated-fibroblasts
#8
Heng Du, Guowei Che
Cancer-associated fibroblasts (CAFs) are one major type of component identified in the tumor microenvironment. Studies have focused on the genetic and epigenetic status of CAFs, since they are critical in tumor progression and differ phenotypically and functionally from normal fibroblasts. The present review summarizes the recent achievements in understanding the gene profiles of CAFs and pays special attention to their possible epigenetic alterations. A total of 7 possible genetic alterations and epigenetic changes in CAFs are discussed, including gene differential expression, karyotype analysis, gene copy number variation, loss of heterozygosis, allelic imbalance, microsatellite instability, post-transcriptional control and DNA methylation...
January 2017: Oncology Letters
https://www.readbyqxmd.com/read/28122348/genome-wide-dna-copy-number-analysis-in-clonally-expanded-human-ovarian-cancer-cells-with-distinct-invasive-migratory-capacities
#9
Lei Li, Huimin Bai, Jiaxin Yang, Dongyan Cao, Keng Shen
Ovarian cancer has the worst prognosis of any gynecological malignancy, and generally presents with metastasis at advanced stages. Copy number variation (CNV) frequently contributes to the alteration of oncogenic drivers. In this study, we sought to identify genetic targets in heterogeneous clones from human ovarian cancers cells. We used array-based technology to systematically assess all the genes with CNVs in cell models clonally expanded from A2780 and SKOV3 ovarian cancer cell lines with distinct highly and minimally invasive/migratory capacities...
January 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28120820/dna-copy-number-changes-define-spatial-patterns-of-heterogeneity-in-colorectal-cancer
#10
Soulafa Mamlouk, Liam Harold Childs, Daniela Aust, Daniel Heim, Friederike Melching, Cristiano Oliveira, Thomas Wolf, Pawel Durek, Dirk Schumacher, Hendrik Bläker, Moritz von Winterfeld, Bastian Gastl, Kerstin Möhr, Andrea Menne, Silke Zeugner, Torben Redmer, Dido Lenze, Sascha Tierling, Markus Möbs, Wilko Weichert, Gunnar Folprecht, Eric Blanc, Dieter Beule, Reinhold Schäfer, Markus Morkel, Frederick Klauschen, Ulf Leser, Christine Sers
Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 most frequently altered genes. In 97 samples, with primary tumours and matched metastases from 27 patients, we observe inter-tumour concordance for coding mutations; in contrast, gene copy numbers are highly discordant between primary tumours and metastases as validated by fluorescent in situ hybridization...
January 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28120777/muir-torre-syndrome-caused-by-exonic-deletion-of-mlh1-due-to-homologous-recombination
#11
Mirei Shiki, Tokimasa Hida, Kokichi Sugano, Rie Kaneko, Takafumi Kamiya, Akihiro Sakurai, Toshiharu Yamashita
BACKGROUND: Muir-Torre syndrome (MTS) is characterized by sebaceous neoplasms with internal malignancies and regarded as a variant of hereditary nonpolyposis colorectal cancer (HNPCC). Pathogenic variations of MTS have been identified in the MSH2, MLH1, and MSH6 genes, with the majority of variations located in MSH2. OBJECTIVES: To present an MTS patient who was the only individual with skin malignancies within a cancer-prone pedigree and to show the usefulness of RNA-based genetic analysis in the investigation of MTS...
February 1, 2017: European Journal of Dermatology: EJD
https://www.readbyqxmd.com/read/28117748/decreased-sp1-expression-mediates-downregulation-of-ship2-in-gastric-cancer-cells
#12
Yan Ye, Xue Yi Qian, Miao Miao Xiao, Yu Ling Shao, Li Mei Guo, Dong Ping Liao, Jie Da, Lin Jie Zhang, Jiegou Xu
Past studies have shown that the Src homology 2-containing inositol 5-phosphatase 2 (SHIP2) is commonly downregulated in gastric cancer, which contributes to elevated activation of PI3K/Akt signaling, proliferation and tumorigenesis of gastric cancer cells. However, the mechanisms underlying the reduced expression of SHIP2 in gastric cancer remain unclear. While gene copy number variation analysis and exon sequencing indicated the absence of genomic alterations of SHIP2, bisulfite genomic sequencing (BGS) showed promoter hypomethylation of SHIP2 in gastric cancer cells...
January 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28104681/copy-number-variations-of-e2f1-a-new-genetic-risk-factor-for-testicular-cancer
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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