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https://www.readbyqxmd.com/read/29673405/gwas-implicated-risk-variants-in-different-genes-contribute-additively-to-increase-the-risk-of-coronary-artery-disease-cad-in-the-pakistani-subjects
#1
Saleem Ullah Shahid, N A Shabana, Abdul Rehman, Steve Humphries
BACKGROUND: Coronary artery disease (CAD) remains the single most important cause of mortality worldwide. Many candidate and GWAS genetic variants have been identified in the recent years. In the current study, we selected six SNPs from various genes that have originally been identified in GWAS studies and examined the association of SNPs individually and as a genetic risk score (GRS) with CAD and blood lipid levels in the Pakistani subjects. METHODS: Six hundred twenty-four (404 cases and 219 controls) subjects were genotyped for variants rs10757274 in CDKN2A gene, rs17465637 in MIA3 gene, rs7025486 in DAB2IP gene, rs17228212 in SMAD3 gene, rs981887 in MRAS gene and rs1746048 in CXCL12 gene, by TaqMan and KASPar allele discrimination techniques...
April 19, 2018: Lipids in Health and Disease
https://www.readbyqxmd.com/read/29670856/cdkn2a-copy-number-loss-is-an-independent-prognostic-factor-in-hpv-negative-head-and-neck-squamous-cell-carcinoma
#2
William S Chen, Ranjit S Bindra, Allen Mo, Thomas Hayman, Zain Husain, Joseph N Contessa, Stephen G Gaffney, Jeffrey P Townsend, James B Yu
Background: HPV infection is associated with high p16 expression and good prognosis in head and neck squamous cell carcinomas (HNSCCs). Analysis of CDKN2A, the gene encoding p16, may further elucidate the association between p16 expression and prognosis. We sought to determine whether CDKN2A copy number loss was associated with poor survival in HPV-negative HNSCCs. Methods: The Cancer Genome Atlas HNSCC clinical and genomic data were obtained and integrated. Patients <80 years old with a primary tumor in the oral cavity, oropharynx, hypopharynx, or larynx were included...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29670052/aneuploid-ctc-and-cec
#3
REVIEW
Peter Ping Lin
Conventional circulating tumor cell (CTC) detection technologies are restricted to large tumor cells (> white blood cells (WBCs)), or those unique carcinoma cells with double positive expression of surface epithelial cell adhesion molecule (EpCAM) for isolation, and intracellular structural protein cytokeratins (CKs) for identification. With respect to detecting the full spectrum of highly heterogeneous circulating rare cells (CRCs), including CTCs and circulating endothelial cells (CECs), it is imperative to develop a strategy systematically coordinating all tri-elements of nucleic acids, biomarker proteins, and cellular morphology, to effectively enrich and comprehensively identify CRCs...
April 18, 2018: Diagnostics
https://www.readbyqxmd.com/read/29667626/eus-fna-in-cystic-pancreatic-lesions-where-are-we-now-and-where-are-we-headed-in-the-future
#4
REVIEW
Jose Lariño-Noia, Julio Iglesias-Garcia, Daniel de la Iglesia-Garcia, J Enrique Dominguez-Muñoz
EUS-FNA is often performed in the evaluation of Cystic Pancreatic Lesions (CPL) for a better preoperative characterization. The objective is to identify premalignant lesions as Mucinous Cystic Neoplasms, and/or a malignant transformation of them (adenocarcinoma). The role of cytological evaluation in this setting is discouraging and intracystic markers analysis, mainly CEA, lacks of a good specificity for the detection of mucinous neoplasms. New devices and approaches have emerged to overcome these problems as the cytology brush (Echobrush), the small mini-biopsy foceps, the cystoscopy and the needle Confocal LASER Endomicroscopy (nCLE), showing in some studies good rates of accuracy for distinguishing among mucinosus and non-mucinous neoplasms...
March 2018: Endoscopic Ultrasound
https://www.readbyqxmd.com/read/29667179/characteristics-of-genomic-alterations-of-lung-adenocarcinoma-in-young-never-smokers
#5
Wenxin Luo, Panwen Tian, Yue Wang, Heng Xu, Lu Chen, Chao Tang, Yang Shu, Shouyue Zhang, Zhoufeng Wang, Jun Zhang, Li Zhang, Lili Jiang, Lunxu Liu, Guowei Che, Chenglin Guo, Hong Zhang, Jiali Wang, Weimin Li
Non-small cell lung cancer (NSCLC) has been recognized as a highly heterogeneous disease with phenotypic and genotypic diversity in each subgroup. While never-smoker patients with NSCLC have been well studied through next generation sequencing, we have yet to recognize the potentially unique molecular features of young never-smoker patients with NSCLC. In this study, we conducted whole genome sequencing (WGS) to characterize the genomic alterations of 36 never-smoker Chinese patients, who were diagnosed with lung adenocarcinoma (LUAD) at 45 years or younger...
April 18, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29661971/cm-score-a-validated-scoring-system-to-predict-cdkn2a-germline-mutations-in-melanoma-families-from-northern-europe
#6
Thomas P Potjer, Hildur Helgadottir, Mirjam Leenheer, Nienke van der Stoep, Nelleke A Gruis, Veronica Höiom, Håkan Olsson, Remco van Doorn, Hans F A Vasen, Christi J van Asperen, Olaf M Dekkers, Frederik J Hes
BACKGROUND: Several factors have been reported that influence the probability of a germline CDKN2A mutation in a melanoma family. Our goal was to create a scoring system to estimate this probability, based on a set of clinical features present in the patient and his or her family. METHODS: Five clinical features and their association with CDKN2A mutations were investigated in a training cohort of 1227 Dutch melanoma families (13.7% with CDKN2A mutation) using multivariate logistic regression...
April 16, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29661773/integrated-genomic-and-immunophenotypic-classification-of-pancreatic-cancer-reveals-three-distinct-subtypes-with-prognostic-predictive-significance
#7
Martin Wartenberg, Silvia Cibin, Inti Zlobec, Erik Vassella, Serenella M M Eppenberger-Castori, Luigi Terracciano, Micha Eichmann, Mathias Worni, Beat Gloor, Aurel Perren, Eva Karamitopoulou
PURPOSE: Current clinical classification of pancreatic ductal adenocarcinoma (PDAC) is unable to predict prognosis or response to chemo- or immunotherapy and does not take into account the host reaction to PDAC-cells. Our aim is to classify PDAC according to host- and tumor-related factors into clinically/biologically relevant subtypes by integrating molecular and microenvironmental findings. EXPERIMENTAL DESIGN: A well-characterized PDAC-cohort (n=110) underwent next-generation sequencing with a hotspot cancer panel, while Next-generation Tissue-Microarrays were immunostained for CD3, CD4, CD8, CD20, PD-L1, p63, hyaluronan-mediated motility receptor (RHAMM) and DNA mismatch-repair proteins...
April 16, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29661169/rna-seq-reveals-the-existence-of-a-cdkn1c-e2f1-tp53-axis-that-is-altered-in-human-t-cell-lymphoblastic-lymphomas
#8
Pilar López-Nieva, Pablo Fernández-Navarro, Concepción Vaquero-Lorenzo, María Villa-Morales, Osvaldo Graña-Castro, María Ángeles Cobos-Fernández, José Luis López-Lorenzo, Pilar Llamas, Laura González-Sanchez, Isabel Sastre, Marina Pollan, Marcos Malumbres, Javier Santos, José Fernández-Piqueras
BACKGROUND: Precursor T-cell lymphoblastic lymphomas (T-LBL) are rare aggressive hematological malignancies that mainly develop in children. As in other cancers, the loss of cell cycle control plays a prominent role in the pathogenesis in these malignancies that is primarily attributed to loss of CDKN2A (encoding protein p16INK4A). However, the impact of the deregulation of other genes such as CDKN1C, E2F1, and TP53 remains to be clarified. Interestingly, experiments in mouse models have proven that conditional T-cell specific deletion of Cdkn1c gene may induce a differentiation block at the DN3 to DN4 transition, and that the loss of this gene in the absence of Tp53 led to aggressive thymic lymphomas...
April 16, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29656754/malignant-cells-from-pleural-fluids-in-malignant-mesothelioma-patients-reveal-novel-mutations
#9
Sophie Sneddon, Ian Dick, Y C Gary Lee, A W Bill Musk, Ann-Marie Patch, John V Pearson, Nicola Waddell, Richard J N Allcock, Robert A Holt, Bruce W S Robinson, Jenette Creaney
OBJECTIVES: Malignant mesothelioma (MM) is an asbestos related tumour affecting cells of serosal cavities. More than 70% of MM patients develop pleural effusions which contain tumour cells, representing a readily accessible source of malignant cells for genetic analysis. Although common somatic mutations and losses have been identified in solid MM tumours, the characterization of tumour cells within pleural effusions could provide novel insights but is little studied. MATERIALS AND METHODS: DNA and RNA were extracted from cells from short term cultures of 27 human MM pleural effusion samples...
May 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29629612/the-9p21-locus-as-a-potential-therapeutic-target-and-prognostic-marker-in-colorectal-cancer
#10
Afsane Bahrami, Seyed Mahdi Hassanian, Majid Khazaei, Masoumeh Gharib, Mahsa Rahmani, Hamid Fiuji, Mir Hadi Jazayeri, Mehrdad Moetamani-Ahmadi, Gordon A Ferns, Amir Avan
Colorectal cancer (CRC) is a major cause of cancer-related-death worldwide. Despite extensive efforts to identify valid biomarkers for the risk stratification of CRC patients, there are few of proven clinical utility. It is recognized that genetic factors play a major role in determining susceptibility to CRC. Recent genome-wide association studies have demonstrated common genetic variants in a region on chromosome 9p21 associated with an increased risk of CRC. Several genetic polymorphisms have been identified in this region that are associated with CRC...
April 9, 2018: Pharmacogenomics
https://www.readbyqxmd.com/read/29618717/the-profiles-and-networks-of-mirna-lncrna-mrna-and-circrna-in-benzo-a-pyrene-transformed-bronchial-epithelial-cells
#11
Xinhang Jiang, Xiaoying Wu, Feiyu Chen, Wei He, Xintong Chen, Linhua Liu, Huanwen Tang
Our aim was to demonstrate the significance of miRNA, lncRNA, and circRNA in the transformation of human bronchial epithelial cells induced by benzo(a)pyrene (BaP), and to investigate their regulatory networks. Hierarchical clustering, gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and network regulation analysis were used to analyze the high-throughput sequencing results of human bronchial epithelial cell line BEAS-2B and BaP-transformed BEAS-2B cells (BEAS-2B-T). 76,191,786 and 3,431differentially-expressed miRNA, lncRNA, mRNA and circRNA were detected, respectively; 43 miRNA, 48 lncRNA, 438 mRNA and 2,079 circRNA were up-regulated; 33 miRNA, 143 lncRNA, 348 mRNA and 1,352 circRNA were down-regulated...
2018: Journal of Toxicological Sciences
https://www.readbyqxmd.com/read/29617669/the-cancer-genome-atlas-comprehensive-molecular-characterization-of-renal-cell-carcinoma
#12
Christopher J Ricketts, Aguirre A De Cubas, Huihui Fan, Christof C Smith, Martin Lang, Ed Reznik, Reanne Bowlby, Ewan A Gibb, Rehan Akbani, Rameen Beroukhim, Donald P Bottaro, Toni K Choueiri, Richard A Gibbs, Andrew K Godwin, Scott Haake, A Ari Hakimi, Elizabeth P Henske, James J Hsieh, Thai H Ho, Rupa S Kanchi, Bhavani Krishnan, David J Kwaitkowski, Wembin Lui, Maria J Merino, Gordon B Mills, Jerome Myers, Michael L Nickerson, Victor E Reuter, Laura S Schmidt, C Simon Shelley, Hui Shen, Brian Shuch, Sabina Signoretti, Ramaprasad Srinivasan, Pheroze Tamboli, George Thomas, Benjamin G Vincent, Cathy D Vocke, David A Wheeler, Lixing Yang, William T Kim, A Gordon Robertson, Paul T Spellman, W Kimryn Rathmell, W Marston Linehan
Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers...
April 3, 2018: Cell Reports
https://www.readbyqxmd.com/read/29615459/genetic-analysis-of-779-advanced-differentiated-and-anaplastic-thyroid-cancers
#13
Nikita Pozdeyev, Laurie Gay, Ethan S Sokol, Ryan J Hartmaier, Kelsi E Deaver, Stephanie N Davis, Jena D French, Pierre Vanden Borre, Daniel V LaBarbera, Aik-Choon Tan, Rebecca E Schweppe, Lauren Fishbein, Jeffrey S Ross, Bryan R Haugen, Daniel W Bowles
PURPOSE: To define the genetic landscape of advanced differentiated and anaplastic thyroid cancer and identify genetic alterations of potential diagnostic, prognostic and therapeutic significance. EXPERIMENTAL DESIGN: The genetic profiles of 583 advanced differentiated and 196 anaplastic thyroid cancers (ATC) generated with targeted next-generation sequencing cancer-associated gene panels MSK-IMPACT and FoundationOne were analyzed. RESULTS: ATC had more genetic alterations per tumor, and pediatric papillary thyroid cancer had fewer genetic alterations per tumor when compared to other thyroid cancer types...
April 3, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29610392/personalized-oncogenomic-analysis-of-metastatic-adenoid-cystic-carcinoma-using-whole-genome-sequencing-to-inform-clinical-decision-making
#14
Manik Chahal, Erin Pleasance, Jasleen Grewal, Eric Zhao, Tony Ng, Erin Chapman, Martin R Jones, Yaoqing Shen, Karen L Mungall, Melika Bonakdar, Gregory A Taylor, Yussanne Ma, Andrew J Mungall, Richard A Moore, Howard Lim, Daniel Renouf, Stephen Yip, Steven J M Jones, Marco A Marra, Janessa Laskin
Metastatic adenoid cystic carcinomas (ACCs) can cause significant morbidity and mortality. Because of their slow growth and relative rarity, there is limited evidence for systemic therapy regimens. Recently, molecular profiling studies have begun to reveal the genetic landscape of these poorly understood cancers, and new treatment possibilities are beginning to emerge. The objective is to use whole-genome and transcriptome sequencing and analysis to better understand the genetic alterations underlying the pathology of metastatic and rare ACCs and determine potentially actionable therapeutic targets...
April 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29596894/pancreatic-neuroendocrine-carcinomas-reveal-a-closer-relationship-to-ductal-adenocarcinomas-than-to-neuroendocrine-tumors-g3
#15
Björn Konukiewitz, Moritz Jesinghaus, Katja Steiger, Anna Melissa Schlitter, Atsuko Kasajima, Bence Sipos, Giuseppe Zamboni, Wilko Weichert, Nicole Pfarr, Günter Klöppel
Pancreatic neuroendocrine carcinoma is a rare aggressive tumor commonly harboring TP53 and RB1 alterations and lacking neuroendocrine related genetic changes such as mutations in MEN1 and ATRX/DAXX. Little is known about its genetic profile with regard to that of pancreatic ductal adenocarcinoma. We therefore conducted a detailed genetic study in 12 pancreatic neuroendocrine carcinomas of large cell (n=9) and small cell type (n=3) using massive parallel sequencing applying a 409 gene panel on an Ion Torrent system...
March 26, 2018: Human Pathology
https://www.readbyqxmd.com/read/29594878/acquired-resistance-to-an-epidermal-growth-factor-receptor-tyrosine-kinase-inhibitor-egfr-tki-in-an-uncommon-g719s-egfr-mutation
#16
Atsushi Osoegawa, Takafumi Hashimoto, Yohei Takumi, Miyuki Abe, Tomonori Yamada, Ryoji Kobayashi, Michiyo Miyawaki, Hideya Takeuchi, Tatsuro Okamoto, Kenji Sugio
Background Acquired resistance (AR) to an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) is a common event, and several underlying mechanisms, including T790 M, MET amplification and PTEN downregulation, have been reported for the common EGFR mutations. EGFR G719X is an uncommon mutation that has been reported to show sensitivity to EGFR-TKIs. However, no established cell lines harboring the EGFR G719X have been reported in the literature. Materials and Methods G719S-GR cells were established from malignant pleural effusion of a patient whose tumor developed AR from gefitinib treatment...
March 28, 2018: Investigational New Drugs
https://www.readbyqxmd.com/read/29590617/regulation-of-cellular-senescence-by-polycomb-chromatin-modifiers-through-distinct-dna-damage-and-histone-methylation-dependent-pathways
#17
Takahiro Ito, Yee Voan Teo, Shane A Evans, Nicola Neretti, John M Sedivy
Polycomb group (PcG) factors maintain facultative heterochromatin and mediate many important developmental and differentiation processes. EZH2, a PcG histone H3 lysine-27 methyltransferase, is repressed in senescent cells. We show here that downregulation of EZH2 promotes senescence through two distinct mechanisms. First, depletion of EZH2 in proliferating cells rapidly initiates a DNA damage response prior to a reduction in the levels of H3K27me3 marks. Second, the eventual loss of H3K27me3 induces p16 (CDKN2A) gene expression independent of DNA damage and potently activates genes of the senescence-associated secretory phenotype (SASP)...
March 27, 2018: Cell Reports
https://www.readbyqxmd.com/read/29581789/integrated-oncogenomic-profiling-of-copy-numbers-and-gene-expression-in-lung-adenocarcinomas-without-egfr-mutations-or-alk-fusion
#18
Yanzhuo Luo, Bingjin Li, Guangxin Zhang, Yuxiao He, Jeeyoo Hope Bae, Fengping Hu, Ranji Cui, Runhua Liu, Zhou Wang, Lizhong Wang
Targeted therapies based on EGFR mutations or on the ALK fusion oncogene have become the standard treatment for certain patients with lung adenocarcinoma (LUAD). However, most LUAD patients have no EGFR mutation or ALK fusion, and their oncogenetic alterations remain to be characterized. Here we conducted an integrated analysis of public datasets to assess the genomic alterations of 23 highly lung cancer-associated genes. The copy numbers of these genes were measured in ten micro-dissected, paired tumors and normal lung tissues of LUAD patients without EGFR mutations or ALK fusion...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29575541/simultaneous-detection-of-abl1-mutation-and-ikzf1-deletion-in-philadelphia-chromosome-positive-acute-lymphoblastic-leukemia-using-a-customized-target-enrichment-system-panel
#19
M Aoe, H Ishida, T Matsubara, S Karakawa, H Kawaguchi, K Fujiwara, K Kanamitsu, K Washio, K Okada, M Shibakura, A Shimada
INTRODUCTION: Recent clinical outcomes of pediatric Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ALL) vastly improved owing to tyrosine kinase inhibitor (TKI). However, the genetic status would be different in each case with ABL1 gene mutation or copy number variants (CNVs) such as IKZF1 deletion. In particular, the TKI resistant clone with ABL1 kinase mutation remains problematic. The comprehensive assessment of genetic status including mutation, insertion and deletion (indel) and CNVs is necessary...
March 25, 2018: International Journal of Laboratory Hematology
https://www.readbyqxmd.com/read/29571084/comprehensive-analysis-of-cancers-of-unknown-primary-for-the-biomarkers-of-response-to-immune-checkpoint-blockade-therapy
#20
Zoran Gatalica, Joanne Xiu, Jeff Swensen, Semir Vranic
BACKGROUND: Cancer of unknown primary (CUP) accounts for approximately 3% of all malignancies. Avoiding immune destruction is a major cancer characteristic and therapies aimed at immune checkpoint blockade are in use for several specific cancer types. A comprehensive survey of predictive biomarkers to immune checkpoint blockade in CUP were explored in this study. METHODS: About 389 cases of CUP were analysed for mutations in 592 genes and 52 gene fusions using a massively parallel DNA sequencing platform (next-generation sequencing [NGS])...
March 20, 2018: European Journal of Cancer
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