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Chromosome 9p21

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https://www.readbyqxmd.com/read/27913867/comparison-of-different-concepts-for-interpretation-of-chromosomal-aberrations-in-urothelial-cells-detected-by-fluorescence-in-situ-hybridization
#1
Johannes Mischinger, Lutz Philipp Guttenberg, Jörg Hennenlotter, Georgios Gakis, Stefan Aufderklamm, Steffen Rausch, Eva Neumann, Jens Bedke, Stefan Kruck, Christian Schwentner, Arnulf Stenzl, Tilman Todenhöfer
PURPOSE: Urine fluorescence in situ hybridization (FISH) has become a broadly used marker for noninvasive detection of bladder cancer (BC). However, it has been discussed whether the interpretation algorithm proposed by the manufacturer could be improved. Aim of the present study was to compare alternative evaluation strategies of FISH for detection of BC. METHODS: We included 1048 patients suspicious for BC, who underwent urine FISH examination before cystoscopy (diagnostic cohort)...
December 2, 2016: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/27905995/cdkn2b-methylation-is-associated-with-carotid-artery-calcification-in-ischemic-stroke-patients
#2
Shuyu Zhou, Yumeng Zhang, Li Wang, Zhizhong Zhang, Biyang Cai, Keting Liu, Hao Zhang, Minhui Dai, Lingli Sun, Xiaomeng Xu, Huan Cai, Xinfeng Liu, Guangming Lu, Gelin Xu
BACKGROUND: Cyclin-dependent kinase inhibitor 2A/2B (CDKN2A/2B) near chromosome 9p21 have been associated with both atherosclerosis and artery calcification, but the underlying mechanisms remained largely unknown. Considering that CDKN2A/2B is a frequently reported site for DNA methylation, this study aimed to evaluate whether carotid artery calcification (CarAC) is related to methylation levels of CDKN2A/2B in patients with ischemic stroke. METHODS: DNA methylation levels of CDKN2A/2B were measured in 322 ischemic stroke patients using peripheral blood leukocytes...
December 1, 2016: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27846637/analysis-on-the-polymorphism-of-chromosome-region-9p21-and-the-susceptibility-of-carotid-plaque
#3
Jialan Sun, Fenghua Sun, Kang Yang, Ningzhen Fu, Longxuan Li
BACKGROUND: Atherosclerosis is a complicated disease governed by genetic, environmental and vascular risk factors, while its relationship with specific genes is still unclear. In recent days, it has been discovered that the single-nucleotide polymorphisms of chromosomal region 9p21 were relevant with the genetic susceptibility of Atherosclerosis. We aimed to figure out the relativity between the gene polymorphism of region 9p21 (rs10757274, rs7044859, rs4977574 and rs496892) and carotid plaque...
November 16, 2016: European Neurology
https://www.readbyqxmd.com/read/27822414/differences-in-mek-inhibitor-efficacy-in-molecularly-characterized-low-grade-serous-ovarian-cancer-cell-lines
#4
Marta Llauradó Fernández, Gabriel E DiMattia, Amy Dawson, Sylvia Bamford, Shawn Anderson, Bryan T Hennessy, Michael S Anglesio, Trevor G Shepherd, Clara Salamanca, Josh Hoenisch, Anna Tinker, David G Huntsman, Mark S Carey
Advanced or recurrent low-grade serous ovarian cancers (LGSC) are resistant to conventional systemic treatments. LGSC carry mutations in RAS or RAF, leading to several clinical trials evaluating MEK inhibitors (MEKi). As LGSC cell lines and xenografts have been difficult to establish, little is known about the efficacy and on-target activity of MEKi treatment in this disease. We compared four different MEKi (trametinib, selumetinib, binimetinib and refametinib) in novel LGSC patient-derived cell lines. Molecular characterization of these cells included copy-number variation and hotspot mutational analysis...
2016: American Journal of Cancer Research
https://www.readbyqxmd.com/read/27773886/cdkn2b-methylation-and-aortic-arch-calcification-in-patients-with-ischemic-stroke
#5
Shuyu Zhou, Biyang Cai, Zhizhong Zhang, Yumeng Zhang, Li Wang, Keting Liu, Hao Zhang, Lingli Sun, Huan Cai, Guangming Lu, Xinfeng Liu, Gelin Xu
AIM: CDKN2A/2B near chromosome 9p21 has been proposed as a potential genetic etiology for both atherosclerosis and arterial calcification. DNA methylation, which can change the expression of CDKN2A/2B, may be an underlying mechanism for this association. This study aimed to evaluate whether CDKN2A/2B methylation is related to aortic arch calcification (AAC) in patients with ischemic stroke. METHODS: DNA methylation levels of CDKN2A/2B was measured using venous blood samples in 322 patients with ischemic stroke...
October 21, 2016: Journal of Atherosclerosis and Thrombosis
https://www.readbyqxmd.com/read/27753829/sy-03-2-pathophysiologic-significance-of-non-coding-rna-in-hypertension
#6
Stephen Harrap
Genetic discovery in blood pressure is generally referenced in relation to protein-coding genes, despite the fact that genes less than 2% of the genome. Recent exploration of the DNA sequences between genes, once called "junk" DNA, has revealed a wealth of transcripts for RNA species that do not encode protein. These non-coding RNAs (ncRNAs) have emerged as dynamic managers of the business of the genome, able to coordinate the expression of genes in time and space to achieve the complexities of normal development and growth...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27721851/association-of-rs10757274-and-rs2383206-polymorphisms-on-9p21-locus-with-coronary-artery-disease-in-turkish-population
#7
Çağrı Yayla, Kaan Okyay, Akın Yılmaz, Asife Şahinarslan, Atiye Seda Yar Sağlam, Azmi Eyiol, Hasan Ata Bolayır, Burak Sezenöz, Sevda Menevşe, Atiye Çengel
BACKGROUND AND OBJECTIVES: Genetic predisposition is an important risk factor for coronary artery disease (CAD). In this study, we aimed to evaluate the impact of rs10757274 and rs2383206 polymorphisms in chromosome 9p21 on presence and severity of CAD in a Turkish population. SUBJECTS AND METHODS: A total of 646 patients who underwent coronary angiography were included in this study. Coronary vessel score and Gensini score were calculated to assess the angiographic severity of CAD...
September 2016: Korean Circulation Journal
https://www.readbyqxmd.com/read/27642882/sy-03-2-pathophysiologic-significance-of-non-coding-rna-in-hypertension
#8
Stephen Harrap
Genetic discovery in blood pressure is generally referenced in relation to protein-coding genes, despite the fact that genes less than 2% of the genome. Recent exploration of the DNA sequences between genes, once called "junk" DNA, has revealed a wealth of transcripts for RNA species that do not encode protein. These non-coding RNAs (ncRNAs) have emerged as dynamic managers of the business of the genome, able to coordinate the expression of genes in time and space to achieve the complexities of normal development and growth...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27635196/loss-of-heterozygosity-and-microsatellite-instability-as-predictive-markers-among-iranian-esophageal-cancer-patients
#9
Mohammad Mahdi Forghanifard, Elham Emami Vahid, Ezzat Dadkhah, Mehran Gholamin, Samaneh Broumand Noghabi, Martha Ghahraman, Mehdi Farzadnia, Mohammad Reza Abbaszadegan
OBJECTIVES: Variation in microsatellite sequences that are dispersed in the genome has been linked to a deficiency in cellular mismatch repair system and defects in several genes of this system are involved in carcinogenesis. Our aim in this study was to illustrate microsatellite DNA alteration in esophageal cancer. MATERIALS AND METHODS: DNA was extracted from formalin fixed paraffin embedded (FFPE) tissues from surgical and matched margin-normal samples. Microsatellite instability (MSI) and loss of heterozygosity (LOH) were studied in 50 cases of esophageal squamous cell carcinoma (ESCC) by amplifying six microsatellite markers: D13S260 (13q12...
July 2016: Iranian Journal of Basic Medical Sciences
https://www.readbyqxmd.com/read/27590390/prenatal-diagnosis-and-molecular-cytogenetic-characterization-of-a-de-novo-unbalanced-reciprocal-translocation-of-der-9-t-9-14-p24-2-q32-11-associated-with-9p-terminal-deletion-and-14q-distal-duplication
#10
Chih-Ping Chen, Chen-Ju Lin, Schu-Rern Chern, Peih-Shan Wu, Yen-Ni Chen, Shin-Wen Chen, Chen-Chi Lee, Li-Feng Chen, Chien-Wen Yang, Wayseen Wang
OBJECTIVE: We present molecular cytogenetic characterization of a prenatally detected derivative chromosome 9 [der(9)] of unknown origin. CASE REPORT: A 35-year-old woman underwent amniocentesis at 18 weeks of gestation because of advanced maternal age, which revealed a der(9) chromosome of unknown origin. The parental karyotypes were normal. Array comparative genomic hybridization (aCGH) analysis revealed a 2.593 Mb deletion of 9p24.3-p24.2 encompassing DOCK8, KANK1, DMRT1, and VLDLR and a 16...
August 2016: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/27569296/loss-of-p16-expression-and-copy-number-changes-of-cdkn2a-in-a-spectrum-of-spitzoid-melanocytic-lesions
#11
Paul W Harms, Thomas L Hocker, Lili Zhao, May P Chan, Aleodor A Andea, Min Wang, Kelly L Harms, Michael L Wang, Shannon Carskadon, Nallasivam Palanisamy, Douglas R Fullen
Spitzoid melanocytic lesions, including Spitz nevi (benign), spitzoid melanoma (malignant), and borderline atypical Spitz tumors (ASTs), frequently present challenges for accurate diagnosis and prognosis. Evaluation for loss of the tumor suppressor p16, encoded by CDKN2A gene on chromosome 9p21.3, has been proposed to be useful for evaluation of spitzoid melanocytic lesions. However, reports on the utility of p16 immunohistochemistry for spitzoid lesions have been conflicting, and few studies have directly compared p16 immunohistochemistry with fluorescence in situ hybridization (FISH) for CDKN2A genomic status...
August 25, 2016: Human Pathology
https://www.readbyqxmd.com/read/27539542/circular-non-coding-rna-anril-modulates-ribosomal-rna-maturation-and-atherosclerosis-in-humans
#12
Lesca M Holdt, Anika Stahringer, Kristina Sass, Garwin Pichler, Nils A Kulak, Wolfgang Wilfert, Alexander Kohlmaier, Andreas Herbst, Bernd H Northoff, Alexandros Nicolaou, Gabor Gäbel, Frank Beutner, Markus Scholz, Joachim Thiery, Kiran Musunuru, Knut Krohn, Matthias Mann, Daniel Teupser
Circular RNAs (circRNAs) are broadly expressed in eukaryotic cells, but their molecular mechanism in human disease remains obscure. Here we show that circular antisense non-coding RNA in the INK4 locus (circANRIL), which is transcribed at a locus of atherosclerotic cardiovascular disease on chromosome 9p21, confers atheroprotection by controlling ribosomal RNA (rRNA) maturation and modulating pathways of atherogenesis. CircANRIL binds to pescadillo homologue 1 (PES1), an essential 60S-preribosomal assembly factor, thereby impairing exonuclease-mediated pre-rRNA processing and ribosome biogenesis in vascular smooth muscle cells and macrophages...
August 19, 2016: Nature Communications
https://www.readbyqxmd.com/read/27465101/microsatellite-alteration-and-immunohistochemical-expression-profile-of-chromosome-9p21-in-patients-with-sporadic-renal-cell-carcinoma-following-surgical-resection
#13
Ismail El-Mokadem, Alison Lim, Thomas Kidd, Katherine Garret, Norman Pratt, David Batty, Stewart Fleming, Ghulam Nabi
BACKGROUND: Long-term prognostic significance of loss of heterozygosity on chromosome 9p21 for localized renal cell carcinoma following surgery remains unreported. The study assessed the frequency of deletions of different loci of chromosome 9p along with immunohistochemical profile of proteins in surgically resected renal cancer tissue and correlated this with long-term outcomes. METHODS: DNA was extracted from renal tumours and corresponding normal kidney tissues in prospectively collected samples of 108 patients who underwent surgical resection for clinically localized disease between January 2001 and December 2005, providing a minimum of 9 years follow-up for each participant...
2016: BMC Cancer
https://www.readbyqxmd.com/read/27461581/anril-lncrna-triggers-efficient-therapeutic-efficacy-by-reprogramming-the-aberrant-ink4-hub-in-melanoma
#14
Shiqiong Xu, Huixue Wang, Hui Pan, Yingyun Shi, Tianyuan Li, Shengfang Ge, Renbing Jia, He Zhang, Xianqun Fan
Melanoma is an extremely aggressive disease with rapid progression, high metastatic potential and recurrence. Simultaneous correction of multiple tumor-specific gene abnormalities has become an attractive approach for developing therapeutics to treat melanoma. To potentiate anti-melanoma activity, we tested a "domino effect-like" therapeutic approach by uniquely targeting one defect and automatically triggering the endogenous corrections of other defects. Using this strategy, in a suspicious INK4b-ARF-INK4a gene cluster at chromosome 9p21, aberrant INK4a and INK4b defects were simultaneously endogenously auto-corrected after targeting the suppression of abnormal ANRIL lncRNA...
October 10, 2016: Cancer Letters
https://www.readbyqxmd.com/read/27356775/the-9p21-locus-and-its-potential-role-in-atherosclerosis-susceptibility-molecular-mechanisms-and-clinical-implications
#15
Amir Tajbakhsh, Seyed Mahdi Hassanian, Mohammad Sadegh Khorrami, Alireza Pasdar, Ehsan Tabatabai, Seyed Mohammad Reza Parizadeh, Mostafa Fazeli, Sharareh Gholamin, Gordon A Ferns, Majid Ghayour-Mobarhan, Amir Avan
Cardiovascular disease (CVD) is the leading cause of global mortality. Although extensive efforts have been made to identify valid biomarkers for CVD risk, relatively ¬¬¬few are of proven clinical utility. It is recognized that genetic factors play a major role in determining the susceptibility to CVD. Recent genome-wide-association-studies have demonstrated common genetic variants in a region on chromosome 9p21 associated with an increased risk of CVD. Several genetic-polymorphisms have been identified in this region that are highly associated with CVD, and these are clustered around the gene loci for CDKN2B (coding for p15ink4b), CDKN2A (coding for p16ink4a and p14ARF) and the 3' end of CDKN2BAS, which has been termed antisense noncoding RNA in the INK4 locus (ANRIL)...
June 27, 2016: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/27329760/genome-wide-association-study-of-40-000-individuals-identifies-two-novel-loci-associated-with-bipolar-disorder
#16
Liping Hou, Sarah E Bergen, Nirmala Akula, Jie Song, Christina M Hultman, Mikael Landén, Mazda Adli, Martin Alda, Raffaella Ardau, Bárbara Arias, Jean-Michel Aubry, Lena Backlund, Judith A Badner, Thomas B Barrett, Michael Bauer, Bernhard T Baune, Frank Bellivier, Antonio Benabarre, Susanne Bengesser, Wade H Berrettini, Abesh Kumar Bhattacharjee, Joanna M Biernacka, Armin Birner, Cinnamon S Bloss, Clara Brichant-Petitjean, Elise T Bui, William Byerley, Pablo Cervantes, Caterina Chillotti, Sven Cichon, Francesc Colom, William Coryell, David W Craig, Cristiana Cruceanu, Piotr M Czerski, Tony Davis, Alexandre Dayer, Franziska Degenhardt, Maria Del Zompo, J Raymond DePaulo, Howard J Edenberg, Bruno Étain, Peter Falkai, Tatiana Foroud, Andreas J Forstner, Louise Frisén, Mark A Frye, Janice M Fullerton, Sébastien Gard, Julie S Garnham, Elliot S Gershon, Fernando S Goes, Tiffany A Greenwood, Maria Grigoroiu-Serbanescu, Joanna Hauser, Urs Heilbronner, Stefanie Heilmann-Heimbach, Stefan Herms, Maria Hipolito, Shashi Hitturlingappa, Per Hoffmann, Andrea Hofmann, Stephane Jamain, Esther Jiménez, Jean-Pierre Kahn, Layla Kassem, John R Kelsoe, Sarah Kittel-Schneider, Sebastian Kliwicki, Daniel L Koller, Barbara König, Nina Lackner, Gonzalo Laje, Maren Lang, Catharina Lavebratt, William B Lawson, Marion Leboyer, Susan G Leckband, Chunyu Liu, Anna Maaser, Pamela B Mahon, Wolfgang Maier, Mario Maj, Mirko Manchia, Lina Martinsson, Michael J McCarthy, Susan L McElroy, Melvin G McInnis, Rebecca McKinney, Philip B Mitchell, Marina Mitjans, Francis M Mondimore, Palmiero Monteleone, Thomas W Mühleisen, Caroline M Nievergelt, Markus M Nöthen, Tomas Novák, John I Nurnberger, Evaristus A Nwulia, Urban Ösby, Andrea Pfennig, James B Potash, Peter Propping, Andreas Reif, Eva Reininghaus, John Rice, Marcella Rietschel, Guy A Rouleau, Janusz K Rybakowski, Martin Schalling, William A Scheftner, Peter R Schofield, Nicholas J Schork, Thomas G Schulze, Johannes Schumacher, Barbara W Schweizer, Giovanni Severino, Tatyana Shekhtman, Paul D Shilling, Christian Simhandl, Claire M Slaney, Erin N Smith, Alessio Squassina, Thomas Stamm, Pavla Stopkova, Fabian Streit, Jana Strohmaier, Szabolcs Szelinger, Sarah K Tighe, Alfonso Tortorella, Gustavo Turecki, Eduard Vieta, Julia Volkert, Stephanie H Witt, Adam Wright, Peter P Zandi, Peng Zhang, Sebastian Zollner, Francis J McMahon
Bipolar disorder (BD) is a genetically complex mental illness characterized by severe oscillations of mood and behavior. Genome-wide association studies (GWAS) have identified several risk loci that together account for a small portion of the heritability. To identify additional risk loci, we performed a two-stage meta-analysis of >9 million genetic variants in 9,784 bipolar disorder patients and 30,471 controls, the largest GWAS of BD to date. In this study, to increase power we used ∼2,000 lithium-treated cases with a long-term diagnosis of BD from the Consortium on Lithium Genetics, excess controls, and analytic methods optimized for markers on the X-chromosome...
June 21, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/27270441/molecular-analysis-of-urothelial-cancer-cell-lines-for-modeling-tumor-biology-and-drug-response
#17
M L Nickerson, N Witte, K M Im, S Turan, C Owens, K Misner, S X Tsang, Z Cai, S Wu, M Dean, J C Costello, D Theodorescu
The utility of tumor-derived cell lines is dependent on their ability to recapitulate underlying genomic aberrations and primary tumor biology. Here, we sequenced the exomes of 25 bladder cancer (BCa) cell lines and compared mutations, copy number alterations (CNAs), gene expression and drug response to BCa patient profiles in The Cancer Genome Atlas (TCGA). We observed a mutation pattern associated with altered CpGs and APOBEC-family cytosine deaminases similar to mutation signatures derived from somatic alterations in muscle-invasive (MI) primary tumors, highlighting a major mechanism(s) contributing to cancer-associated alterations in the BCa cell line exomes...
June 6, 2016: Oncogene
https://www.readbyqxmd.com/read/27244233/a-pilot-study-on-commonality-and-specificity-of-copy-number-variants-in-schizophrenia-and-bipolar-disorder
#18
J Chen, V D Calhoun, N I Perrone-Bizzozero, G D Pearlson, J Sui, Y Du, J Liu
Schizophrenia (SZ) and bipolar disorder (BD) are known to share genetic risks. In this work, we conducted whole-genome scanning to identify cross-disorder and disorder-specific copy number variants (CNVs) for these two disorders. The Database of Genotypes and Phenotypes (dbGaP) data were used for discovery, deriving from 2416 SZ patients, 592 BD patients and 2393 controls of European Ancestry, as well as 998 SZ patients, 121 BD patients and 822 controls of African Ancestry. PennCNV and Birdsuite detected high-confidence CNVs that were aggregated into CNV regions (CNVRs) and compared with the database of genomic variants for confirmation...
2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27240780/the-correlation-between-9p21-chromosome-rs4977574-polymorphism-genotypes-and-the-development-of-coronary-artery-heart-disease
#19
Oushan Tang, Jin Lv, Yinhong Cheng, Fengming Qin
Our aim is to investigate the correlation between 9p21 chromosome rs4977574 polymorphism genotypes and the development of coronary artery heart disease (CHD). Two hundred and eighty-nine patients with angiography-confirmed CHD were recruited as the CHD group, while 338 subjects without CHD symptoms were enrolled as the control group. For all participating subjects, the genotypes of rs4977574 polymorphism were examined by the real-time PCR analysis. Analyses acquired from single-locus technique showed that genotype distribution of rs4977574 polymorphism was significantly different (p = 0...
May 30, 2016: Cardiovascular Toxicology
https://www.readbyqxmd.com/read/27207013/whole-genome-profiling-helps-to-classify-phyllodes-tumours-of-the-breast
#20
Marick Laé, Philippe La Rosa, Jonas Mandel, Fabien Reyal, Philippe Hupé, Philippe Terrier, Jérôme Couturier
AIMS: The aim of this study was to analyse a series of borderline and malignant phyllodes tumours (PTs) of the breast by whole-genome profiling to identify genomic markers that could help to recognise potentially malignant tumours within borderline tumours. METHODS: We evaluated the genetic imbalances of a series of 53 PTs (30 borderline, 23 malignant) using the Human CNV370 BeadChip microarray (Illumina), containing 370 000 SNP markers and correlate this alterations with clinicopathological features...
May 20, 2016: Journal of Clinical Pathology
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