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Chromosome 9p21

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
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
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
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
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
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
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...
2016: Nature Communications
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
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
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
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
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
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
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
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
Ryan C Romano, Wonwoo Shon, William R Sukov
Background Malignant melanoma of the nail apparatus is exceedingly rare. Increasingly, genetic studies have been employed to aid in distinguishing between malignant melanoma and benign melanocytic nevi. Methods Archived nail apparatus melanomas were analyzed by fluorescence in situ hybridization (FISH) using probes targeting the genes at 6p25 (RREB1), 11q13 (CCND1), 8q24.1 (MYC), 6q23 (MYB), 9p21 (CDKN2A) and the centromeres of chromosomes 8 (D8Z2) and 6 (D6Z1). The results were correlated with clinical and demographic information...
September 2016: International Journal of Surgical Pathology
Pierre Chirac, Denis Maillet, Frédéric Leprêtre, Sylvie Isaac, Olivier Glehen, Martin Figeac, Laurent Villeneuve, Julien Péron, Fernando Gibson, Françoise Galateau-Sallé, François-Noël Gilly, Marie Brevet
Malignant peritoneal mesotheliomas (MPM) are rare, accounting for approximately 8% of cases of mesothelioma in France. We performed comparative genomic hybridization (CGH) on frozen MPM samples using the Agilent Human Genome CGH 180 K array. Samples were taken from a total of 33 French patients, comprising 20 men and 13 women with a mean (range) age of 58.4 (17-76) years. Asbestos exposure was reported in 8 patients (24.2%). Median (range) overall survival (OS) was 39 (0-119) months. CGH analysis demonstrated the presence of chromosomal instability in patients with MPM, with a genomic pattern that was similar to that described for pleural mesothelioma, including the loss of chromosomal regions 3p21, 9p21, and 22q12...
September 2016: Human Pathology
Mariela C Coccé, Balca R Mardin, Susanne Bens, Adrian M Stütz, Fabiana Lubieniecki, Inga Vater, Jan O Korbel, Reiner Siebert, Cristina N Alonso, Marta S Gallego
Congenital gliobastoma multiforme (GBM) is rare and little is known about the molecular defects underlying the initiation and progression of this tumor type. We present a case of congenital GBM analyzed by conventional cytogenetics, fluorescence in situ hybridization, array comparative genomic hybridization and next generation sequencing. On cytogenetic analysis we detected a reciprocal translocation t(6;12)(q21;q24.3). By sequencing, the translocation was shown to form a fusion between the 5' region of ZCCHC8 and the 3' region of ROS1...
September 2016: Genes, Chromosomes & Cancer
Tea Kaartokallio, A Inkeri Lokki, Hanna Peterson, Katja Kivinen, Leena Hiltunen, Elina Salmela, Tuuli Lappalainen, Paula Maanselkä, Sanna Heino, Sakari Knuutila, Ayat Sayed, Lucilla Poston, Shaun P Brennecke, Matthew P Johnson, Linda Morgan, Eric K Moses, Juha Kere, Hannele Laivuori
INTRODUCTION: Preeclampsia is a common and partially genetic pregnancy complication characterized by hypertension and proteinuria. Association with cardiovascular disease and type 2 diabetes has been reported in 9p21 by several genome-wide association studies. It has been hypothesized that cardiometabolic diseases may share common etiology with preeclampsia. MATERIALS AND METHODS: We tested association with the 9p21 region to preeclampsia in the Finnish population by genotyping 23 tagging single nucleotide polymorphisms (SNPs) in 15 extended preeclampsia families and in a nationwide cohort consisting of 281 cases and 349 matched controls...
August 2016: Annals of Medicine
Xiao-Li Cao, Rui-Xing Yin, Feng Huang, Jin-Zhen Wu, Wu-Xian Chen
The single nucleotide polymorphisms (SNPs) related to both coronary heart disease (CHD) and ischemic stroke (IS) in Chinese individuals have not been identified definitely. This study was developed to evaluate the genetic susceptibility to CHD and IS on the chromosome 9p21 and the adenosine triphosphate (ATP)-binding cassette transporter A1 genes (ABCA1) in a Chinese Han population. Genotypes of the rs1333040, rs1333042, rs4977574, rs2066715 and rs2740483 SNPs were determined in 1134 unrelated patients (CHD, 565 and IS, 569) and 541 controls...
2016: International Journal of Molecular Sciences
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