Psychiatric Syndromes in Individuals with Chromosome 18 Abnormalities
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
18P Deletions FTNW
18p deletions rarechromo.org 18p deletions A deletion of 18p means that the cells of the body have a small but variable amount of genetic material missing from one of their 46 chromosomes – chromosome 18. For healthy development, chromosomes should contain just the right amount of material – not too much and not too little. Like most other chromosome disorders, 18p deletions increase the risk of birth defects, developmental delay and learning difficulties. However, the problems vary and depend very much on what genetic material is missing. Chromosomes are made up mostly of DNA and are the structures in the nucleus of the body’s cells that carry genetic information (known as genes), telling the body how to develop, grow and function. Base pairs are the chemicals in DNA that form the ends of the ‘rungs’ of its ladder-like structure. Chromosomes usually come in pairs, one chromosome from each parent. Of these 46 chromosomes, two are a pair of sex chromosomes, XX (a pair of X chromosomes) in females and XY (one X chromosome and one Y chromosome) in males. The remaining 44 chromosomes are grouped in 22 pairs, numbered 1 to 22 approximately from the largest to the smallest. Each chromosome has a short ( p) arm (shown at the top in the diagram on the facing page) and a long ( q) arm (the bottom part of the chromosome). People with an 18p deletion have one intact chromosome 18, but the other is missing a smaller or larger piece from the short arm and this can affect their learning and physical development. -
Chromosome 18
Chromosome 18 Description Humans normally have 46 chromosomes in each cell, divided into 23 pairs. Two copies of chromosome 18, one copy inherited from each parent, form one of the pairs. Chromosome 18 spans about 78 million DNA building blocks (base pairs) and represents approximately 2.5 percent of the total DNA in cells. Identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to predict the number of genes on each chromosome, the estimated number of genes varies. Chromosome 18 likely contains 200 to 300 genes that provide instructions for making proteins. These proteins perform a variety of different roles in the body. Health Conditions Related to Chromosomal Changes The following chromosomal conditions are associated with changes in the structure or number of copies of chromosome 18. Distal 18q deletion syndrome Distal 18q deletion syndrome occurs when a piece of the long (q) arm of chromosome 18 is missing. The term "distal" means that the missing piece (deletion) occurs near one end of the chromosome arm. The signs and symptoms of distal 18q deletion syndrome include delayed development and learning disabilities, short stature, weak muscle tone ( hypotonia), foot abnormalities, and a wide variety of other features. The deletion that causes distal 18q deletion syndrome can occur anywhere between a region called 18q21 and the end of the chromosome. The size of the deletion varies among affected individuals. The signs and symptoms of distal 18q deletion syndrome are thought to be related to the loss of multiple genes from this part of the long arm of chromosome 18. -
A Minimum-Labeling Approach for Reconstructing Protein Networks Across Multiple Conditions
A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions Arnon Mazza1, Irit Gat-Viks2, Hesso Farhan3, and Roded Sharan1 1 Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel. Email: [email protected]. 2 Dept. of Cell Research and Immunology, Tel Aviv University, Tel Aviv 69978, Israel. 3 Biotechnology Institute Thurgau, University of Konstanz, Unterseestrasse 47, CH-8280 Kreuzlingen, Switzerland. Abstract. The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to fa- cilitate the interpretation and representation of these data. A fundamen- tal challenge in this domain is the reconstruction of a protein-protein sub- network that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorith- mic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza in- fection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes. 1 Introduction With the increasing availability of high-throughput data, network biol- arXiv:1307.7803v1 [q-bio.QM] 30 Jul 2013 ogy has become the method of choice for filtering, interpreting and rep- resenting these data. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Low Abundance of the Matrix Arm of Complex I in Mitochondria Predicts Longevity in Mice
ARTICLE Received 24 Jan 2014 | Accepted 9 Apr 2014 | Published 12 May 2014 DOI: 10.1038/ncomms4837 OPEN Low abundance of the matrix arm of complex I in mitochondria predicts longevity in mice Satomi Miwa1, Howsun Jow2, Karen Baty3, Amy Johnson1, Rafal Czapiewski1, Gabriele Saretzki1, Achim Treumann3 & Thomas von Zglinicki1 Mitochondrial function is an important determinant of the ageing process; however, the mitochondrial properties that enable longevity are not well understood. Here we show that optimal assembly of mitochondrial complex I predicts longevity in mice. Using an unbiased high-coverage high-confidence approach, we demonstrate that electron transport chain proteins, especially the matrix arm subunits of complex I, are decreased in young long-living mice, which is associated with improved complex I assembly, higher complex I-linked state 3 oxygen consumption rates and decreased superoxide production, whereas the opposite is seen in old mice. Disruption of complex I assembly reduces oxidative metabolism with concomitant increase in mitochondrial superoxide production. This is rescued by knockdown of the mitochondrial chaperone, prohibitin. Disrupted complex I assembly causes premature senescence in primary cells. We propose that lower abundance of free catalytic complex I components supports complex I assembly, efficacy of substrate utilization and minimal ROS production, enabling enhanced longevity. 1 Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne NE4 5PL, UK. 2 Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle upon Tyne NE4 5PL, UK. 3 Newcastle University Protein and Proteome Analysis, Devonshire Building, Devonshire Terrace, Newcastle upon Tyne NE1 7RU, UK. Correspondence and requests for materials should be addressed to T.v.Z. -
WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT (51) International Patent Classification: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, C12Q 1/68 (2018.01) A61P 31/18 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/70 (2006.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2018/056167 OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (22) International Filing Date: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 16 October 2018 (16. 10.2018) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (30) Priority Data: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 62/573,025 16 October 2017 (16. 10.2017) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, ΓΕ , IS, IT, LT, LU, LV, (71) Applicant: MASSACHUSETTS INSTITUTE OF MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TECHNOLOGY [US/US]; 77 Massachusetts Avenue, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, Cambridge, Massachusetts 02139 (US). -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Epigenetic Abnormalities Associated with a Chromosome 18(Q21-Q22) Inversion and a Gilles De La Tourette Syndrome Phenotype
Epigenetic abnormalities associated with a chromosome 18(q21-q22) inversion and a Gilles de la Tourette syndrome phenotype Matthew W. State*†‡, John M. Greally§, Adam Cuker¶, Peter N. Bowersʈ, Octavian Henegariu**, Thomas M. Morgan†, Murat Gunel††, Michael DiLuna††, Robert A. King*, Carol Nelson†, Abigail Donovan¶, George M. Anderson*, James F. Leckman*, Trevor Hawkins‡‡, David L. Pauls§§, Richard P. Lifton†**¶¶, and David C. Ward†¶¶ *Child Study Center and Departments of †Genetics, ¶¶Molecular Biochemistry and Biophysics, **Internal Medicine, ʈPediatrics, and ††Neurosurgery, ¶Yale University School of Medicine, New Haven, CT 06511; §Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461; §§Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129; and ‡‡Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA 94598 Contributed by David C. Ward, February 6, 2003 Gilles de la Tourette syndrome (GTS) is a potentially debilitating In addition to linkage and association strategies, multiple neuropsychiatric disorder defined by the presence of both vocal investigators have studied chromosomal abnormalities in indi- and motor tics. Despite evidence that this and a related phenotypic viduals and families with GTS in the hopes of identifying a gene spectrum, including chronic tics (CT) and Obsessive Compulsive or genes of major effect disrupted by the rearrangement (14–16). Disorder (OCD), are genetically mediated, no gene involved in This strategy is predicated on the notion that such patients, disease etiology has been identified. Chromosomal abnormalities although unusual, may help to identify genes that are of conse- have long been proposed to play a causative role in isolated cases quence for a subgroup of patients with GTS, OCD, and CT, and of GTS spectrum phenomena, but confirmation of this hypothesis provide important insights into physiologic pathways that more has yet to be forthcoming. -
PROTEOME of the HUMAN CHROMOSOME 18: GENE-CENTRIC IDENTIFICATION of TRANSCRIPTS, PROTEINS and PEPTIDES Addendum to the Roadmap
PROTEOME OF THE HUMAN CHROMOSOME 18: GENE-CENTRIC IDENTIFICATION OF TRANSCRIPTS, PROTEINS AND PEPTIDES Addendum to the Roadmap: HEALTH ASPECTS 1. PROTEOMICS MEETS MEDICINE At its very beginning, one of the goals of human proteomics became a disease biomarker discovery. Many works compared diseased and normal tissues and liquids to get diagnostic profiles by many proteomics methods. Of them, some cancer proteome profiling studies were considered too optimistic in terms of clinical applicability due to incorrect experimental design [Petricoin], thereby conferring the negative expectations from proteomics in translational medicine [Diamantidis, Nature]. The interlaboratory reproducibility of proteomics pipelines also was considered as a shortage in some papers, e.g. in the works of Bell et al [2009] who tested the proteome MS methods with 20-protein standard sample. These difficulties at the early stage of proteomics were partly caused by the fact that many attempts were mostly directed to the technique adjustment rather than to the clinically relevant result. However, the recent advances in mass-spectrometry including the use of MRM to quantify peptides of proteome [Anderson Hunter 2006] made the community to have a view of cautious optimism on the problem of translation to medicine [Nilsson 2010]. A reproducibility problem stated in [Bell 2009] was shown to be mainly caused by the bioinformatics misinterpretation whereas the MS itself worked properly. The readiness of MRM-based platforms to the clinical use is illustrated by the attempt to pass FDA with the mock application which describes MS-based quantitation test for 10 proteins [Regnier FE 2010]. In its current state, the test has not got a clearance. -
Overview of Research on Fusion Genes in Prostate Cancer
2011 Review Article Overview of research on fusion genes in prostate cancer Chunjiao Song1,2, Huan Chen3 1Medical Research Center, Shaoxing People’s Hospital, Shaoxing University School of Medicine, Shaoxing 312000, China; 2Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing 312000, China; 3Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310000, China Contributions: (I) Conception and design: C Song; (II) Administrative support: Shaoxing Municipal Health and Family Planning Science and Technology Innovation Project (2017CX004) and Shaoxing Public Welfare Applied Research Project (2018C30058); (III) Provision of study materials or patients: None; (IV) Collection and assembly of data: C Song; (V) Data analysis and interpretation: H Chen; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. Correspondence to: Chunjiao Song. No. 568 Zhongxing Bei Road, Shaoxing 312000, China. Email: [email protected]. Abstract: Fusion genes are known to drive and promote carcinogenesis and cancer progression. In recent years, the rapid development of biotechnologies has led to the discovery of a large number of fusion genes in prostate cancer specimens. To further investigate them, we summarized the fusion genes. We searched related articles in PubMed, CNKI (Chinese National Knowledge Infrastructure) and other databases, and the data of 92 literatures were summarized after preliminary screening. In this review, we summarized approximated 400 fusion genes since the first specific fusion TMPRSS2-ERG was discovered in prostate cancer in 2005. Some of these are prostate cancer specific, some are high-frequency in the prostate cancer of a certain ethnic group. This is a summary of scientific research in related fields and suggests that some fusion genes may become biomarkers or the targets for individualized therapies. -
Human Artificial Chromosomes Generated by Modification of a Yeast Artificial Chromosome Containing Both Human Alpha Satellite and Single-Copy DNA Sequences
Proc. Natl. Acad. Sci. USA Vol. 96, pp. 592–597, January 1999 Genetics Human artificial chromosomes generated by modification of a yeast artificial chromosome containing both human alpha satellite and single-copy DNA sequences KARLA A. HENNING*, ELIZABETH A. NOVOTNY*, SHEILA T. COMPTON*, XIN-YUAN GUAN†,PU P. LIU*, AND MELISSA A. ASHLOCK*‡ *Genetics and Molecular Biology Branch and †Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 Communicated by Francis S. Collins, National Institutes of Health, Bethesda, MD, November 6, 1998 (received for review September 3, 1998) ABSTRACT A human artificial chromosome (HAC) vec- satellite repeats also have been shown to be capable of human tor was constructed from a 1-Mb yeast artificial chromosome centromere function (13, 14). As for the third required ele- (YAC) that was selected based on its size from among several ment, the study of origins of DNA replication also has led to YACs identified by screening a randomly chosen subset of the conflicting reports, with no apparent consensus sequence Centre d’E´tude du Polymorphisme Humain (CEPH) (Paris) having yet been determined for the initiation of DNA synthesis YAC library with a degenerate alpha satellite probe. This in human cells (15, 16). YAC, which also included non-alpha satellite DNA, was mod- The production of HACs from cloned DNA sources should ified to contain human telomeric DNA and a putative origin help to define the elements necessary for human chromosomal of replication from the human b-globin locus. The resultant function and to provide an important vector suitable for the HAC vector was introduced into human cells by lipid- manipulation of large DNA sequences in human cells. -
Identifying Mitochondrial-Related Genes NDUFA10 and NDUFV2 As Prognostic Markers for Prostate Cancer Through Biclustering
Hindawi BioMed Research International Volume 2021, Article ID 5512624, 15 pages https://doi.org/10.1155/2021/5512624 Research Article Identifying Mitochondrial-Related Genes NDUFA10 and NDUFV2 as Prognostic Markers for Prostate Cancer through Biclustering Haokun Zhang ,1,2 Yuanhua Shao,1 Weijun Chen,1 and Xin Chen 1 1Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou 510006, China 2School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China Correspondence should be addressed to Xin Chen; [email protected] Received 15 February 2021; Accepted 5 May 2021; Published 24 May 2021 Academic Editor: Mohsin Khurshid Copyright © 2021 Haokun Zhang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Prostate cancer is currently associated with higher morbidity and mortality in men in the United States and Western Europe, so it is important to identify genes that regulate prostate cancer. The high-dimension gene expression profile impedes the discovery of biclusters which are of great significance to the identification of the basic cellular processes controlled by multiple genes and the identification of large-scale unknown effects hidden in the data. We applied the biclustering method MCbiclust to explore large biclusters in the TCGA cohort through a large number of iterations. Two biclusters were found with the highest silhouette coefficient value. The expression patterns of one bicluster are highly similar to those found by the gene expression profile of the known androgen-regulated genes.