Division of Immunogenetics Division of Immunogenetics
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Strokovno Poročilo UKCL 2019
STROKOVNO POROČILO 2019 STROKOVNO POROČILO 2019 Univerzitetni klinični center Ljubljana, Zaloška cesta 2, 1000 Ljubljana Odgovorna oseba: prof. dr. Jadranka Buturović Ponikar, dr. med., strokovna direktorica UKC Ljubljana Besedila za poročilo so prispevali: prof. dr. Zlatko Fras, mag. Jana Brguljan Hitij, prof. dr. Aleš Blinc, prof. dr. Matjaž Šinkovec, prof. dr. Marko Noč, prof. dr. Marjeta Terčelj, prof. dr. Borut Štabuc, prof. dr. Miha Arnol, doc. dr. Andrej Janež, prof. dr. Samo Zver, prof. dr. Matija Tomšič, Gregor Veninšek, doc. dr. Miran Brvar, dr. Hugon Možina, prof. dr. Matjaž Veselko, dr. Nikola Lakić, prof. dr. Roman Bošnjak, prof. dr. Uroš Ahčan, prof. dr. Matej Cimerman, prof. dr. Aleš Tomažič, dr. Tomaž Štupnik, asist. Bojan Štrus, prof. dr. Andrej Kansky, prof. dr. Vesna Novak Jankovič, doc. dr. Igor Frangež, prof. dr. Simon Podnar, prof. dr. Uroš Rot, doc., prof. dr. Adolf Lukanovič, doc. dr. Borut Kobal, Mag. Gorazd Kavšek, prof. dr. Eda Vrtačnik Bokal, Leon Meglič, prof. dr. Borut Peterlin, doc.dr. Marko Pokorn, doc. dr. Anamarija Meglič, prim. Mojca Brecelj Kobe, prof. dr.Tadej Avčin, Uroš Krivec, prof. dr. Rok Orel, prof. dr. Tadej Battellino, prof. dr. Tanja Kersnik Levart, prof. dr. Janez Jazbec, prof. dr. Darja Paro Panjan, prof. dr. David Neubauer, mag. Mojca Tomažič, asist. dr. Veronika Velenšek, prof. dr. Milan Petelin, prof. dr. Martina Drevenšek, dr. Rok Kosem, doc.dr. Milan Kuhar, doc. dr. Tatjana Lejko Zupanc, prof. dr. Mojca Globočnik Petrović, prof. dr. Vane Antolič, doc. dr. Aleksandar Aničin, prim. asist. Tanja Planinšek Ručigaj, doc.dr.. Dimitrij Kuhelj, doc. dr. Katja Zaletel, prof. dr. Milan Skitek, prof. -
Newsletteralumni News of the Newyork-Presbyterian Hospital/Columbia University Department of Surgery Volume 13, Number 1 Summer 2010
NEWSLETTERAlumni News of the NewYork-Presbyterian Hospital/Columbia University Department of Surgery Volume 13, Number 1 Summer 2010 CUMC 2007-2009 Transplant Activity Profile* Activity Kidney Liver Heart Lung Pancreas Baseline list at year start 694 274 174 136 24 Deceased donor transplant 123 124 93 57 11 Living donor transplant 138 17 — 0 — Transplant rate from list 33% 50% 51% 57% 35% Mortality rate while on list 9% 9% 9% 15% 0% New listings 411 217 144 68 23 Wait list at year finish 735 305 204 53 36 2007-June 2008 Percent 1-Year Survival No % No % No % No % No % Adult grafts 610 91 279 86 169 84 123 89 6 100 Adult patients 517 96 262 88 159 84 116 91 5 100 Pediatric grafts 13 100 38 86 51 91 3 100 0 — Pediatric patients 11 100 34 97 47 90 2 100 0 — Summary Data Total 2009 living donor transplants 155 (89% Kidney) Total 2009 deceased donor transplants 408 (30% Kidney, 30% Liver) 2007-June 2008 adult 1-year patient survival range 84% Heart to 100% Pancreas 2007-June 2008 pediatric 1-year patient survival range 90% Heart to 100% Kidney or lung *Health Resource and Service Administration’s Scientific Registry of Transplant Recipients (SRTR) Ed Note. The figure shows the US waiting list for whole organs which will only be partially fulfilled by some 8,000 deceased donors, along with 6,600 living donors, who will provide 28,000 to 29,000 organs in 2010. The Medical Center’s role in this process is summarized in the table, and the articles that follow my note expand on this incredible short fall and its potential solutions. -
Single Nucleotide Polymorphism (SNP)
Aquaculture Genome Technologies Zhanjiang (John) Liu Copyright © 2007 by Blackwell Publishing Chapter 6 Single Nucleotide Polymorphism (SNP) Zhanjiang Liu Single nucleotide polymorphism (SNP) describes polymorphisms caused by point mutations that give rise to different alleles containing alternative bases at a given nucleotide position within a locus. Such sequence differences due to base substitu- tions have been well characterized since the beginning of DNA sequencing in 1977, but the ability to genotype SNPs rapidly in large numbers of samples was not possible until several major technological advances in the late 1990s. With the development of the TaqMan technology, gene chip technology, pyrosequencing, and MALDI-TOF, which is matrix-assisted laser desorption ionization-time of flight mass spectrometry (Haff et al. 1997, Tost et al. 2005), SNPs are again becoming a focal point in molecular marker development because they are the most abundant polymorphism in any organ- ism (as shown in Table 6.1), adaptable to automation, and reveal hidden polymor- phism not detected with other markers and methods. SNP markers are regarded by many as the projected markers of choice for the future. In this chapter, I will summa- rize methods for SNP discovery, review the traditional approaches for SNP genotyp- ing and their principles, present several major platforms for SNP genotyping using recently developed technologies, and discuss the pros and cons of SNP markers for aquaculture genome research. What Are SNP Markers and Why Are They the Future Markers of Choice? SNP can be defined as base variation at any site of the genome among individuals, or an alternative base at a given DNA site (Figure 6.1). -
Genetic, Epidemiological and Biological Analysis of Interleukin-10
Genes and Immunity (2009) 10, 174–180 & 2009 Macmillan Publishers Limited All rights reserved 1466-4879/09 $32.00 www.nature.com/gene ORIGINAL ARTICLE Genetic, epidemiological and biological analysis of interleukin-10 promoter single-nucleotide polymorphisms suggests a definitive role for À819C/T in leprosy susceptibility AC Pereira1,5, VN Brito-de-Souza1,5, CC Cardoso2, IMF Dias-Baptista1, FPC Parelli1,3, J Venturini1,3, FR Villani-Moreno1, AG Pacheco4 and MO Moraes2 1Instituto Lauro de Souza Lima, Bauru, Sa˜o Paulo, Brazil; 2Laborato´rio de Hansenı´ase, Departamento de Micobacterioses, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil; 3Tropical Diseases Area, Botucatu Medical School, Sao Paulo State University, UNESP, Botucatu, Sa˜o Paulo, Brazil and 4Departamento de Epidemiologia e Me´todos Quantitativos em Sau´de (DEMQS), Escola Nacional de Sau´de Pu´blica (ENSP)/PROCC, FIOCRUZ, Rio de Janeiro, Brazil Leprosy is a complex infectious disease influenced by genetic and environmental factors. The genetic contributing factors are considered heterogeneous and several genes have been consistently associated with susceptibility like PARK2, tumor necrosis factor (TNF), lymphotoxin-a (LTA) and vitamin-D receptor (VDR). Here, we combined a case–control study (374 patients and 380 controls), with meta-analysis (5 studies; 2702 individuals) and biological study to test the epidemiological and physiological relevance of the interleukin-10 (IL-10) genetic markers in leprosy. We observed that the À819T allele is associated with leprosy susceptibility either in the case–control or in the meta-analysis studies. Haplotypes combining promoter single-nucleotide polymorphisms also implicated a haplotype carrying the À819T allele in leprosy susceptibility (odds ratio (OR) ¼ 1.40; P ¼ 0.01). -
Application of NGS Technology in Understanding the Pathology of Autoimmune Diseases
Journal of Clinical Medicine Review Application of NGS Technology in Understanding the Pathology of Autoimmune Diseases Anna Wajda 1 , Larysa Sivitskaya 2,* and Agnieszka Paradowska-Gorycka 1 1 Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland; [email protected] (A.W.); [email protected] (A.P.-G.) 2 Institute of Genetics and Cytology, National Academy of Sciences of Belarus, 220072 Minsk, Belarus * Correspondence: [email protected] Abstract: NGS technologies have transformed clinical diagnostics and broadly used from neonatal emergencies to adult conditions where the diagnosis cannot be made based on clinical symptoms. Autoimmune diseases reveal complicate molecular background and traditional methods could not fully capture them. Certainly, NGS technologies meet the needs of modern exploratory research, diagnostic and pharmacotherapy. Therefore, the main purpose of this review was to briefly present the application of NGS technology used in recent years in the understanding of autoimmune diseases paying particular attention to autoimmune connective tissue diseases. The main issues are presented in four parts: (a) panels, whole-genome and -exome sequencing (WGS and WES) in diagnostic, (b) Human leukocyte antigens (HLA) as a diagnostic tool, (c) RNAseq, (d) microRNA and (f) microbiome. Although all these areas of research are extensive, it seems that epigenetic impact on the development of systemic autoimmune diseases will set trends for future studies on this area. Citation: Wajda, A.; Sivitskaya, L.; Keywords: next-generation sequencing; autoimmune diseases; autoimmune connective tissue dis- Paradowska-Gorycka, A. Application eases; HLA; microRNA; microbiome of NGS Technology in Understanding the Pathology of Autoimmune Diseases. J. Clin. -
IMGT-Choreography for Immunogenetics and Immunoinformatics
In Silico Biology 5 (2005) 45–60 45 IOS Press IMGT-Choreography for Immunogenetics and Immunoinformatics Marie-Paule Lefranc∗, Oliver Clement,´ Quentin Kaas, Elodie Duprat, Patrick Chastellan, Isabelle Coelho, Kora Combres, Chantal Ginestoux, Veronique´ Giudicelli, Denys Chaume and Gerard´ Lefranc IMGT, the international ImMunoGeneTics information system , Universite´ Montpellier II, Laboratoire d’ImmunoGen´ etique´ Moleculaire´ LIGM, UPR CNRS 1142, Institut de Gen´ etique´ Humaine IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France Tel.: +33 4 99 61 99 65; Fax: +33 4 99 61 99 01 Edited by H. Michael; received 11 September 2004; revised and accepted 14 December 2004; published 24 December 2004 ABSTRACT: IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), was created in 1989 at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). IMGT provides a common access to standardized data from genome, proteome, genetics and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY has been formalized using XML Schema (IMGT-ML) for interoperability with other information systems. We are developing Web services to automatically query IMGT databases and tools. This is the first step towards IMGT-Choreography which will trigger and coordinate dynamic interactions between IMGT Web services to process complex significant biological and clinical requests. -
Multiple Sclerosis: Shall We Target CD33?
G C A T T A C G G C A T genes Article Multiple Sclerosis: Shall We Target CD33? Vasileios Siokas 1, Zisis Tsouris 1, Athina-Maria Aloizou 1 , Christos Bakirtzis 2, Ioannis Liampas 1 , Georgios Koutsis 3 , Maria Anagnostouli 4 , Dimitrios P. Bogdanos 5, Nikolaos Grigoriadis 2, Georgios M. Hadjigeorgiou 1,6 and Efthimios Dardiotis 1,* 1 Laboratory of Neurogenetics, Department of Neurology, University Hospital of Larissa, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; [email protected] (V.S.); [email protected] (Z.T.); [email protected] (A.-M.A.); [email protected] (I.L.); [email protected] (G.M.H.) 2 Multiple Sclerosis Center, B’ Department of Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, GR54636 Thessaloniki, Greece; [email protected] (C.B.); [email protected] (N.G.) 3 Neurogenetics Unit, 1st Department of Neurology, Eginition Hospital, School of Medicine, National and Kapodistrian University of Athens, Vassilissis Sofias 72-74 Ave, 11528 Athens, Greece; [email protected] 4 Multiple Sclerosis and Demyelinating Diseases Unit and Immunogenetics Laboratory, 1st Department of Neurology, Eginition Hospital, School of Medicine, National and Kapodistrian University of Athens, 115 28 Athens, Greece; [email protected] 5 Department of Rheumatology and Clinical Immunology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; [email protected] 6 Department of Neurology, Medical School, University of Cyprus, 1678 Nicosia, Cyprus * Correspondence: [email protected]; Tel.: +30-241-350-1137 Received: 23 September 2020; Accepted: 5 November 2020; Published: 12 November 2020 Abstract: Background: Multiple sclerosis (MS) is a chronic disease of the central nervous system (CNS). -
Transplanted Thymus Thymus Nor the Development of Impairs Neither the Recovery of Recipient Depleted Lymphocyte Infusion
CD4+ T Cell −Depleted Lymphocyte Infusion Impairs Neither the Recovery of Recipient Thymus nor the Development of Transplanted Thymus This information is current as of September 26, 2021. Ming Shi, Ming Li, Yunze Cui, Lin Liu, Yasushi Adachi and Susumu Ikehara J Immunol 2013; 190:2976-2983; Prepublished online 4 February 2013; doi: 10.4049/jimmunol.1201605 Downloaded from http://www.jimmunol.org/content/190/6/2976 Supplementary http://www.jimmunol.org/content/suppl/2013/02/04/jimmunol.120160 http://www.jimmunol.org/ Material 5.DC1 References This article cites 36 articles, 10 of which you can access for free at: http://www.jimmunol.org/content/190/6/2976.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 26, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Author Choice Freely available online through The Journal of Immunology Author Choice option Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology CD4+ T Cell–Depleted Lymphocyte Infusion Impairs Neither the Recovery of Recipient Thymus nor the Development of Transplanted Thymus Ming Shi,* Ming Li,* Yunze Cui,*,† Lin Liu,* Yasushi Adachi,*,‡ and Susumu Ikehara* Thymus transplantation, in conjunction with bone marrow transplantation (BMT), has been attracting attention for the treatment of various diseases. -
Thymus Transplantation Reference Number: CP.MP.189 Coding Implications Date of Last Revision: 06/21 Revision Log
Clinical Policy: Thymus Transplantation Reference Number: CP.MP.189 Coding Implications Date of Last Revision: 06/21 Revision Log See Important Reminder at the end of this policy for important regulatory and legal information. Description Complete DiGeorge anomaly is a disorder in which a person has no thymus function. Without thymus function, bone marrow stem cells do not develop into T cells, which results in immunodeficiency. Without successful treatment, patients usually die by 2 years of age. Thymus transplantation with and without immunosuppression has resulted in the development good T cell function in complete DiGeorge anomaly subjects.1 Policy/Criteria I. It is the policy of health plans affiliated with Centene Corporation® that thymus transplant (use of RVT-802) requires secondary review, due to limited evidence, when meeting all of the following: A. Complete or “atypical” DiGeorge syndrome with poor thymus function, per medical testing laboratory studies and physical examination, as confirmed by the thymus transplant clinical trial (NCT01220531); B. Immunodeficiency, or severe autoimmunity for which development of naïve T cells would be expected to lead to clinical improvement; C. Flow cytometry and phytohaemagglutinin (PHA) studies are planned to occur twice, once within 3 months of transplantation and once within one month of transplantation. Studies must be performed in a CLIA or CAP certified laboratory, preferably Duke Clinical Immunology Laboratory; D. None of the following contraindications: 1. Malignancy, except for non-melanoma localized skin cancer that has been treated appropriately, a malignancy that has been completely resected, or a treated malignancy determined to have a small likelihood of recurrence and acceptable future risks; 2. -
Thymocytes May Persist and Differentiate Without Any Input from Bone Marrow Progenitors
Brief Definitive Report Thymocytes may persist and differentiate without any input from bone marrow progenitors Laetitia Peaudecerf,1 Sara Lemos,1 Alessia Galgano,1 Gerald Krenn,1 Florence Vasseur,1 James P. Di Santo,2 Sophie Ezine,1 and Benedita Rocha1 1Institut National de la Santé et de la Recherche Médicale, Unit 1020, Faculty of Medicine Descartes Paris V, 75015 Paris, France 2Innate Immunity Unit, Pasteur Institute, 75724 Paris, France Thymus transplants can correct deficiencies of the thymus epithelium caused by the com- plete DiGeorge syndrome or FOXN1 mutations. However, thymus transplants were never used to correct T cell–intrinsic deficiencies because it is generally believed that thymocytes have short intrinsic lifespans. This notion is based on thymus transplantation experiments where it was shown that thymus-resident cells were rapidly replaced by progenitors origi- nating in the bone marrow. In contrast, here we show that neonatal thymi transplanted into interleukin 7 receptor–deficient hosts harbor populations with extensive capacity to self-renew, and maintain continuous thymocyte generation and export. These thymus transplants reconstitute the full diversity of peripheral T cell repertoires one month after surgery, which is the earliest time point studied. Moreover, transplantation experiments performed across major histocompatibility barriers show that allogeneic transplanted thymi are not rejected, and allogeneic cells do not induce graft-versus-host disease; transplants induced partial or total protection to infection. These results challenge the current dogma that thymocytes cannot self-renew, and indicate a potential use of neonatal thymus trans- plants to correct T cell–intrinsic deficiencies. Finally, as found with mature T cells, they show that thymocyte survival is determined by the competition between incoming progeni- tors and resident cells. -
Course of Study M. Sc. in Molecular & Human Genetics
Course of Study M. Sc. in Molecular & Human Genetics DISTRIBUTION OF DIFFERENT COURSES AND CREDITS IN VARIOUS SEMESTERS Semester-I Course Code Title Credits MGM101 Transmission Genetics 2 MGM102 Molecular Genetics 3 MGM103 Basic Human Genetics 3 MGM104 Cytogenetics 2 MGM105 Biochemistry 3 MGM106 Cell Biology 3 MGM107 Lab work based on courses MGM101 &MGM102 2 MGM108 Lab work based on courses MGM103 & MGM104 2 MGM109 Lab work based on courses MGM105 & MGM106 2 Total 22 Semester-II Course Code Title Credits MGM201 DNA Technology & Genetic Engineering 3 MGM202 Bioinformatics and Biotechniques 3 MGM203 Model Genetic Systems 2 MGM204 Genomic Instability and Cancer 3 MGM205 Human Genome 3 MGM206 Reproductive Genetics 2 MGM207 Lab work based on courses MGM201 & MGM202 2 MGM208 Lab work based on courses MGM203 & MGM204 2 MGM209 SWAYAM Course 2 Total 22 Semester-III Course Code Title Credits MGM301 Human Molecular Genetics 3 MGM302 Clinical Genetics 3 MGM303 Developmental Genetics 3 MGM304 Immunogenetics 3 MGM305 Population & Evolutionary Genetics 2 MGM306 Lab work based on courses MGM301 & MGM302 2 MGM307 Lab work based on courses MGM303 & MGM304 2 MGM308 SWAYAM Course 2 Total 20 Semester-IV Course Code Title Credits MGM401 Neurogenetics 3 MGM402 Genetic Counseling and Intellectual Property Rights 2 MGM403 Lab work based on course MGM401 1 MGM404 Seminar & Formulation of Research Project 2 MGM405 Comprehensive Viva-voce 2 MGM406 Dissertation 6 Total 16 Grand Total 80 SEMESTER - I MGM101: Transmission Genetics Credits: 2 Lecture hours 1. Introduction to Genetics 1 2.Mendelism 5 2.1.Mendel and his experiments 2.2.Law of segregation 2.3.Law of independent assortment 2.4.Application of laws of probability (product rule, sum rule) 2.5. -
GENETICS of LIVER DISEASE: IMMUNOGENETICS and DISEASE Gut: First Published As 10.1136/Gut.2003.031732 on 11 March 2004
RECENT ADVANCES IN CLINICAL PRACTICE GENETICS OF LIVER DISEASE: IMMUNOGENETICS AND DISEASE Gut: first published as 10.1136/gut.2003.031732 on 11 March 2004. Downloaded from PATHOGENESIS 599 PTDonaldson Gut 2004;53:599–608. doi: 10.1136/gut.2003.031732 nderstanding the genetic basis of ‘‘complex disease’’ has been heralded as one of the major challenges of the post genome era.1 However what are ‘‘complex diseases’’ and how will understanding the genetics of such diseases advance medical science? There has been a U 2 great deal of ‘‘hype’’ about the potential of the human genome mapping project. The three major claims are that this information will: (a) be used in diagnosis; (b) provide useful prognostic indices for disease management (including the development of individualised treatment regimens, based on the findings of both immunogenetic and pharmacogenetic studies); and (c) provide insight into the pathogenesis of these diseases. Of these three objectives the last has the greatest potential and is the least exaggerated claim. In this review I shall highlight major associations, discuss some of the practical issues that arise, and outline how current knowledge of the immunogenetic basis of chronic liver disease is beginning to inform the debate about disease pathogenesis. c AN INTRODUCTION TO COMPLEX TRAITS Complex traits are defined as those where inheritance does not follow a Mendelian (that is, simple) pattern. This is not a new science; studies of complex traits were first performed in the mid-20th century. However, in the 21st century, the prevailing language has changed. Previously complex traits were called ‘‘polygenic’’ (involving more than one gene), multifactorial (depending on the interaction of the host genome and one or more environmental factors), or oligogenic (whereby individual mutations in several different genes in one or more common pathways lead to the same clinical syndrome but each patient with the disease may possess a single disease causing mutation only) (see box 1).