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Whole Exome Sequencing Gene Package Vision Disorders, Version 6.1, 31-1-2020
Whole Exome Sequencing Gene package Vision disorders, version 6.1, 31-1-2020 Technical information DNA was enriched using Agilent SureSelect DNA + SureSelect OneSeq 300kb CNV Backbone + Human All Exon V7 capture and paired-end sequenced on the Illumina platform (outsourced). The aim is to obtain 10 Giga base pairs per exome with a mapped fraction of 0.99. The average coverage of the exome is ~50x. Duplicate and non-unique reads are excluded. Data are demultiplexed with bcl2fastq Conversion Software from Illumina. Reads are mapped to the genome using the BWA-MEM algorithm (reference: http://bio-bwa.sourceforge.net/). Variant detection is performed by the Genome Analysis Toolkit HaplotypeCaller (reference: http://www.broadinstitute.org/gatk/). The detected variants are filtered and annotated with Cartagenia software and classified with Alamut Visual. It is not excluded that pathogenic mutations are being missed using this technology. At this moment, there is not enough information about the sensitivity of this technique with respect to the detection of deletions and duplications of more than 5 nucleotides and of somatic mosaic mutations (all types of sequence changes). HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x ABCA4 Cone-rod dystrophy 3, 604116 601691 94 100 100 97 Fundus flavimaculatus, 248200 {Macular degeneration, age-related, 2}, 153800 Retinal dystrophy, early-onset severe, 248200 Retinitis pigmentosa 19, 601718 Stargardt disease -
Genes in Eyecare Geneseyedoc 3 W.M
Genes in Eyecare geneseyedoc 3 W.M. Lyle and T.D. Williams 15 Mar 04 This information has been gathered from several sources; however, the principal source is V. A. McKusick’s Mendelian Inheritance in Man on CD-ROM. Baltimore, Johns Hopkins University Press, 1998. Other sources include McKusick’s, Mendelian Inheritance in Man. Catalogs of Human Genes and Genetic Disorders. Baltimore. Johns Hopkins University Press 1998 (12th edition). http://www.ncbi.nlm.nih.gov/Omim See also S.P.Daiger, L.S. Sullivan, and B.J.F. Rossiter Ret Net http://www.sph.uth.tmc.edu/Retnet disease.htm/. Also E.I. Traboulsi’s, Genetic Diseases of the Eye, New York, Oxford University Press, 1998. And Genetics in Primary Eyecare and Clinical Medicine by M.R. Seashore and R.S.Wappner, Appleton and Lange 1996. M. Ridley’s book Genome published in 2000 by Perennial provides additional information. Ridley estimates that we have 60,000 to 80,000 genes. See also R.M. Henig’s book The Monk in the Garden: The Lost and Found Genius of Gregor Mendel, published by Houghton Mifflin in 2001 which tells about the Father of Genetics. The 3rd edition of F. H. Roy’s book Ocular Syndromes and Systemic Diseases published by Lippincott Williams & Wilkins in 2002 facilitates differential diagnosis. Additional information is provided in D. Pavan-Langston’s Manual of Ocular Diagnosis and Therapy (5th edition) published by Lippincott Williams & Wilkins in 2002. M.A. Foote wrote Basic Human Genetics for Medical Writers in the AMWA Journal 2002;17:7-17. A compilation such as this might suggest that one gene = one disease. -
Genetic and Developmental Basis of Renal Coloboma (Papillorenal) Syndrome
Perspective Genetic and developmental basis of renal coloboma (papillorenal) syndrome Expert Rev. Ophthalmol. 4(2), 135–xxx (2009) Lisa A Schimmenti Renal coloboma syndrome, also known as papillorenal syndrome, is characterized by optic Department of Pediatrics and nerve anomalies and kidney hypodysplasia. Autosomal dominant mutations in the gene Ophthalmology, University of encoding the paired box transcription factor PAX2 can be identified in nearly half of all Minnesota Medical School, 420 patients with this phenotype. The primary ophthalmologic findings include congenital central Delaware Street Southeast, retinal vasculature absence associated with abnormalities in retinal blood vessel patterning MMC 730, Minnesota, and deeply excavated optic discs. Other published findings include optic nerve hypoplasia, MN 55455, USA optic nerve cyst, optic nerve pits, retinal coloboma, microphthalmia and scleral staphyloma. Tel.: +1 612 624 5613 Visual acuity ranges from normal to severe impairment. Up to one third of affected patients Fax: +1 612 626 2993 will develop end-stage renal disease. Mouse and zebrafish withPax2/pax2a mutations provide [email protected] developmentally based explanations for the observed phenotypic observations in affected patients. KEYWORDS: optic nerve coloboma • optic nerve dysplasia • papillorenal syndrome • PAX2 • renal coloboma syndrome The clinical presentation of optic nerve anomalies total of 10 years later, Weaver et al. reported a case associated with renal hypodysplasia should alert the of two brothers, both with optic nerve colobomas, clinician to the possibility that a patient may have interstitial nephritis and renal failure [3]. Weaver renal coloboma syndrome, a condition also known noted the similarity of the optic nerve colobomas as papillorenal syndrome (OMIM#120330). The in his patients with the ‘morning glory anomaly’, optic nerve findings could be described as a ‘dys- previously reported by Karcher et al. -
WES Gene Package Multiple Congenital Anomalie.Xlsx
Whole Exome Sequencing Gene package Multiple congenital anomalie, version 5, 1‐2‐2018 Technical information DNA was enriched using Agilent SureSelect Clinical Research Exome V2 capture and paired‐end sequenced on the Illumina platform (outsourced). The aim is to obtain 8.1 Giga base pairs per exome with a mapped fraction of 0.99. The average coverage of the exome is ~50x. Duplicate reads are excluded. Data are demultiplexed with bcl2fastq Conversion Software from Illumina. Reads are mapped to the genome using the BWA‐MEM algorithm (reference: http://bio‐bwa.sourceforge.net/). Variant detection is performed by the Genome Analysis Toolkit HaplotypeCaller (reference: http://www.broadinstitute.org/gatk/). The detected variants are filtered and annotated with Cartagenia software and classified with Alamut Visual. It is not excluded that pathogenic mutations are being missed using this technology. At this moment, there is not enough information about the sensitivity of this technique with respect to the detection of deletions and duplications of more than 5 nucleotides and of somatic mosaic mutations (all types of sequence changes). HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x A4GALT [Blood group, P1Pk system, P(2) phenotype], 111400 607922 101 100 100 99 [Blood group, P1Pk system, p phenotype], 111400 NOR polyagglutination syndrome, 111400 AAAS Achalasia‐addisonianism‐alacrimia syndrome, 231550 605378 73 100 100 100 AAGAB Keratoderma, palmoplantar, -
Orphanet Report Series Rare Diseases Collection
Marche des Maladies Rares – Alliance Maladies Rares Orphanet Report Series Rare Diseases collection DecemberOctober 2013 2009 List of rare diseases and synonyms Listed in alphabetical order www.orpha.net 20102206 Rare diseases listed in alphabetical order ORPHA ORPHA ORPHA Disease name Disease name Disease name Number Number Number 289157 1-alpha-hydroxylase deficiency 309127 3-hydroxyacyl-CoA dehydrogenase 228384 5q14.3 microdeletion syndrome deficiency 293948 1p21.3 microdeletion syndrome 314655 5q31.3 microdeletion syndrome 939 3-hydroxyisobutyric aciduria 1606 1p36 deletion syndrome 228415 5q35 microduplication syndrome 2616 3M syndrome 250989 1q21.1 microdeletion syndrome 96125 6p subtelomeric deletion syndrome 2616 3-M syndrome 250994 1q21.1 microduplication syndrome 251046 6p22 microdeletion syndrome 293843 3MC syndrome 250999 1q41q42 microdeletion syndrome 96125 6p25 microdeletion syndrome 6 3-methylcrotonylglycinuria 250999 1q41-q42 microdeletion syndrome 99135 6-phosphogluconate dehydrogenase 67046 3-methylglutaconic aciduria type 1 deficiency 238769 1q44 microdeletion syndrome 111 3-methylglutaconic aciduria type 2 13 6-pyruvoyl-tetrahydropterin synthase 976 2,8 dihydroxyadenine urolithiasis deficiency 67047 3-methylglutaconic aciduria type 3 869 2A syndrome 75857 6q terminal deletion 67048 3-methylglutaconic aciduria type 4 79154 2-aminoadipic 2-oxoadipic aciduria 171829 6q16 deletion syndrome 66634 3-methylglutaconic aciduria type 5 19 2-hydroxyglutaric acidemia 251056 6q25 microdeletion syndrome 352328 3-methylglutaconic -
Basement Membranes in Diseases Affecting the Eye, Kidney
Van Agtmael, T. and Bruckner-Tuderman, L. (2010) Basement membranes and human disease. Cell and Tissue Research, 339 (1). pp. 167-188. ISSN 0302-766X http://eprints.gla.ac.uk/35275/ Deposited on: 30 August 2010 Enlighten – Research publications by members of the University of Glasgow http://eprints.gla.ac.uk Basement membranes and human disease Tom van Agtmael§ and Leena Bruckner-Tuderman* § Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow, U.K. and * Dept. of Dermatology, University Medical Center Freiburg and Freiburg Institute for Advanced Studies, Freiburg, Germany Corresponding authors: Tom Van Agtmael Faculty of Biomedical and Life Sciences, Davidson Building, University of Glasgow, University Avenue, Glasgow UK, [email protected],. Leena Bruckner-Tuderman Department of Dermatology, University Medical Center Freiburg, Hauptstr. 7, 79104 Freiburg, Germany. E-mail: [email protected] Keywords: basement membrane, laminin, collagen, laminin, nidogen Abbreviations BM: basement membrane, NMJ neuromuscular junction, DEJ dermo epidermal junction, SJS Schwartz Jampel syndrome, DDSH Dyssegmental dysplasia silverman handmaker type, EB epidermolysis bullosa, GBM glomerular basement membrane 1 Abstract In 1990 the role of basement membranes in human disease was established by the identification of COL4A5 mutations in Alport’s syndrome. Since then the number of diseases caused by mutations in basement membrane components has steadily increased as has our understanding of the roles of basement membranes in organ development and function. However, many questions remain as to the molecular and cellular consequences of these mutations and how they lead to the observed disease phenotypes. Despite this, exciting progress has recently been made with potential treatment options for some of these so far incurable diseases. -
Mackenzie's Mission Gene & Condition List
Mackenzie’s Mission Gene & Condition List What conditions are being screened for in Mackenzie’s Mission? Genetic carrier screening offered through this research study has been carefully developed. It is focused on providing people with information about their chance of having children with a severe genetic condition occurring in childhood. The screening is designed to provide genetic information that is relevant and useful, and to minimise uncertain and unclear information. How the conditions and genes are selected The Mackenzie’s Mission reproductive genetic carrier screen currently includes approximately 1300 genes which are associated with about 750 conditions. The reason there are fewer conditions than genes is that some genetic conditions can be caused by changes in more than one gene. The gene list is reviewed regularly. To select the conditions and genes to be screened, a committee comprised of experts in genetics and screening was established including: clinical geneticists, genetic scientists, a genetic pathologist, genetic counsellors, an ethicist and a parent of a child with a genetic condition. The following criteria were developed and are used to select the genes to be included: • Screening the gene is technically possible using currently available technology • The gene is known to cause a genetic condition • The condition affects people in childhood • The condition has a serious impact on a person’s quality of life and/or is life-limiting o For many of the conditions there is no treatment or the treatment is very burdensome for the child and their family. For some conditions very early diagnosis and treatment can make a difference for the child. -
Eleventh Edition
SUPPLEMENT TO April 15, 2009 A JOBSON PUBLICATION www.revoptom.com Eleventh Edition Joseph W. Sowka, O.D., FAAO, Dipl. Andrew S. Gurwood, O.D., FAAO, Dipl. Alan G. Kabat, O.D., FAAO Supported by an unrestricted grant from Alcon, Inc. 001_ro0409_handbook 4/2/09 9:42 AM Page 4 TABLE OF CONTENTS Eyelids & Adnexa Conjunctiva & Sclera Cornea Uvea & Glaucoma Viitreous & Retiina Neuro-Ophthalmic Disease Oculosystemic Disease EYELIDS & ADNEXA VITREOUS & RETINA Blow-Out Fracture................................................ 6 Asteroid Hyalosis ................................................33 Acquired Ptosis ................................................... 7 Retinal Arterial Macroaneurysm............................34 Acquired Entropion ............................................. 9 Retinal Emboli.....................................................36 Verruca & Papilloma............................................11 Hypertensive Retinopathy.....................................37 Idiopathic Juxtafoveal Retinal Telangiectasia...........39 CONJUNCTIVA & SCLERA Ocular Ischemic Syndrome...................................40 Scleral Melt ........................................................13 Retinal Artery Occlusion ......................................42 Giant Papillary Conjunctivitis................................14 Conjunctival Lymphoma .......................................15 NEURO-OPHTHALMIC DISEASE Blue Sclera .........................................................17 Dorsal Midbrain Syndrome ..................................45 -
Psykisk Utviklingshemming Og Forsinket Utvikling
Psykisk utviklingshemming og forsinket utvikling Genpanel, versjon v03 Tabellen er sortert på gennavn (HGNC gensymbol) Navn på gen er iht. HGNC >x10 Andel av genet som har blitt lest med tilfredstillende kvalitet flere enn 10 ganger under sekvensering x10 er forventet dekning; faktisk dekning vil variere. Gen Gen (HGNC Transkript >10x Fenotype (symbol) ID) AAAS 13666 NM_015665.5 100% Achalasia-addisonianism-alacrimia syndrome OMIM AARS 20 NM_001605.2 100% Charcot-Marie-Tooth disease, axonal, type 2N OMIM Epileptic encephalopathy, early infantile, 29 OMIM AASS 17366 NM_005763.3 100% Hyperlysinemia OMIM Saccharopinuria OMIM ABCB11 42 NM_003742.2 100% Cholestasis, benign recurrent intrahepatic, 2 OMIM Cholestasis, progressive familial intrahepatic 2 OMIM ABCB7 48 NM_004299.5 100% Anemia, sideroblastic, with ataxia OMIM ABCC6 57 NM_001171.5 93% Arterial calcification, generalized, of infancy, 2 OMIM Pseudoxanthoma elasticum OMIM Pseudoxanthoma elasticum, forme fruste OMIM ABCC9 60 NM_005691.3 100% Hypertrichotic osteochondrodysplasia OMIM ABCD1 61 NM_000033.3 77% Adrenoleukodystrophy OMIM Adrenomyeloneuropathy, adult OMIM ABCD4 68 NM_005050.3 100% Methylmalonic aciduria and homocystinuria, cblJ type OMIM ABHD5 21396 NM_016006.4 100% Chanarin-Dorfman syndrome OMIM ACAD9 21497 NM_014049.4 99% Mitochondrial complex I deficiency due to ACAD9 deficiency OMIM ACADM 89 NM_000016.5 100% Acyl-CoA dehydrogenase, medium chain, deficiency of OMIM ACADS 90 NM_000017.3 100% Acyl-CoA dehydrogenase, short-chain, deficiency of OMIM ACADVL 92 NM_000018.3 100% VLCAD -
Inherited Connective Tissue Disorders of Collagens: Lessons from Targeted Mutagenesis
13 Inherited Connective Tissue Disorders of Collagens: Lessons from Targeted Mutagenesis Christelle Bonod-Bidaud and Florence Ruggiero Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon, UMR CNRS 5242, University Lyon 1, France 1. Introduction The extracellular matrix (ECM) is the cell structural environment in tissues and organs. The ECM is a dynamic structure that it is constantly remodelled. It contributes to tissue integrity and mechanical properties. It is also essential for maintaining tissue homeostasis, morphogenesis and differentiation, which it does, through specific interactions with cells. The ECM is composed of a mixture of water and macromolecules classified into four main categories: collagens, proteoglycans, elastic proteins, and non-collagenous glycoproteins (also called adhesive glycoproteins). The nature, concentration and ratio of the different ECM components are all important factors in the regulation of the assembly of complex tissue-specific networks tuned to meet mechanical and biological requirements of tissues. Collagens form a superfamily of 28 trimeric proteins, distinguishable from the other ECM components by their particular abundance in tissues (collagens represent up to 80-90% of total proteins in skin, tendon and bones) and their capacity to self-assemble into supramolecular organized structures (the best known being the banded fibers). The collagen superfamily is highly complex and shows a remarkable diversity in structure, tissue distribution and function (Ricard-Blum and Ruggiero, 2005). The importance -
Albinism: Modern Molecular Diagnosis
British Journal of Ophthalmology 1998;82:189–195 189 Br J Ophthalmol: first published as 10.1136/bjo.82.2.189 on 1 February 1998. Downloaded from PERSPECTIVE Albinism: modern molecular diagnosis Susan M Carden, Raymond E Boissy, Pamela J Schoettker, William V Good Albinism is no longer a clinical diagnosis. The past cytes and into which melanin is confined. In the skin, the classification of albinism was predicated on phenotypic melanosome is later transferred from the melanocyte to the expression, but now molecular biology has defined the surrounding keratinocytes. The melanosome precursor condition more accurately. With recent advances in arises from the smooth endoplasmic reticulum. Tyrosinase molecular research, it is possible to diagnose many of the and other enzymes regulating melanin synthesis are various albinism conditions on the basis of genetic produced in the rough endoplasmic reticulum, matured in causation. This article seeks to review the current state of the Golgi apparatus, and translocated to the melanosome knowledge of albinism and associated disorders of hypo- where melanin biosynthesis occurs. pigmentation. Tyrosinase is a copper containing, monophenol, mono- The term albinism (L albus, white) encompasses geneti- oxygenase enzyme that has long been known to have a cally determined diseases that involve a disorder of the critical role in melanogenesis.5 It catalyses three reactions melanin system. Each condition of albinism is due to a in the melanin pathway. The rate limiting step is the genetic mutation on a diVerent chromosome. The cutane- hydroxylation of tyrosine into dihydroxyphenylalanine ous hypopigmentation in albinism ranges from complete (DOPA) by tyrosinase, but tyrosinase does not act alone. -
Blueprint Genetics Vitreoretinopathy Panel
Vitreoretinopathy Panel Test code: OP0701 Is a 24 gene panel that includes assessment of non-coding variants. Is ideal for patients with a clinical suspicion / diagnosis of vitreoretinopathy. The genes on this panel are included in the Retinal Dystropy Panel. About Vitreoretinopathy Vitreoretinal diseases are characterised by the degeneration of the vitreous and retina of the eye. Several types of vitreoretinopathies exist giving rise to a spectrum of phenotypic presentations such as retinal detachment, optically empty vitreous, fibrillary condensation, cataract, and neovascularization. The condition includes familial exudative vitreoretinopathy, snowflake vitreoretinal degeneration, Norrie disease, Wagner syndrome, Stickler syndrome and Knobloch syndrome. The vitreoretinopathies may be inherited in an autosomal dominant, autosomal recessive, or X-linked manner. For instance, autosomal dominant familial exudative vitreoretinopathy (FEVR) is caused by mutations in FZD4; LRP5 has been associated with both autosomal dominant and recessive cases and NDP with X-linked FEVR. The clinical presentation and the disease course can be highly variable. The prevalence of FEVR is unknown, but it is a rare disorder. Availability 4 weeks Gene Set Description Genes in the Vitreoretinopathy Panel and their clinical significance Gene Associated phenotypes Inheritance ClinVar HGMD ATOH7 Persistent hyperplastic primary vitreous, autosomal recessive AR 4 9 BEST1 Vitreoretinochoroidopathy, Microcornea, Rod-cone dystrophy, Posterior AD/AR 62 318 staphyloma, Bestrophinopathy,