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Rubinstein YR, Robinson PN, Gahl WA, Avillach P, Baynam G, Cederroth H, Goodwin RM, Groft SC, Hansson MG, Harris NL, Huser V, Mascalzoni D, McMurry JA, Might M, Nellaker C, Mons B, Paltoo DN, Pevsner J, Posada M, Rockett-Frase AP, Roos M, Rubinstein TB, Taruscio D, van Enckevort E, Haendel MA. The case for open science: rare diseases. JAMIA Open 2020; 3:472-486. [PMID: 33426479 PMCID: PMC7660964 DOI: 10.1093/jamiaopen/ooaa030] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/30/2020] [Accepted: 06/23/2020] [Indexed: 01/04/2023] Open
Abstract
The premise of Open Science is that research and medical management will progress faster if data and knowledge are openly shared. The value of Open Science is nowhere more important and appreciated than in the rare disease (RD) community. Research into RDs has been limited by insufficient patient data and resources, a paucity of trained disease experts, and lack of therapeutics, leading to long delays in diagnosis and treatment. These issues can be ameliorated by following the principles and practices of sharing that are intrinsic to Open Science. Here, we describe how the RD community has adopted the core pillars of Open Science, adding new initiatives to promote care and research for RD patients and, ultimately, for all of medicine. We also present recommendations that can advance Open Science more globally.
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Affiliation(s)
- Yaffa R Rubinstein
- Special Volunteer in the Office of Strategic Initiatives, National Library of Medicine, Bethesda, Maryland, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - William A Gahl
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, Maryland, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Telethon Kids Institute, Perth, Australia
| | | | - Rebecca M Goodwin
- Department of Health and Human Services, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen C Groft
- NCATS, National Institutes of Health, Bethesda, Maryland, USA
| | - Mats G Hansson
- Center for Research Ethics and Bioethics, Uppsala Universitet, Uppsala, Sweden
| | - Nomi L Harris
- Department of Environmental Genomics & System Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vojtech Huser
- Department of Health and Human Services, NCBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Deborah Mascalzoni
- Center for Research Ethics and Bioethics, Uppsala University, Sweden and EURAC Research, Bolzano, Italy
| | - Julie A McMurry
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, USA
| | - Matthew Might
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christoffer Nellaker
- Nuffield Department of Women's and Reproductive Health, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Barend Mons
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Dina N Paltoo
- Department of Health and Human Services, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute and Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Manuel Posada
- Rare Diseases Research Institute & CIBERER, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Marco Roos
- Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Tamar B Rubinstein
- Children Hospital at Montefiore/Albert Einstein College of Medicine—Pediatrics, Bronx, New York, USA
| | - Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Esther van Enckevort
- Department of Genetics, University Medical Center Groningen, University of Groningen, Leiden, Netherlands
| | - Melissa A Haendel
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, USA
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Johnstone T, Wang J, Ross D, Balanda N, Huang Y, Godfrey R, Groden C, Barton BR, Gahl W, Toro C, Malicdan MCV. Biallelic variants in two complex I genes cause abnormal splicing defects in probands with mild Leigh syndrome. Mol Genet Metab 2020; 131:98-106. [PMID: 33097395 PMCID: PMC7749052 DOI: 10.1016/j.ymgme.2020.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/25/2022]
Abstract
Leigh syndrome is a genetically heterogeneous disorder resulting from deficient oxidative energy biogenesis. The syndrome is characterized by subacute episodic decompensations, transiently elevated lactate, and necrotizing brain lesions most often in the striatum and brainstem. Acute decompensation is often triggered by viral infections. Sequalae from repeated episodes leads to progressive neurological deterioration and death. The severity of Leigh syndrome varies widely, from a rapid demise in childhood to rare adult presentations. Although the causes of Leigh syndrome include genes affecting a variety of different pathways, more than 75 of them are nuclear or mitochondrial encoded genes involved in the assembly and catalytic activity of mitochondrial respiratory complex I. Here we report the detailed clinical and molecular phenotype of two adults with mild presentations of NDUFS3 and NDUFAF6-related Leigh Syndrome. Mitochondrial assays revealed slightly reduced complex I activity in one proband and normal complex I activity in the other. The proband with NDUFS3-related Leigh syndrome was mildly affected and lived into adulthood with novel biallelic variants causing aberrant mRNA splicing (NM_004551.2:c.419G > A; p.Arg140Gln; NM_004551.2:c.381 + 6 T > C). The proband with NDUFAF6-related Leigh syndrome had biallelic variants that cause defects in mRNA splicing (NM_152416.3:c.371 T > C; p.Ile124Thr; NM_152416.3:c.420 + 2_420 + 3insTA). The mild phenotypes of these two individuals may be attributed to some residual production of normal NDUFS3 and NDUFAF6 proteins by NDUFS3 and NDUFAF6 mRNA isoforms alongside mutant transcripts. Taken together, these cases reported herein suggest that splice-regulatory variants to complex I proteins could result in milder phenotypes.
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Affiliation(s)
- Thomas Johnstone
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; United States Naval Academy, Annapolis, MD, USA
| | - Jennifer Wang
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA
| | - Daron Ross
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas Balanda
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA
| | - Yan Huang
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA
| | - Rena Godfrey
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Catherine Groden
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brandon R Barton
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - William Gahl
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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Chennen K, Weber T, Lornage X, Kress A, Böhm J, Thompson J, Laporte J, Poch O. MISTIC: A prediction tool to reveal disease-relevant deleterious missense variants. PLoS One 2020; 15:e0236962. [PMID: 32735577 PMCID: PMC7394404 DOI: 10.1371/journal.pone.0236962] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/16/2020] [Indexed: 12/20/2022] Open
Abstract
The diffusion of next-generation sequencing technologies has revolutionized research and diagnosis in the field of rare Mendelian disorders, notably via whole-exome sequencing (WES). However, one of the main issues hampering achievement of a diagnosis via WES analyses is the extended list of variants of unknown significance (VUS), mostly composed of missense variants. Hence, improved solutions are needed to address the challenges of identifying potentially deleterious variants and ranking them in a prioritized short list. We present MISTIC (MISsense deleTeriousness predICtor), a new prediction tool based on an original combination of two complementary machine learning algorithms using a soft voting system that integrates 113 missense features, ranging from multi-ethnic minor allele frequencies and evolutionary conservation, to physiochemical and biochemical properties of amino acids. Our approach also uses training sets with a wide spectrum of variant profiles, including both high-confidence positive (deleterious) and negative (benign) variants. Compared to recent state-of-the-art prediction tools in various benchmark tests and independent evaluation scenarios, MISTIC exhibits the best and most consistent performance, notably with the highest AUC value (> 0.95). Importantly, MISTIC maintains its high performance in the specific case of discriminating deleterious variants from benign variants that are rare or population-specific. In a clinical context, MISTIC drastically reduces the list of VUS (<30%) and significantly improves the ranking of "causative" deleterious variants. Pre-computed MISTIC scores for all possible human missense variants are available at http://lbgi.fr/mistic.
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Affiliation(s)
- Kirsley Chennen
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory – CNRS, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Thomas Weber
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory – CNRS, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
| | - Xavière Lornage
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Arnaud Kress
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory – CNRS, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
| | - Johann Böhm
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Julie Thompson
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory – CNRS, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
| | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Olivier Poch
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory – CNRS, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
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54
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Blanco-Sánchez B, Clément A, Stednitz SJ, Kyle J, Peirce JL, McFadden M, Wegner J, Phillips JB, Macnamara E, Huang Y, Adams DR, Toro C, Gahl WA, Malicdan MCV, Tifft CJ, Zink EM, Bloodsworth KJ, Stratton KG, Koeller DM, Metz TO, Washbourne P, Westerfield M. yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development. PLoS Genet 2020; 16:e1008841. [PMID: 32544203 PMCID: PMC7319359 DOI: 10.1371/journal.pgen.1008841] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 06/26/2020] [Accepted: 05/08/2020] [Indexed: 12/30/2022] Open
Abstract
Hypomyelination, a neurological condition characterized by decreased production of myelin sheets by glial cells, often has no known etiology. Elucidating the genetic causes of hypomyelination provides a better understanding of myelination, as well as means to diagnose, council, and treat patients. Here, we present evidence that YIPPEE LIKE 3 (YPEL3), a gene whose developmental role was previously unknown, is required for central and peripheral glial cell development. We identified a child with a constellation of clinical features including cerebral hypomyelination, abnormal peripheral nerve conduction, hypotonia, areflexia, and hypertrophic peripheral nerves. Exome and genome sequencing revealed a de novo mutation that creates a frameshift in the open reading frame of YPEL3, leading to an early stop codon. We used zebrafish as a model system to validate that YPEL3 mutations are causative of neuropathy. We found that ypel3 is expressed in the zebrafish central and peripheral nervous system. Using CRISPR/Cas9 technology, we created zebrafish mutants carrying a genomic lesion similar to that of the patient. Our analysis revealed that Ypel3 is required for development of oligodendrocyte precursor cells, timely exit of the perineurial glial precursors from the central nervous system (CNS), formation of the perineurium, and Schwann cell maturation. Consistent with these observations, zebrafish ypel3 mutants have metabolomic signatures characteristic of oligodendrocyte and Schwann cell differentiation defects, show decreased levels of Myelin basic protein in the central and peripheral nervous system, and develop defasciculated peripheral nerves. Locomotion defects were observed in adult zebrafish ypel3 mutants. These studies demonstrate that Ypel3 is a novel gene required for perineurial cell development and glial myelination.
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Affiliation(s)
| | - Aurélie Clément
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Sara J. Stednitz
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Jennifer Kyle
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Judy L. Peirce
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Marcie McFadden
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Jeremy Wegner
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Jennifer B. Phillips
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Ellen Macnamara
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yan Huang
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David R. Adams
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Camilo Toro
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - William A. Gahl
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - May Christine V. Malicdan
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cynthia J. Tifft
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Erika M. Zink
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kent J. Bloodsworth
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kelly G. Stratton
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | | | - David M. Koeller
- Molecular and Medical Genetics, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Thomas O. Metz
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Philip Washbourne
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
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55
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Ates KM, Wang T, Moreland T, Veeranan-Karmegam R, Ma M, Jeter C, Anand P, Wenzel W, Kim HG, Wolfe LA, Stephen J, Adams DR, Markello T, Tifft CJ, Settlage R, Gahl WA, Gonsalvez GB, Malicdan MC, Flanagan-Steet H, Pan YA. Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development. Dis Model Mech 2020; 13:dmm041913. [PMID: 32152089 PMCID: PMC7272357 DOI: 10.1242/dmm.041913] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022] Open
Abstract
A critical barrier in the treatment of endosomal and lysosomal diseases is the lack of understanding of the in vivo functions of the putative causative genes. We addressed this by investigating a key pair of endocytic adaptor proteins, PH domain-containing endocytic trafficking adaptor 1 and 2 (PHETA1/2; also known as FAM109A/B, Ses1/2, IPIP27A/B), which interact with the protein product of OCRL, the causative gene for Lowe syndrome. Here, we conducted the first study of PHETA1/2 in vivo, utilizing the zebrafish system. We found that impairment of both zebrafish orthologs, pheta1 and pheta2, disrupted endocytosis and ciliogenesis in renal tissues. In addition, pheta1/2 mutant animals exhibited reduced jaw size and delayed chondrocyte differentiation, indicating a role in craniofacial development. Deficiency of pheta1/2 resulted in dysregulation of cathepsin K, which led to an increased abundance of type II collagen in craniofacial cartilages, a marker of immature cartilage extracellular matrix. Cathepsin K inhibition rescued the craniofacial phenotypes in the pheta1/2 double mutants. The abnormal renal and craniofacial phenotypes in the pheta1/2 mutant animals were consistent with the clinical presentation of a patient with a de novo arginine (R) to cysteine (C) variant (R6C) of PHETA1. Expressing the patient-specific variant in zebrafish exacerbated craniofacial deficits, suggesting that the R6C allele acts in a dominant-negative manner. Together, these results provide insights into the in vivo roles of PHETA1/2 and suggest that the R6C variant is contributory to the pathogenesis of disease in the patient.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Kristin M Ates
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, VA 24016, USA
| | - Tong Wang
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Trevor Moreland
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Manxiu Ma
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, VA 24016, USA
| | - Chelsi Jeter
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Priya Anand
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Hyung-Goo Kim
- Neurological Disorder Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Lynne A Wolfe
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshi Stephen
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R Adams
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Markello
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cynthia J Tifft
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert Settlage
- Advanced Research Computing Unit, Division of Information Technology, Virginia Tech, Blacksburg, VA 24060, USA
| | - William A Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- National Institutes of Health Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD 20892, USA
| | - Graydon B Gonsalvez
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - May Christine Malicdan
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- National Institutes of Health Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Y Albert Pan
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, VA 24016, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA
- Department of Psychiatry and Behavioral Medicine, Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
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56
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Davids M, Menezes M, Guo Y, McLean SD, Hakonarson H, Collins F, Worgan L, Billington CJ, Maric I, Littlejohn RO, Onyekweli T, Adams DR, Tifft CJ, Gahl WA, Wolfe LA, Christodoulou J, Malicdan MCV. Homozygous splice-variants in human ARV1 cause GPI-anchor synthesis deficiency. Mol Genet Metab 2020; 130:49-57. [PMID: 32165008 PMCID: PMC7303973 DOI: 10.1016/j.ymgme.2020.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/15/2020] [Accepted: 02/07/2020] [Indexed: 10/25/2022]
Abstract
BACKGROUND Mutations in the ARV1 Homolog, Fatty Acid Homeostasis Modulator (ARV1), have recently been described in association with early infantile epileptic encephalopathy 38. Affected individuals presented with epilepsy, ataxia, profound intellectual disability, visual impairment, and central hypotonia. In S. cerevisiae, Arv1 is thought to be involved in sphingolipid metabolism and glycophosphatidylinositol (GPI)-anchor synthesis. The function of ARV1 in human cells, however, has not been elucidated. METHODS Mutations were discovered through whole exome sequencing and alternate splicing was validated on the cDNA level. Expression of the variants was determined by qPCR and Western blot. Expression of GPI-anchored proteins on neutrophils and fibroblasts was analyzed by FACS and immunofluorescence microscopy, respectively. RESULTS Here we describe seven patients from two unrelated families with biallelic splice mutations in ARV1. The patients presented with early onset epilepsy, global developmental delays, profound hypotonia, delayed speech development, cortical visual impairment, and severe generalized cerebral and cerebellar atrophy. The splice variants resulted in decreased ARV1 expression and significant decreases in GPI-anchored protein on the membranes of neutrophils and fibroblasts, indicating that the loss of ARV1 results in impaired GPI-anchor synthesis. CONCLUSION Loss of GPI-anchored proteins on our patients' cells confirms that the yeast Arv1 function of GPI-anchor synthesis is conserved in humans. Overlap between the phenotypes in our patients and those reported for other GPI-anchor disorders suggests that ARV1-deficiency is a GPI-anchor synthesis disorder.
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Affiliation(s)
- Mariska Davids
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Minal Menezes
- Genetic Metabolic Disorders Research Unit, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child and Adolescent Health and Genomic Medicine, Sydney Medical School, Sydney University, Sydney, NSW, Australia
| | - Yiran Guo
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Scott D McLean
- Department of Clinical Genetics, The Children's Hospital of San Antonio, San Antonio, TX, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Felicity Collins
- Discipline of Child and Adolescent Health and Genomic Medicine, Sydney Medical School, Sydney University, Sydney, NSW, Australia; Department of Clinical Genetics, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Lisa Worgan
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, NSW, Australia
| | - Charles J Billington
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irina Maric
- Hematology Service, Clinical Center, NIH, Bethesda, MD, USA
| | | | - Tito Onyekweli
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lynne A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - John Christodoulou
- Genetic Metabolic Disorders Research Unit, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child and Adolescent Health and Genomic Medicine, Sydney Medical School, Sydney University, Sydney, NSW, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Pediatrics, Melbourne Medical School, University of Melbourne, Melbourne, VIC, Australia.
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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Grineski S, Morales DX, Collins T, Wilkes J, Bonkowsky JL. Geographic and Specialty Access Disparities in US Pediatric Leukodystrophy Diagnosis. J Pediatr 2020; 220:193-199. [PMID: 32143930 PMCID: PMC7186149 DOI: 10.1016/j.jpeds.2020.01.063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/05/2020] [Accepted: 01/29/2020] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To examine disparities in the diagnosis of leukodystrophies including geographic factors and access to specialty centers. STUDY DESIGN Retrospective cohort study of pediatric patients admitted to Pediatric Health Information System hospitals. Patients with leukodystrophy were identified with International Classification of Diseases, Tenth Revision, Clinical Modification diagnostic codes for any of 4 leukodystrophies (X-linked adrenoleukodystrophy, Hurler disease, Krabbe disease, and metachromatic leukodystrophy). We used 3-level hierarchical generalized logistic modeling to predict diagnosis of a leukodystrophy based on distance traveled for hospital, neighborhood composition, urban/rural context, and access to specialty center. RESULTS We identified 501 patients with leukodystrophy. Patients seen at a leukodystrophy center of excellence hospital were 1.73 times more likely to be diagnosed than patients at non-center of excellence hospitals. Patients who traveled farther were more likely to be diagnosed than those who traveled shorter. Patients living in a Health Professionals Shortage Area zip code were 0.86 times less likely to be diagnosed than those living in a non-Health Professionals Shortage Area zip code. CONCLUSIONS Geographic factors affect the diagnosis of leukodystrophies in pediatric patients, particularly in regard to access to a center with expertise in leukodystrophies. Our findings suggest a need for improving access to pediatric specialists and possibly deploying specialists or diagnostic testing more broadly.
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Affiliation(s)
- Sara Grineski
- Department of Sociology, University of Utah, Salt Lake City, Utah
| | - Danielle X. Morales
- Department of Sociology & Anthropology. University of Texas at El Paso, El Paso, Texas
| | - Timothy Collins
- Department of Geography, University of Utah, Salt Lake City, Utah
| | | | - Joshua L. Bonkowsky
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah,Brain and Spine Center, Primary Children’s Hospital, Salt Lake City, Utah,Primary Children’s Center for Personalized Medicine, Salt Lake City, Utah,Address correspondence to: Josh Bonkowsky, Department of Pediatrics, 295 Chipeta Way/Williams Building, Salt Lake City, Utah 84108, , Phone: 801-581-6756, Fax: 801-581-4233
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58
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Taruscio D, Baynam G, Cederroth H, Groft SC, Klee EW, Kosaki K, Lasko P, Melegh B, Riess O, Salvatore M, Gahl WA. The Undiagnosed Diseases Network International: Five years and more! Mol Genet Metab 2020; 129:243-254. [PMID: 32033911 DOI: 10.1016/j.ymgme.2020.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 11/23/2022]
Abstract
Undiagnosed rare diseases (URDs) account for a significant portion of the overall rare disease burden, depending upon the country. Hence, URDs represent an unmet medical need. A specific challenge posed by the ensemble of the URD patient cohort is the heterogeneity of its composition; the group, indeed, includes very rare, still unidentified conditions as well as clinical variants of recognized rare diseases. Exact disease recognition requires new approaches that cut across national and institutional boundaries, may need the implementation of methods new to diagnostics, and embrace clinical care and research. To address these issues, the Undiagnosed Diseases Network International (UDNI) was established in 2014, with the major aims of providing diagnoses to patients, implementing additional diagnostic tools, and fostering research on novel diseases, their mechanisms, and their pathways. The UDNI involves centres with internationally recognized expertise, and its scientific resources and know-how aim to fill the knowledge gaps that impede diagnosis, in particularly for ultra-rare diseases. Consequently, the UDNI fosters the translation of research into medical practice, aided by active patient involvement. The goals of the UDNI are to work collaboratively and at an international scale to: 1) provide diagnoses for individuals who have conditions that have eluded diagnosis by clinical experts; 2) gain insights into the etiology and pathogenesis of novel diseases; 3) contribute to standards of diagnosing unsolved patients; and 4) share the results of UDNI research in a timely manner and as broadly as possible.
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Affiliation(s)
- D Taruscio
- National Centre for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy.
| | - G Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of WA, WA Health Department, Perth, Australia; Faculty of Health and Medical Sciences, Division of Paediatrics and Telethon Kids Institute, Perth, Australia
| | | | - S C Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - E W Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - K Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - P Lasko
- Department of Biology, McGill University, Montréal, Québec, Canada; Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - B Melegh
- Department of Medical Genetics, University of Pécs, School of Medicine, Clinical Center, Pecs, Hungary
| | - O Riess
- Institute of Medical Genetics and Applied Genomics, Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - M Salvatore
- National Centre for Rare Diseases, Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, Rome, Italy
| | - W A Gahl
- NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Institute, National Institutes of Health, Bethesda, MD, USA
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59
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Burke EA, Reichard KE, Wolfe LA, Brooks BP, DiGiovanna JJ, Hadley DW, Lehky TJ, Gropman AL, Tifft CJ, Gahl WA, Toro C, Adams D. A novel frameshift mutation in SOX10 causes Waardenburg syndrome with peripheral demyelinating neuropathy, visual impairment and the absence of Hirschsprung disease. Am J Med Genet A 2020; 182:1278-1283. [PMID: 32150337 DOI: 10.1002/ajmg.a.61542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/31/2020] [Accepted: 02/14/2020] [Indexed: 11/09/2022]
Abstract
Waardenburg syndrome (WS) is a group of genetic disorders associated with varying components of sensorineural hearing loss and abnormal pigmentation of the hair, skin, and eyes. There exist four different WS subtypes, each defined by the absence or presence of additional features. One of the genes associated with WS is SOX10, a key transcription factor for the development of neural crest-derived lineages. Here we report a 12-year-old boy with a novel de novo SOX10 frameshift mutation and unique combination of clinical features including primary peripheral demyelinating neuropathy, hearing loss and visual impairment but absence of Hirschsprung disease and the typical pigmentary changes of hair or skin. This expands the spectrum of currently recognized phenotypes associated with WS and illustrates the phenotypic heterogeneity of SOX10-associated WS.
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Affiliation(s)
- Elizabeth A Burke
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Kyle E Reichard
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Lynne A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, USA
| | - John J DiGiovanna
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Donald W Hadley
- Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Human Development Section, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Tanya J Lehky
- Electromyography Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Andrea L Gropman
- Human Development Section, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Department of Neurology, Children's National Medical Center, Washington, District of Columbia, USA
| | - Cynthia J Tifft
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Section on Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - David Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
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60
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Ziats MN, Ahmad A, Bernat JA, Fisher R, Glassford M, Hannibal MC, Jacher JE, Weiser N, Keegan CE, Lee KN, Marzulla TB, O'Connor BC, Quinonez SC, Seemann L, Turner L, Bielas S, Harris NL, Ogle JD, Innis JW, Martin DM. Genotype-phenotype analysis of 523 patients by genetics evaluation and clinical exome sequencing. Pediatr Res 2020; 87:735-739. [PMID: 31618753 PMCID: PMC7082194 DOI: 10.1038/s41390-019-0611-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 09/05/2019] [Accepted: 10/02/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND As clinical exome sequencing (CES) becomes more common, understanding which patients are most likely to benefit and in what manner is critical for the general pediatrics community to appreciate. METHODS Five hundred and twenty-three patients referred to the Pediatric Genetics clinic at Michigan Medicine were systematically phenotyped by the presence or absence of abnormalities for 13 body/organ systems by a Clinical Genetics team. All patients then underwent CES. RESULTS Overall, 30% of patients who underwent CES had an identified pathogenic mutation. The most common phenotypes were developmental delay (83%), neuromuscular system abnormalities (81%), and multiple congenital anomalies (42%). In all, 67% of patients had a variant of uncertain significance (VUS) or gene of uncertain significance (GUS); 23% had no variants reported. There was a significant difference in the average number of body systems affected among these groups (pathogenic 5.89, VUS 6.0, GUS 6.12, and no variant 4.6; P < 0.00001). Representative cases highlight four ways in which CES is changing clinical pediatric practice. CONCLUSIONS Patients with identified variants are enriched for multiple organ system involvement. Furthermore, our phenotyping provides broad insights into which patients are most likely to benefit from genetics referral and CES and how those results can help guide clinical practice more generally.
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Affiliation(s)
- Mark N Ziats
- Department of Internal Medicine, University of Michigan, Arbor, MI, USA
| | - Ayesha Ahmad
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
| | - John A Bernat
- Division of Medical Genetics, Stead Family Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Rachel Fisher
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
| | - Megan Glassford
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
| | - Mark C Hannibal
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
| | - Joseph E Jacher
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
| | - Natasha Weiser
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
| | - Catherine E Keegan
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Arbor, MI, USA
- Children's Clinical Trial Support Unit, University of Michigan, Arbor, MI, USA
| | - Kristen N Lee
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
| | - Tessa B Marzulla
- Department of Human Genetics, University of Michigan, Arbor, MI, USA
- Children's Clinical Trial Support Unit, University of Michigan, Arbor, MI, USA
| | - Bridget C O'Connor
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
| | - Shane C Quinonez
- Department of Internal Medicine, University of Michigan, Arbor, MI, USA
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
| | - Lauren Seemann
- Department of Human Genetics, University of Michigan, Arbor, MI, USA
- Children's Clinical Trial Support Unit, University of Michigan, Arbor, MI, USA
| | - Lauren Turner
- Department of Human Genetics, University of Michigan, Arbor, MI, USA
- Children's Clinical Trial Support Unit, University of Michigan, Arbor, MI, USA
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Arbor, MI, USA
- Children's Clinical Trial Support Unit, University of Michigan, Arbor, MI, USA
| | - Nicholas L Harris
- Children's Clinical Trial Support Unit, University of Michigan, Arbor, MI, USA
| | - Jacob D Ogle
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Arbor, MI, USA
- Children's Clinical Trial Support Unit, University of Michigan, Arbor, MI, USA
| | - Jeffrey W Innis
- Department of Internal Medicine, University of Michigan, Arbor, MI, USA
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Arbor, MI, USA
- Children's Clinical Trial Support Unit, University of Michigan, Arbor, MI, USA
| | - Donna M Martin
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan, Arbor, MI, USA.
- Department of Human Genetics, University of Michigan, Arbor, MI, USA.
- Children's Clinical Trial Support Unit, University of Michigan, Arbor, MI, USA.
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61
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Aday AW, Krier JB, Pallais JC, Fieg EL, MacRae CA, Loscalzo J. The Undiagnosed Diseases Network as a Tool for Graduate Medical Education. Am J Med 2020; 133:e18-e22. [PMID: 31301294 PMCID: PMC7610137 DOI: 10.1016/j.amjmed.2019.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 11/18/2022]
Affiliation(s)
- Aaron W Aday
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass.
| | - Joel B Krier
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - J Carl Pallais
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Elizabeth L Fieg
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Calum A MacRae
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass.
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62
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Joolharzadeh P, St Hilaire C. CD73 (Cluster of Differentiation 73) and the Differences Between Mice and Humans. Arterioscler Thromb Vasc Biol 2020; 39:339-348. [PMID: 30676071 DOI: 10.1161/atvbaha.118.311579] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As vascular disease is complex and the various manifestations are influenced by differences in vascular bed architecture, exposure to shear and mechanical forces, cell types involved, and inflammatory responses, in vivo models are necessary to recapitulate the complex physiology and dynamic cellular interactions during pathogenesis. Murine knockout models are commonly used tools for investigators to study the role of a specific gene or pathway in multifaceted disease traits. Although valuable, these models are not perfect, and this is particularly true in regard to CD73 (cluster of differentiation 73), the extracellular enzyme that generates adenosine from AMP. At baseline, CD73-deficient mice do not present with an overt phenotype, whereas CD73-deficient humans present with the complex phenotype of vascular calcification, arteriomegaly and tortuosity, and calcification in small joints. In this review, we highlight the differences between the mouse and human systems and discuss the potential to leverage findings in mice to inform us on the human conditions.
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Affiliation(s)
- Pouya Joolharzadeh
- From the Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, PA; and Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, PA
| | - Cynthia St Hilaire
- From the Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, PA; and Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, PA
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63
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Gochuico BR, Ziegler SG, Ten NS, Balanda NJ, Mason CE, Zumbo P, Evans CA, Van Waes C, Gahl WA, Malicdan MCV. A comprehensive, multidisciplinary, precision medicine approach to discover effective therapy for an undiagnosed, progressive, fibroinflammatory disease. Transl Res 2020; 215:31-40. [PMID: 31520587 PMCID: PMC6939610 DOI: 10.1016/j.trsl.2019.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/15/2019] [Accepted: 08/22/2019] [Indexed: 11/21/2022]
Abstract
Precision medicine has generated diagnoses for many patients with challenging undiagnosed disorders. Some individuals remain without a diagnosis despite comprehensive testing, and this impedes their treatment. This report addresses the role of personalized medicine in identifying effective therapy for an undiagnosed disease. A 22-year-old woman presented with chronic severe recurrent trismus, facial pain, progressive multicentric inflammatory and fibrotic masses, and high C-reactive protein. Sites of disease included the pterygomaxillary region, masseter muscles, mandible, lung, pericardium, intrabdominal cavity, and retroperitoneum. A diagnosis was not established after an extensive assessment, including multiple biopsies. The patient was subsequently evaluated under the Undiagnosed Diseases Program at the National Institutes of Health. Large scale genotyping, proteomic studies, and in vitro and gene expression analyses of fibroblasts obtained from a major disease locus were performed. Germline genetic testing did not identify strong candidate genes; proteomic studies of the patient's serum and bronchoalveolar lavage fluid and gene expression analyses of her cells were consistent with dysregulation of the tumor necrosis factor-alpha pathway. The patient's cultured fibroblasts were incubated with selected drugs, and cell proliferation was inhibited by hydroxychloroquine. Treatment of the patient with hydroxychloroquine conferred prolonged beneficial clinical effects, including stabilization of trismus and reduction of corticosteroid dose, C-reactive protein, and size of masses. This case represents an example of precision medicine applied to discover effective treatments for individuals with enigmatic undiagnosed disorders.
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Affiliation(s)
- Bernadette R Gochuico
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.
| | - Shira G Ziegler
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland; Department of Genetics and Pediatrics, Johns Hopkins University School of Medicine, Bloomberg Children's Center, Baltimore, Maryland
| | - Nicholas S Ten
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Nicholas J Balanda
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York; The World Quant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Colleen A Evans
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Carter Van Waes
- Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesda, Maryland
| | - William A Gahl
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland; NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - May C V Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland; NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
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Abstract
Advances in precision medicine require high-throughput, inexpensive, point-of-care diagnostic methods with multiomics capability for detecting a wide range of biomolecules and their molecular variants. Optical techniques have offered many promising advances toward such diagnostics. However, the inability to squeeze light with several hundred nanometer wavelengths into angstrom-scale volume for single-nucleotide measurements has hindered further progress. This limitation has been circumvented by analyzing the relative nucleobase content with Raman spectroscopy, in an optical sequencing method. Here, we performed optical sequencing measurements on positively charged silver nanoparticles to achieve 93.3% accuracy for predicting nucleobase content in label-free DNA k-mer blocks (where k = 10) as well as measurements on RNA and chemically modified nucleobases for extensions to transcriptomic and epigenetic studies. Our high-accuracy measurements were then used with a content-scoring database searching algorithm to correctly identify a β-lactamase gene from the MEGARes antibiotic resistance database and confirm the Pseudomonas aeruginosa pathogen of origin from <12 block content measurements (<15% coverage) of the gene. These results prove the feasibility of an optical sequencing platform as a diagnostic method. With the versatile range of available plasmonic substrates offering simple data acquisition, varying resolution (single-molecule to the ensemble), and multiplexing, this optical sequencing platform has potential as the rapid, cost-effective method needed for broad-spectrum biomarker detection.
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65
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Wise AL, Manolio TA, Mensah GA, Peterson JF, Roden DM, Tamburro C, Williams MS, Green ED. Genomic medicine for undiagnosed diseases. Lancet 2019; 394:533-540. [PMID: 31395441 PMCID: PMC6709871 DOI: 10.1016/s0140-6736(19)31274-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/08/2019] [Accepted: 05/16/2019] [Indexed: 12/23/2022]
Abstract
One of the primary goals of genomic medicine is to improve diagnosis through identification of genomic conditions, which could improve clinical management, prevent complications, and promote health. We explore how genomic medicine is being used to obtain molecular diagnoses for patients with previously undiagnosed diseases in prenatal, paediatric, and adult clinical settings. We focus on the role of clinical genomic sequencing (exome and genome) in aiding patients with conditions that are undiagnosed even after extensive clinical evaluation and testing. In particular, we explore the impact of combining genomic and phenotypic data and integrating multiple data types to improve diagnoses for patients with undiagnosed diseases, and we discuss how these genomic sequencing diagnoses could change clinical management.
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Affiliation(s)
- Anastasia L Wise
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - George A Mensah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cecelia Tamburro
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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66
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Kanca O, Andrews JC, Lee PT, Patel C, Braddock SR, Slavotinek AM, Cohen JS, Gubbels CS, Aldinger KA, Williams J, Indaram M, Fatemi A, Yu TW, Agrawal PB, Vezina G, Simons C, Crawford J, Lau CC, Chung WK, Markello TC, Dobyns WB, Adams DR, Gahl WA, Wangler MF, Yamamoto S, Bellen HJ, Malicdan MCV. De Novo Variants in WDR37 Are Associated with Epilepsy, Colobomas, Dysmorphism, Developmental Delay, Intellectual Disability, and Cerebellar Hypoplasia. Am J Hum Genet 2019; 105:413-424. [PMID: 31327508 PMCID: PMC6699142 DOI: 10.1016/j.ajhg.2019.06.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 06/14/2019] [Indexed: 12/16/2022] Open
Abstract
WD40 repeat-containing proteins form a large family of proteins present in all eukaryotes. Here, we identified five pediatric probands with de novo variants in WDR37, which encodes a member of the WD40 repeat protein family. Two probands shared one variant and the others have variants in nearby amino acids outside the WD40 repeats. The probands exhibited shared phenotypes of epilepsy, colobomas, facial dysmorphology reminiscent of CHARGE syndrome, developmental delay and intellectual disability, and cerebellar hypoplasia. The WDR37 protein is highly conserved in vertebrate and invertebrate model organisms and is currently not associated with a human disease. We generated a null allele of the single Drosophila ortholog to gain functional insights and replaced the coding region of the fly gene CG12333/wdr37 with GAL4. These flies are homozygous viable but display severe bang sensitivity, a phenotype associated with seizures in flies. Additionally, the mutant flies fall when climbing the walls of the vials, suggesting a defect in grip strength, and repeat the cycle of climbing and falling. Similar to wall clinging defect, mutant males often lose grip of the female abdomen during copulation. These phenotypes are rescued by using the GAL4 in the CG12333/wdr37 locus to drive the UAS-human reference WDR37 cDNA. The two variants found in three human subjects failed to rescue these phenotypes, suggesting that these alleles severely affect the function of this protein. Taken together, our data suggest that variants in WDR37 underlie a novel syndromic neurological disorder.
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Affiliation(s)
- Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan C Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029, Australia
| | - Stephen R Braddock
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Medical Center, St. Louis, MO 63104, USA; Department of Pediatrics, Saint Louis University Hospital, St. Louis, MO 63104, USA
| | - Anne M Slavotinek
- Department of Pediatrics, University of California, San Francisco, CA 94143-2711, USA
| | - Julie S Cohen
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Cynthia S Gubbels
- Division of Genetics and Genomics, Boston Children's Hospital/Harvard Medical School/Broad Institute of MIT and Harvard, Boston, MA 02138, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Judy Williams
- Paediatric Department, Bundaberg Hospital, Bundaberg, QLD 4670, Australia
| | - Maanasa Indaram
- Department of Ophthalmology, University of California, San Francisco, CA 94143-2711, USA
| | - Ali Fatemi
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Timothy W Yu
- Division of Genetics and Genomics, Boston Children's Hospital/Harvard Medical School/Broad Institute of MIT and Harvard, Boston, MA 02138, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine and Genetics and Genomics, Manton Center for Orphan Disease Research, Harvard Medical School, Boston, MA 02115, USA
| | - Gilbert Vezina
- Division of Diagnostic Imaging & Radiology, Children's National Health System, 111 Michigan Ave. NW, Washington, DC 20010, USA
| | - Cas Simons
- The Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Murdoch Childrens Research Institute, Melbourne, VIC 3052 Australia
| | - Joanna Crawford
- The Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - C Christopher Lau
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD 20892, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD 20892-1851, USA
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics (Genetics), University of Washington, Seattle, WA 98195, USA; Department of Neurology, University of Washington, Seattle, WA 98195, USA
| | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD 20892-1851, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD 20892-1851, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD 20892-1851, USA.
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Korshoj LE, Nagpal P. BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage. Comput Biol Med 2019; 110:196-206. [PMID: 31173943 DOI: 10.1016/j.compbiomed.2019.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 01/10/2023]
Abstract
A single, inexpensive diagnostic test capable of rapidly identifying a wide range of genetic biomarkers would prove invaluable in precision medicine. Previous work has demonstrated the potential for high-throughput, label-free detection of A-G-C-T content in DNA k-mers, providing an alternative to single-letter sequencing while also having inherent lossy data compression and massively parallel data acquisition. Here, we apply a new bioinformatics algorithm - block optical content scoring (BOCS) - capable of using the high-throughput content k-mers for rapid, broad-spectrum identification of genetic biomarkers. BOCS uses content-based sequence alignment for probabilistic mapping of k-mer contents to gene sequences within a biomarker database, resulting in a probability ranking of genes on a content score. Simulations of the BOCS algorithm reveal high accuracy for identification of single antibiotic resistance genes, even in the presence of significant sequencing errors (100% accuracy for no sequencing errors, and >90% accuracy for sequencing errors at 20%), and at well below full coverage of the genes. Simulations for detecting multiple resistance genes within a methicillin-resistant Staphylococcus aureus (MRSA) strain showed 100% accuracy at an average gene coverage of merely 0.515, when the k-mer lengths were variable and with 4% sequencing error within the k-mer blocks. Extension of BOCS to cancer and other genetic diseases met or exceeded the results for resistance genes. Combined with a high-throughput content-based sequencing technique, the BOCS algorithm potentiates a test capable of rapid diagnosis and profiling of genetic biomarkers ranging from antibiotic resistance to cancer and other genetic diseases.
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Affiliation(s)
- Lee E Korshoj
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Prashant Nagpal
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, 80303, USA; Materials Science and Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA.
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The prevalence and impact of psychiatric symptoms in an undiagnosed diseases clinical program. PLoS One 2019; 14:e0216937. [PMID: 31170170 PMCID: PMC6553712 DOI: 10.1371/journal.pone.0216937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/01/2019] [Indexed: 12/12/2022] Open
Abstract
In 2008, the NIH launched an undiagnosed diseases program to investigate difficult to diagnose, and typically, multi-system diseases. The objective of this study was to evaluate the presence of psychiatric symptoms or psychiatric diagnoses in a cohort of patients seeking care at the Emory Special Diagnostic Service clinic. We hypothesized that psychiatric symptoms would be prevalent and associated with trauma exposure, and a decreased quality of life and functioning. This is a cross-sectional, retrospective analysis of 247 patients seen between February 7, 2014 and May 31, 2017. The sources for data included the Emory Health History Questionnaire (HHQ) that had the work and social adjustment and quality of life enjoyment and satisfaction questionnaire–short form (QLSQ) embedded in it; medical records, and the comprehensive standardized special diagnostic clinic forms. Primary outcomes were presence of any psychiatric symptom, based on report of the symptom on the HHQ or medical record, or presence of a confirmed preexisting psychiatric disorder. Seventy-two percent of patients had at least one psychiatric symptom while 24.3% of patients had a pre-existing psychiatric diagnosis. Patients with any psychiatric symptom had significantly diminished Q-LES-Q scores (45.27 ± 18.63) versus patients with no psychiatric symptoms (62.01 ± 21.57, t = 5.60, df = 225, p<0.0001) and they had significantly greater functional disability. Patients with a psychiatric disorder also had significantly diminished Q-LES-Q scores (45.16 ± 17.28) versus those without a psychiatric diagnosis (51.85 ± 21.54, t = 2.11, df = 225, p = 0.036) but did not have significantly increased functional impairment. Both patients with psychiatric symptoms and ones with psychiatric disorders had an increased prevalence of trauma. Psychiatric symptoms are prevalent in patients evaluated for undiagnosed disorders. The presence of any psychiatric symptom, with or without a formal psychiatric diagnosis, significantly decreases quality of life and functioning. This suggests that assessment for psychiatric symptoms should be part of the evaluation of individuals with undiagnosed disorders and may have important diagnostic and treatment implications.
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Sharma P, Reichert M, Lu Y, Markello TC, Adams DR, Steinbach PJ, Fuqua BK, Parisi X, Kaler SG, Vulpe CD, Anderson GJ, Gahl WA, Malicdan MCV. Biallelic HEPHL1 variants impair ferroxidase activity and cause an abnormal hair phenotype. PLoS Genet 2019; 15:e1008143. [PMID: 31125343 PMCID: PMC6534290 DOI: 10.1371/journal.pgen.1008143] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/16/2019] [Indexed: 11/18/2022] Open
Abstract
Maintenance of the correct redox status of iron is functionally important for critical biological processes. Multicopper ferroxidases play an important role in oxidizing ferrous iron, released from the cells, into ferric iron, which is subsequently distributed by transferrin. Two well-characterized ferroxidases, ceruloplasmin (CP) and hephaestin (HEPH) facilitate this reaction in different tissues. Recently, a novel ferroxidase, Hephaestin like 1 (HEPHL1), also known as zyklopen, was identified. Here we report a child with compound heterozygous mutations in HEPHL1 (NM_001098672) who presented with abnormal hair (pili torti and trichorrhexis nodosa) and cognitive dysfunction. The maternal missense mutation affected mRNA splicing, leading to skipping of exon 5 and causing an in-frame deletion of 85 amino acids (c.809_1063del; p.Leu271_ala355del). The paternal mutation (c.3176T>C; p.Met1059Thr) changed a highly conserved methionine that is part of a typical type I copper binding site in HEPHL1. We demonstrated that HEPHL1 has ferroxidase activity and that the patient's two mutations exhibited loss of this ferroxidase activity. Consistent with these findings, the patient's fibroblasts accumulated intracellular iron and exhibited reduced activity of the copper-dependent enzyme, lysyl oxidase. These results suggest that the patient's biallelic variants are loss-of-function mutations. Hence, we generated a Hephl1 knockout mouse model that was viable and had curly whiskers, consistent with the hair phenotype in our patient. These results enhance our understanding of the function of HEPHL1 and implicate altered ferroxidase activity in hair growth and hair disorders.
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Affiliation(s)
- Prashant Sharma
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marie Reichert
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yan Lu
- Iron Metabolism Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Thomas C. Markello
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland Bethesda, Maryland, United States of America
| | - David R. Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter J. Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brie K. Fuqua
- Department of Medicine, University of California, Los Angeles, United States of America
| | - Xenia Parisi
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephen G. Kaler
- Section on Translational Neuroscience, Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christopher D. Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Gregory J. Anderson
- Iron Metabolism Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - William A. Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland Bethesda, Maryland, United States of America
| | - May Christine V. Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Benson LA, Li H, Henderson LA, Solomon IH, Soldatos A, Murphy J, Bielekova B, Kennedy AL, Rivkin MJ, Davies KJ, Hsu AP, Holland SM, Gahl WA, Sundel RP, Lehmann LE, Lee MA, Alexandrescu S, Degar BA, Duncan CN, Gorman MP. Pediatric CNS-isolated hemophagocytic lymphohistiocytosis. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2019; 6:e560. [PMID: 31044148 PMCID: PMC6467688 DOI: 10.1212/nxi.0000000000000560] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/15/2019] [Indexed: 11/15/2022]
Abstract
Objective To highlight a novel, treatable syndrome, we report 4 patients with CNS-isolated inflammation associated with familial hemophagocytic lymphohistiocytosis (FHL) gene mutations (CNS-FHL). Methods Retrospective chart review. Results Patients with CNS-FHL are characterized by chronic inflammation restricted to the CNS that is not attributable to any previously described neuroinflammatory etiology and have germline mutations in known FHL-associated genes with no signs of systemic inflammation. Hematopoietic stem cell transplantation (HCT) can be well tolerated and effective in achieving or maintaining disease remission in patients with CNS-FHL. Conclusions Early and accurate diagnosis followed by treatment with HCT can reduce morbidity and mortality in CNS-FHL, a novel, treatable syndrome. Classification of evidence This study provides Class IV evidence that HCT is well tolerated and effective in treating CNS-FHL.
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Affiliation(s)
- Leslie A Benson
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Hojun Li
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Lauren A Henderson
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Isaac H Solomon
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Ariane Soldatos
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Jennifer Murphy
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Bibiana Bielekova
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Alyssa L Kennedy
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Michael J Rivkin
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Kimberly J Davies
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Amy P Hsu
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Steven M Holland
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - William A Gahl
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Robert P Sundel
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Leslie E Lehmann
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Michelle A Lee
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Sanda Alexandrescu
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Barbara A Degar
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Christine N Duncan
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
| | - Mark P Gorman
- Department of Neurology (L.A.B., M.J.R., M.P.G.), Boston Children's Hospital; Dana-Farber/Boston Children's Cancer and Blood Disorders Center (H.L., A.L.K., L.E.L., B.A.D., C.N.D.); Department of Rheumatology (L.A.H., R.P.S.), Boston Children's Hospital; Department of Pathology (I.H.S002E, S.A.), Boston Children's Hospital, Boston, MA; Undiagnosed Diseases Program (A.S., J.M., W.A.G.), National Human Genome Research Institute; Neuroimmunological Diseases Section (B.B.), Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases; Laboratory of Clinical Immunology and Microbiology (A.P.H., S.M.H.), National Institute of Allergy and Infectious Diseases, Bethesda, MD; and Division of Hematology, Oncology (M.L.A.), and Marrow and Blood Cell Transplantation, Children's Hospital at Montefiore, Bronx, NY
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Glycomics in rare diseases: from diagnosis tomechanism. Transl Res 2019; 206:5-17. [PMID: 30423312 DOI: 10.1016/j.trsl.2018.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/22/2018] [Accepted: 10/15/2018] [Indexed: 12/16/2022]
Abstract
The National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP) studies rare genetic disorders not only to achieve diagnoses, but to understand human biology. To ascertain the contribution of protein glycosylation to rare diseases, the NIH UDP used mass spectrometry to agnostically identify abnormalities of N-linked and O-linked glycans in plasma and free oligosaccharides in the urine of 207 patients. 60% of UDP patients had a glycome profile that deviated from control values in at least 1 fluid. Additional evaluation of the fibroblast glycome in 66 patients with abnormalities in plasma and/or urine revealed a consistent glycome phenotype in 83% of these cases. Many of these patients may have secondary glycosylation defects, since it is unlikely that they all have congenital disorders of glycosylation (CDGs). In fact, whole exome sequencing revealed only a few patients with CDGs, along with several others having disorders indirectly altering glycosylation. In summary, we describe a biochemical phenotyping screen to identify defects in protein glycosylation that can elucidate mechanisms of disease among NIH UDP patients.
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Niknejad N, Jafar-Nejad H. Unbiased glycomics: a powerful tool in rare disease diagnosis and research. Transl Res 2019; 206:1-4. [PMID: 30528322 DOI: 10.1016/j.trsl.2018.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 11/25/2022]
Affiliation(s)
- Nima Niknejad
- Department of Molecular and Human Genetics, Program in Developmental Biology, Baylor College of Medicine, Houston, Texas
| | - Hamed Jafar-Nejad
- Department of Molecular and Human Genetics, Program in Developmental Biology, Baylor College of Medicine, Houston, Texas.
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Kahn-Kirby AH, Amagata A, Maeder CI, Mei JJ, Sideris S, Kosaka Y, Hinman A, Malone SA, Bruegger JJ, Wang L, Kim V, Shrader WD, Hoff KG, Latham JC, Ashley EA, Wheeler MT, Bertini E, Carrozzo R, Martinelli D, Dionisi-Vici C, Chapman KA, Enns GM, Gahl W, Wolfe L, Saneto RP, Johnson SC, Trimmer JK, Klein MB, Holst CR. Targeting ferroptosis: A novel therapeutic strategy for the treatment of mitochondrial disease-related epilepsy. PLoS One 2019; 14:e0214250. [PMID: 30921410 PMCID: PMC6438538 DOI: 10.1371/journal.pone.0214250] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/08/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Mitochondrial disease is a family of genetic disorders characterized by defects in the generation and regulation of energy. Epilepsy is a common symptom of mitochondrial disease, and in the vast majority of cases, refractory to commonly used antiepileptic drugs. Ferroptosis is a recently-described form of iron- and lipid-dependent regulated cell death associated with glutathione depletion and production of lipid peroxides by lipoxygenase enzymes. Activation of the ferroptosis pathway has been implicated in a growing number of disorders, including epilepsy. Given that ferroptosis is regulated by balancing the activities of glutathione peroxidase-4 (GPX4) and 15-lipoxygenase (15-LO), targeting these enzymes may provide a rational therapeutic strategy to modulate seizure. The clinical-stage therapeutic vatiquinone (EPI-743, α-tocotrienol quinone) was reported to reduce seizure frequency and associated morbidity in children with the mitochondrial disorder pontocerebellar hypoplasia type 6. We sought to elucidate the molecular mechanism of EPI-743 and explore the potential of targeting 15-LO to treat additional mitochondrial disease-associated epilepsies. METHODS Primary fibroblasts and B-lymphocytes derived from patients with mitochondrial disease-associated epilepsy were cultured under standardized conditions. Ferroptosis was induced by treatment with the irreversible GPX4 inhibitor RSL3 or a combination of pharmacological glutathione depletion and excess iron. EPI-743 was co-administered and endpoints, including cell viability and 15-LO-dependent lipid oxidation, were measured. RESULTS EPI-743 potently prevented ferroptosis in patient cells representing five distinct pediatric disease syndromes with associated epilepsy. Cytoprotection was preceded by a dose-dependent decrease in general lipid oxidation and the specific 15-LO product 15-hydroxyeicosatetraenoic acid (15-HETE). CONCLUSIONS These findings support the continued clinical evaluation of EPI-743 as a therapeutic agent for PCH6 and other mitochondrial diseases with associated epilepsy.
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Affiliation(s)
- Amanda H. Kahn-Kirby
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Akiko Amagata
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Celine I. Maeder
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Janet J. Mei
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Steve Sideris
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Yuko Kosaka
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Andrew Hinman
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Stephanie A. Malone
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Joel J. Bruegger
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Leslie Wang
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Virna Kim
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - William D. Shrader
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Kevin G. Hoff
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Joey C. Latham
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Euan A. Ashley
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, California, United States of America
| | - Matthew T. Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, California, United States of America
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children’s Research Hospital, Rome, Italy
| | - Rosalba Carrozzo
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children’s Research Hospital, Rome, Italy
| | - Diego Martinelli
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children’s Research Hospital, Rome, Italy
| | - Carlo Dionisi-Vici
- Clinical Division and Research Unit of Metabolic Diseases, Bambino Gesù Children's Hospital, Rome, Italy
| | - Kimberly A. Chapman
- Children’s National Rare Disease Institute, Children's National Health System, Washington, D.C., United States of America
| | - Gregory M. Enns
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - William Gahl
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lynne Wolfe
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, Maryland, United States of America
| | - Russell P. Saneto
- Division of Pediatric Neurology, Department of Neurology, Neuroscience Institute, Seattle Children's Hospital, Seattle, Washington, United States of America
| | - Simon C. Johnson
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Neurology, University of Washington, Seattle, Washington, United States of America
| | - Jeffrey K. Trimmer
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Matthew B. Klein
- BioElectron Technology Corporation, Mountain View, California, United States of America
| | - Charles R. Holst
- BioElectron Technology Corporation, Mountain View, California, United States of America
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Silverman EK, Allard P, Loscalzo J, Mulvihill JJ, Korrick SA. Reported environmental exposures are inversely associated with obtaining a genetic diagnosis in the Undiagnosed Diseases Network. Am J Med Genet A 2019; 179:958-965. [DOI: 10.1002/ajmg.a.61132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/26/2019] [Accepted: 03/07/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Edwin K. Silverman
- Channing Division of Network Medicine, Department of MedicineBrigham and Women's Hospital Boston Massachusetts
- Department of MedicineBrigham and Women's Hospital Boston Massachusetts
- Department of Medicine, Harvard Medical School Boston Massachusetts
| | - Patrick Allard
- Institute for Society and GeneticsUniversity of California at Los Angeles Los Angeles California
| | - Joseph Loscalzo
- Channing Division of Network Medicine, Department of MedicineBrigham and Women's Hospital Boston Massachusetts
- Department of MedicineBrigham and Women's Hospital Boston Massachusetts
- Department of Medicine, Harvard Medical School Boston Massachusetts
- Division of Cardiovascular MedicineBrigham and Women's Hospital Boston Massachusetts
| | - John J. Mulvihill
- Division of Genomic MedicineNational Human Genome Research Institute Bethesda Maryland
- Department of Pediatrics, University of Oklahoma Health Sciences Center Oklahoma City Oklahoma
| | - Susan A. Korrick
- Channing Division of Network Medicine, Department of MedicineBrigham and Women's Hospital Boston Massachusetts
- Department of MedicineBrigham and Women's Hospital Boston Massachusetts
- Department of Medicine, Harvard Medical School Boston Massachusetts
- Department of Environmental HealthHarvard T.H. Chan School of Public Health Boston Massachusetts
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The Korean undiagnosed diseases program: lessons from a one-year pilot project. Orphanet J Rare Dis 2019; 14:68. [PMID: 30894207 PMCID: PMC6427886 DOI: 10.1186/s13023-019-1041-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/28/2019] [Indexed: 11/12/2022] Open
Abstract
Background The Korean Undiagnosed Diseases Program (KUDP) was launched in January 2017 as a one-year pilot project to address the increasing global interest in patients with undiagnosed rare diseases. The purpose of this paper is to summarize the project results and emphasize the unmet research needs among patients with undiagnosed rare diseases in Korea. Results Patient enrollment, assessment, and diagnostic processes were determined by the KUDP clinical expert consortium. Patients followed a diagnostic workflow after being categorized into one of four groups: I) insufficient clinical information or lack of standard diagnostic processes; II) undiagnosed due to low disease awareness; III) clinically diagnosed but unconfirmed genetically due to genetic heterogeneities; or IV) unknown disease due to complex, atypical clinical presentations. After excluding two patients from group I, 97 patients were enrolled, including 10 in group II, 67 in group III, and 20 in group IV. Most of them (92 of 97, 94.8%) were pediatric patients (< 18 years old) and 59 (60.8%) were male. The primary symptoms for 80 patients (82.5%) were neurologic. During the one-year pilot study, 72 patients completed a diagnostic assessment including clinical and molecular genetic analyses; some patients also underwent pathological or biochemical analysis. Twenty-eight of these patients (28/72, 38.9%) achieved molecular genetic diagnosis. Thirteen patients were diagnosed based on traditional tests, including biochemical assay, single or targeted genetic analysis, and chromosomal microarray. We performed whole exome sequencing on 52 patients, among whom 15 (28.8%, 15/52) reached a final diagnosis. One new disorder was identified via international collaboration. Conclusions Using an efficient clinical diagnostic workflow, this KUDP pilot study resulted in a fair diagnostic success rate, improving the potential for additional diagnoses and new scientific discovery of complex and rare diseases. KUDP also satisfied unmet needs for rare diseases with multisystem involvement, highlighting the value of emerging genomic technologies for further research into rare and still-undiagnosed conditions. Electronic supplementary material The online version of this article (10.1186/s13023-019-1041-5) contains supplementary material, which is available to authorized users.
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76
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Kuo ME, Theil AF, Kievit A, Malicdan MC, Introne WJ, Christian T, Verheijen FW, Smith DEC, Mendes MI, Hussaarts-Odijk L, van der Meijden E, van Slegtenhorst M, Wilke M, Vermeulen W, Raams A, Groden C, Shimada S, Meyer-Schuman R, Hou YM, Gahl WA, Antonellis A, Salomons GS, Mancini GMS. Cysteinyl-tRNA Synthetase Mutations Cause a Multi-System, Recessive Disease That Includes Microcephaly, Developmental Delay, and Brittle Hair and Nails. Am J Hum Genet 2019; 104:520-529. [PMID: 30824121 DOI: 10.1016/j.ajhg.2019.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/15/2019] [Indexed: 02/06/2023] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes responsible for charging tRNA molecules with cognate amino acids. Consistent with the essential function and ubiquitous expression of ARSs, mutations in 32 of the 37 ARS-encoding loci cause severe, early-onset recessive phenotypes. Previous genetic and functional data suggest a loss-of-function mechanism; however, our understanding of the allelic and locus heterogeneity of ARS-related disease is incomplete. Cysteinyl-tRNA synthetase (CARS) encodes the enzyme that charges tRNACys with cysteine in the cytoplasm. To date, CARS variants have not been implicated in any human disease phenotype. Here, we report on four subjects from three families with complex syndromes that include microcephaly, developmental delay, and brittle hair and nails. Each affected person carries bi-allelic CARS variants: one individual is compound heterozygous for c.1138C>T (p.Gln380∗) and c.1022G>A (p.Arg341His), two related individuals are compound heterozygous for c.1076C>T (p.Ser359Leu) and c.1199T>A (p.Leu400Gln), and one individual is homozygous for c.2061dup (p.Ser688Glnfs∗2). Measurement of protein abundance, yeast complementation assays, and assessments of tRNA charging indicate that each CARS variant causes a loss-of-function effect. Compared to subjects with previously reported ARS-related diseases, individuals with bi-allelic CARS variants are unique in presenting with a brittle-hair-and-nail phenotype, which most likely reflects the high cysteine content in human keratins. In sum, our efforts implicate CARS variants in human inherited disease, expand the locus and clinical heterogeneity of ARS-related clinical phenotypes, and further support impaired tRNA charging as the primary mechanism of recessive ARS-related disease.
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Affiliation(s)
- Molly E Kuo
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus Medical Center, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 CN Rotterdam, the Netherlands
| | - Anneke Kievit
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - May Christine Malicdan
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wendy J Introne
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Christian
- Department of Biochemistry and Molecular Biochemistry, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Frans W Verheijen
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Desiree E C Smith
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Center and Amsterdam Gastroenterology and Metabolism, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HZ Amsterdam, the Netherlands
| | - Marisa I Mendes
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Center and Amsterdam Gastroenterology and Metabolism, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HZ Amsterdam, the Netherlands
| | - Lidia Hussaarts-Odijk
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Eric van der Meijden
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus Medical Center, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 CN Rotterdam, the Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus Medical Center, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 CN Rotterdam, the Netherlands
| | - Catherine Groden
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shino Shimada
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rebecca Meyer-Schuman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ya Ming Hou
- Department of Biochemistry and Molecular Biochemistry, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - William A Gahl
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony Antonellis
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Gajja S Salomons
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam University Medical Center and Amsterdam Gastroenterology and Metabolism, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, 1081 HZ Amsterdam, the Netherlands; Genetic Metabolic Diseases, Amsterdam University Medical Center, University of Amsterdam, 1081 HZ Amsterdam, the Netherlands.
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus Medical Center, University Medical Center, 3015 GD Rotterdam, the Netherlands
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Abstract
Massively parallel sequencing is emerging from research settings into clinical practice, helping the vision of precision medicine to become a reality. The most successful applications are using the tools of implementation science within the framework of the learning health-care system. This article examines the application of massively parallel sequencing to four clinical scenarios: pharmacogenomics, diagnostic testing, somatic testing for molecular tumor characterization, and population screening. For each application, it highlights an exemplar program to illustrate the enablers and challenges of implementation. International examples are also presented. These early lessons will allow other programs to account for these factors, helping to accelerate the implementation of precision medicine and health.
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Affiliation(s)
- Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania 17822-2620, USA;
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Lim SS, Lee W, Kim YK, Kim J, Park JH, Park BR, Yoon JH. The cumulative incidence and trends of rare diseases in South Korea: a nationwide study of the administrative data from the National Health Insurance Service database from 2011-2015. Orphanet J Rare Dis 2019; 14:49. [PMID: 30777110 PMCID: PMC6379926 DOI: 10.1186/s13023-019-1032-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 02/11/2019] [Indexed: 12/13/2022] Open
Abstract
Background The burden of rare diseases on society and patients’ families has increased in Korea. However, because of the infrequency of rare diseases, there is a lack of resources and information to address these cases and inadequate funding for the management of these patients. We investigated the average annual cumulative incidence of rare diseases and the trends in annual cumulative incidence from 2011 to 2015 in Korea by using nationwide administrative data from the Korean National Health Insurance Service (NHIS) database for patients registered with the co-payment assistance policy for rare and incurable diseases. Annual cumulative incidence per 10,000,000 was calculated as the total number of newly enrolled patients with the Korean Standard Classification of Diseases (KCD)-7 code in the register, divided by the number of residents with health insurance coverage during each year. We employed simple linear regression analysis to evaluate the trends in annual cumulative incidence/10,000,000 population per year for each rare disease. Results Overall, national support was provided for patients with 415 KCD codes listed among the targeted rare diseases. The total number of newly enrolled patients with rare diseases was 53,831 in 2011, 52,658 in 2012, 52,955 in 2013, 71,530 in 2014, and 70,559 in 2015. The number of rare diseases with an average annual cumulative incidence of 100/10,000,000 and above was 22 (5.30%), while there were 227 (54.70%) and 148 (35.66%) with an average cumulative incidence between 1/10,000,000 and 100/10,000,000 and less than 1/10,000,000, respectively. The trends in the annual cumulative incidence for 43 rare diseases were statistically significant (p-value < 0.05). The rare diseases for which the incremental trend per year was statistically significant were sarcoidosis (D86, D86.0, D86.1, D86.2, D86.3, D86.8, D86.9), Parkinson’s disease (G20), Guillain-Barré syndrome (G61.0), primary biliary cirrhosis (K74.3) and Sjogren’s syndrome (M35.0). Conclusions The number of rare diseases showing an increasing trend in annual cumulative incidence was higher than the number of diseases showing a decreasing trend in annual cumulative incidence. Given that the definition and diagnosis vary based on country and that there is difficulty in identifying valid cases, further detection strategies are needed to establish the incidence of each rare disease considering the importance of establishing a health policy based on the actual incidence of the targeted diseases. Electronic supplementary material The online version of this article (10.1186/s13023-019-1032-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sung-Shil Lim
- Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea.,The Institute for Occupational Health, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Wanhyung Lee
- Department of Occupational and Environmental Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Yeong-Kwang Kim
- Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea.,The Institute for Occupational Health, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jihyun Kim
- Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea.,The Institute for Occupational Health, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Heon Park
- Department of Big Data Steering, National Health Insurance Service, Seoul, South Korea
| | - Bo Ram Park
- Department of Big Data Steering, National Health Insurance Service, Seoul, South Korea
| | - Jin-Ha Yoon
- The Institute for Occupational Health, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Department of Preventive Medicine and Public Health, Yonsei University College of Medicine, Seoul, Republic of Korea.
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Chin JJ, Behnam B, Davids M, Sharma P, Zein WM, Wang C, Chepa-Lotrea X, Gallantine WB, Toro C, Adams DR, Tifft CJ, Gahl WA, Malicdan MCV. Novel mutations in CLN6 cause late-infantile neuronal ceroid lipofuscinosis without visual impairment in two unrelated patients. Mol Genet Metab 2019; 126:188-195. [PMID: 30528883 DOI: 10.1016/j.ymgme.2018.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/02/2018] [Accepted: 12/02/2018] [Indexed: 12/25/2022]
Abstract
CLN6 is a transmembrane protein located in the endoplasmic reticulum that is involved in lysosomal acidification. Mutations in CLN6 cause late-infantile neuronal ceroid lipofuscinosis (LINCL), and teenage and adult onset NCL without visual impairment. Here we describe two pediatric patients with LINCL from unrelated families who were evaluated at the National Institutes of Health. Both children exhibited typical phenotypes associated with LINCL except that they lacked the expected visual impairment. Whole exome sequencing identified novel biallelic mutations in CLN6, i.e., c.218-220dupGGT (p.Trp73dup) and c.296A > G (p.Lys99Arg) in Proband 1 and homozygous c.723G > T (p.Met241Ile) in Proband 2. Expression analysis in dermal fibroblasts showed a small increase in CLN6 protein levels. Electron micrographs of these fibroblasts demonstrated large numbers of small membrane-bound vesicles, in addition to lipofuscin deposits. LysoTracker™ Red intensity was increased in fibroblasts from both patients. This study supports a role for CLN6 in lysosomal homeostasis, and highlights the importance of considering CLN6 mutations in the diagnosis of Batten Disease even in patients with normal vision.
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Affiliation(s)
- Joseph J Chin
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Babak Behnam
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mariska Davids
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Prashant Sharma
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Wadih M Zein
- National Eye Institute, National Institute of Health, Bethesda, MD, United States
| | - Camille Wang
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Xenia Chepa-Lotrea
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | | | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Cynthia J Tifft
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States.
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80
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Gu F, Wu A, Gordon MG, Vlahos L, Macnamara S, Burke E, Malicdan MC, Adams DR, Tifft CJ, Toro C, Gahl WA, Markello TC. A suite of automated sequence analyses reduces the number of candidate deleterious variants and reveals a difference between probands and unaffected siblings. Genet Med 2019; 21:1772-1780. [PMID: 30700791 PMCID: PMC6669106 DOI: 10.1038/s41436-019-0434-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/03/2019] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Develop an automated exome analysis workflow that can produce a very small number of candidate variants yet still detect different numbers of deleterious variants between probands and unaffected siblings. METHODS Ninety-seven outbred nuclear families from the Undiagnosed Diseases Program/Network included single probands and the corresponding unaffected sibling(s). Single-nucleotide polymorphism (SNP) chip and exome analyses were performed on all, with proband and unaffected sibling considered independently as the target. The total burden of candidate genetic variants was summed for probands and siblings over all considered disease models. RESULTS Exome analysis workflow include automated programs for ethnicity-matched genotype calling, salvage pathway for Mendelian inconsistency, compound heterozygous recessive detection, BAM file regional curation, population frequency filtering, pedigree-aware BAM file noise evaluation, and exon deletion filtration. This workflow relied heavily on BAM file analysis. A greater average pathogenic variant number was found compared with unaffected siblings. This was significant (p < 0.05) when using published recommended thresholds, and implies that causal variants are retained in many probands' lists. CONCLUSION Using Mendelian and non-Mendelian models, this agnostic exome analysis shows a difference between a small group of probands and their unaffected siblings. This workflow produces candidate lists small enough to pursue with laboratory validation.
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Affiliation(s)
- Fangning Gu
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Anchi Wu
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - M Grace Gordon
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Lukas Vlahos
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Shane Macnamara
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth Burke
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - May C Malicdan
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - William A Gahl
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Thomas C Markello
- Office of the Clinical Director, National Human Genome Research Institute, and Undiagnosed Diseases Program and Network, Office of the Director, National Institutes of Health, Bethesda, MD, USA.
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81
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Jaitovich Groisman I, Hurlimann T, Godard B. Parents of a child with epilepsy: Views and expectations on receiving genetic results from Whole Genome Sequencing. Epilepsy Behav 2019; 90:178-190. [PMID: 30583270 DOI: 10.1016/j.yebeh.2018.11.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/02/2018] [Accepted: 11/19/2018] [Indexed: 01/03/2023]
Abstract
PURPOSE The use of Next Generation Sequencing technologies (NGS), such as Whole Genome Sequencing (WGS), is expected to improve the often complex and protracted course of treatment of patients with epilepsy by providing an earlier and more accurate diagnosis. As part of the "Personalized medicine in the treatment of epilepsy" project, which aimed to determine whether WGS could be used as a valuable "diagnostic tool" in pharmacoresistant epilepsies, we examined parents' expectations, hopes, and concerns upon receiving results related to their child's epilepsy, comorbidities, resistance to medication, and genetic information on unrelated conditions, and how these results could impact their and their child's life. METHODS Parents of 32 children participating in the genetic study completed either paper or online questionnaires. A descriptive analysis of responses and comments was conducted regarding parents' experience with their child's epilepsy, as well as their views on WGS, and expectations and concerns surrounding such test results. RESULTS Most respondents had trouble explaining the medical causes of their child's epilepsy (n = 27), and a majority (n = 26) feared that their child may be treated unjustly because of their epilepsy, although some acknowledged that their child had never actually been treated unjustly (n = 13). A majority of respondents had also experienced feelings of guilt due to their child's epilepsy (n = 23), and some expected WGS results to have an impact on those feelings. The anticipation of benefits for their child was the parents' primary reason to get involved in a genomic research project, closely followed by altruism. A majority expressed strong intentions to receive as many WGS results as possible, considering that any could be beneficial for them and their child, even when mutations were not found. Respondents were divided as to how and when to tell their child that they might have newly discovered predispositions to develop another disease. In proportion, more parents expressed concerns about sharing unexpected results with their family members compared with sharing results linked to epilepsy, comorbidities, and pharmacoresistance. CONCLUSION Our results reinforce the importance of having clear guidelines to help parents manage their expectations and better navigate the complexities of receiving and sharing WGS results. Despite the small size of our sample, we believe that our results are meaningful to clinical practice.
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Affiliation(s)
| | - Thierry Hurlimann
- Université de Montréal, PO Box 6128, Station Centre-ville, Montreal H3C 3J7, Canada
| | - Béatrice Godard
- Université de Montréal, PO Box 6128, Station Centre-ville, Montreal H3C 3J7, Canada.
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Gartner V, Markello TC, Macnamara E, De Biase A, Thurm A, Joseph L, Beggs A, Schmahmann JD, Berry GT, Anselm I, Boslet E, Tifft CJ, Gahl WA, Lee PR. Novel variants in SPTAN1 without epilepsy: An expansion of the phenotype. Am J Med Genet A 2018; 176:2768-2776. [PMID: 30548380 PMCID: PMC11157598 DOI: 10.1002/ajmg.a.40628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/19/2018] [Accepted: 08/13/2018] [Indexed: 11/11/2022]
Abstract
We describe two unrelated children with de novo variants in the non-erythrocytic alpha-II-spectrin (SPTAN1) gene who have hypoplastic brain structures, intellectual disability, and both fine and gross motor impairments. Using agnostic exome sequencing, we identified a nonsense variant creating a premature stop codon in exon 21 of SPTAN1, and in a second patient we identified an intronic substitution in SPTAN1 prior to exon 50 creating a new donor acceptor site. Neither of these variants has been described previously. Although some of these patients' features are consistent with the known SPTAN1 encephalopathy phenotype, these two children do not have epilepsy, in contrast to reports about nearly every other patient with heterozygous SPTAN1 variants and in all patients with a variant near the C-terminal coding region. Moreover, both children have abnormal thyroid function, which has not been previously reported in association with SPTAN1 variant. We present a detailed discussion of the clinical manifestations of these two unique SPTAN1 variants and provide evidence that both variants result in reduced mRNA expression despite different locations within the gene and clinical phenotypes. These findings expand the motor, cognitive, and behavioral spectrum of the SPTAN1-associated phenotype and invite speculation about underlying pathophysiologies.
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Affiliation(s)
- Valerie Gartner
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Thomas C. Markello
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Ellen Macnamara
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | | | - Audrey Thurm
- Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Lisa Joseph
- Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Alan Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jeremy D. Schmahmann
- Ataxia Unit, Cognitive Behavioral Neurology Unit, Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gerard T. Berry
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Irina Anselm
- Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Emma Boslet
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Cynthia J. Tifft
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - William A. Gahl
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Paul R. Lee
- Office of the Clinical Director, NHGRI, and NIH Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, Maryland
- Division of Neurology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
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83
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Splinter K, Adams DR, Bacino CA, Bellen HJ, Bernstein JA, Cheatle-Jarvela AM, Eng CM, Esteves C, Gahl WA, Hamid R, Jacob HJ, Kikani B, Koeller DM, Kohane IS, Lee BH, Loscalzo J, Luo X, McCray AT, Metz TO, Mulvihill JJ, Nelson SF, Palmer CGS, Phillips JA, Pick L, Postlethwait JH, Reuter C, Shashi V, Sweetser DA, Tifft CJ, Walley NM, Wangler MF, Westerfield M, Wheeler MT, Wise AL, Worthey EA, Yamamoto S, Ashley EA. Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease. N Engl J Med 2018; 379:2131-2139. [PMID: 30304647 PMCID: PMC6481166 DOI: 10.1056/nejmoa1714458] [Citation(s) in RCA: 244] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Many patients remain without a diagnosis despite extensive medical evaluation. The Undiagnosed Diseases Network (UDN) was established to apply a multidisciplinary model in the evaluation of the most challenging cases and to identify the biologic characteristics of newly discovered diseases. The UDN, which is funded by the National Institutes of Health, was formed in 2014 as a network of seven clinical sites, two sequencing cores, and a coordinating center. Later, a central biorepository, a metabolomics core, and a model organisms screening center were added. METHODS We evaluated patients who were referred to the UDN over a period of 20 months. The patients were required to have an undiagnosed condition despite thorough evaluation by a health care provider. We determined the rate of diagnosis among patients who subsequently had a complete evaluation, and we observed the effect of diagnosis on medical care. RESULTS A total of 1519 patients (53% female) were referred to the UDN, of whom 601 (40%) were accepted for evaluation. Of the accepted patients, 192 (32%) had previously undergone exome sequencing. Symptoms were neurologic in 40% of the applicants, musculoskeletal in 10%, immunologic in 7%, gastrointestinal in 7%, and rheumatologic in 6%. Of the 382 patients who had a complete evaluation, 132 received a diagnosis, yielding a rate of diagnosis of 35%. A total of 15 diagnoses (11%) were made by clinical review alone, and 98 (74%) were made by exome or genome sequencing. Of the diagnoses, 21% led to recommendations regarding changes in therapy, 37% led to changes in diagnostic testing, and 36% led to variant-specific genetic counseling. We defined 31 new syndromes. CONCLUSIONS The UDN established a diagnosis in 132 of the 382 patients who had a complete evaluation, yielding a rate of diagnosis of 35%. (Funded by the National Institutes of Health Common Fund.).
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Affiliation(s)
- Kimberly Splinter
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - David R Adams
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Carlos A Bacino
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Hugo J Bellen
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Jonathan A Bernstein
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Alys M Cheatle-Jarvela
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Christine M Eng
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Cecilia Esteves
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - William A Gahl
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Rizwan Hamid
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Howard J Jacob
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Bijal Kikani
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - David M Koeller
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Isaac S Kohane
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Brendan H Lee
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Joseph Loscalzo
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Xi Luo
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Alexa T McCray
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Thomas O Metz
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - John J Mulvihill
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Stanley F Nelson
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Christina G S Palmer
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - John A Phillips
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Leslie Pick
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - John H Postlethwait
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Chloe Reuter
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Vandana Shashi
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - David A Sweetser
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Cynthia J Tifft
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Nicole M Walley
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Michael F Wangler
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Monte Westerfield
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Matthew T Wheeler
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Anastasia L Wise
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Elizabeth A Worthey
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Shinya Yamamoto
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Euan A Ashley
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
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84
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Davids M, Markello T, Wolfe LA, Chepa-Lotrea X, Tifft CJ, Gahl WA, Malicdan MCV. Early infantile-onset epileptic encephalopathy 28 due to a homozygous microdeletion involving the WWOX gene in a region of uniparental disomy. Hum Mutat 2018; 40:42-47. [PMID: 30362252 DOI: 10.1002/humu.23675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/25/2018] [Accepted: 10/21/2018] [Indexed: 01/28/2023]
Abstract
The genetic etiologies of many rare disorders, including early infantile epileptic encephalopathies, are largely undiagnosed. A 6-year-old girl was admitted to the National Institutes of Health Undiagnosed Diseases Program with profound intellectual disability, infantile-onset seizures, chronic respiratory failure, facial dysmorphisms, skeletal abnormalities, and atrial septum defect. A large region of homozygosity was discovered on chromosome 16, spanning 16q22.1-16q24.3' caused by uniparental disomy (UPD) that included a maternally inherited homozygous microdeletion covering exon 6 of WWOX (NM_016373.3). mRNA expression analysis revealed that the deletion led to nonsense-mediated decay of the NM_016373.3 transcript; the exon 6 of an alternative transcript (NM_130791.3), lacking the short-chain dehydrogenase, was utilized. The microdeletion in WWOX explains the seizures and intellectual disability, while pathogenic variants in another gene, HSPG2, are likely responsible for the patient's skeletal abnormalities. This report describes a rare autosomal recessive disorder with multiple genetic etiologies, one of which involves UPD.
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Affiliation(s)
- Mariska Davids
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland
| | - Thomas Markello
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - Lynne A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - Xenia Chepa-Lotrea
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland
| | - Cynthia J Tifft
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
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85
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Morimoto M, Waller-Evans H, Ammous Z, Song X, Strauss KA, Pehlivan D, Gonzaga-Jauregui C, Puffenberger EG, Holst CR, Karaca E, Brigatti KW, Maguire E, Coban-Akdemir ZH, Amagata A, Lau CC, Chepa-Lotrea X, Macnamara E, Tos T, Isikay S, Nehrebecky M, Overton JD, Klein M, Markello TC, Posey JE, Adams DR, Lloyd-Evans E, Lupski JR, Gahl WA, Malicdan MCV. Bi-allelic CCDC47 Variants Cause a Disorder Characterized by Woolly Hair, Liver Dysfunction, Dysmorphic Features, and Global Developmental Delay. Am J Hum Genet 2018; 103:794-807. [PMID: 30401460 PMCID: PMC6218603 DOI: 10.1016/j.ajhg.2018.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/26/2018] [Indexed: 01/06/2023] Open
Abstract
Ca2+ signaling is vital for various cellular processes including synaptic vesicle exocytosis, muscle contraction, regulation of secretion, gene transcription, and cellular proliferation. The endoplasmic reticulum (ER) is the largest intracellular Ca2+ store, and dysregulation of ER Ca2+ signaling and homeostasis contributes to the pathogenesis of various complex disorders and Mendelian disease traits. We describe four unrelated individuals with a complex multisystem disorder characterized by woolly hair, liver dysfunction, pruritus, dysmorphic features, hypotonia, and global developmental delay. Through whole-exome sequencing and family-based genomics, we identified bi-allelic variants in CCDC47 that encodes the Ca2+-binding ER transmembrane protein CCDC47. CCDC47, also known as calumin, has been shown to bind Ca2+ with low affinity and high capacity. In mice, loss of Ccdc47 leads to embryonic lethality, suggesting that Ccdc47 is essential for early development. Characterization of cells from individuals with predicted likely damaging alleles showed decreased CCDC47 mRNA expression and protein levels. In vitro cellular experiments showed decreased total ER Ca2+ storage, impaired Ca2+ signaling mediated by the IP3R Ca2+ release channel, and reduced ER Ca2+ refilling via store-operated Ca2+ entry. These results, together with the previously described role of CCDC47 in Ca2+ signaling and development, suggest that bi-allelic loss-of-function variants in CCDC47 underlie the pathogenesis of this multisystem disorder.
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Affiliation(s)
- Marie Morimoto
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Zineb Ammous
- The Community Health Clinic, Topeka, IN 46571, USA
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Charles R Holst
- BioElectron Technology Corporation, Mountain View, CA 94043, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Emily Maguire
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Zeynep H Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Akiko Amagata
- BioElectron Technology Corporation, Mountain View, CA 94043, USA
| | - C Christopher Lau
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xenia Chepa-Lotrea
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ellen Macnamara
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tulay Tos
- Department of Medical Genetics, Dr. Sami Ulus Research and Training Hospital of Women's and Children's Health and Diseases, Ankara 06080, Turkey
| | - Sedat Isikay
- Department of Physiotherapy and Rehabilitation, Hasan Kalyoncu University, School of Health Sciences, Gaziantep 27000, Turkey
| | - Michele Nehrebecky
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA
| | - John D Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Matthew Klein
- BioElectron Technology Corporation, Mountain View, CA 94043, USA
| | - Thomas C Markello
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David R Adams
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA; Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - William A Gahl
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA; Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - May Christine V Malicdan
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA; Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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86
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Taveira-DaSilva AM, Markello TC, Kleiner DE, Jones AM, Groden C, Macnamara E, Yokoyama T, Gahl WA, Gochuico BR, Moss J. Expanding the phenotype of COPA syndrome: a kindred with typical and atypical features. J Med Genet 2018; 56:778-782. [PMID: 30385646 PMCID: PMC6860403 DOI: 10.1136/jmedgenet-2018-105560] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/14/2018] [Accepted: 09/30/2018] [Indexed: 11/19/2022]
Abstract
Background Copa syndrome is a rare autosomal dominant disorder with abnormal intracellular vesicle trafficking. The objective of this work is to expand the knowledge about this disorder by delineating phenotypic features of an unreported COPA family. Methods and results A heterozygous missense variant (c.698 G>A, p.Arg233His) in COPA was identified in four members of a three-generation kindred with lung, autoimmune and malignant disease of unknown aetiology. Ages of onset were 56, 26, 16 and 1 year, with earlier age of onset in successive generations. Presenting symptoms were cough and dyspnoea. Findings included small lung cysts, follicular bronchiolitis, interstitial lung disease, neuroendocrine cell hyperplasia, rheumatoid arthritis, avascular necrosis and select abnormal autoimmune serologies. Neither alveolar haemorrhage nor glomerular disease were present. Features not previously associated with Copa syndrome included neuromyelitis optica, pulmonary carcinoid tumour, clear cell renal carcinoma, renal cysts, hepatic cysts, nephrolithiasis, pyelonephritis and meningitis. Longitudinal evaluations demonstrated slow progression of lung disease and extrapulmonary cysts. Conclusions Worsening severity with successive generations may be observed in Copa syndrome. Extrapulmonary cysts, malignancies, autoimmune neurological disorders and infections are clinical features that may be associated with Copa syndrome. Further studies are indicated to fully define the phenotypic spectrum of this disorder.
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Affiliation(s)
- Angelo M Taveira-DaSilva
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - David E Kleiner
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Amanda M Jones
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | - Tadafumi Yokoyama
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Bethesda, Maryland, USA.,Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Bernadette R Gochuico
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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87
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Hurlimann T, Jaitovich Groisman I, Godard B. Exploring neurologists' perspectives on the return of next generation sequencing results to their patients: a needed step in the development of guidelines. BMC Med Ethics 2018; 19:81. [PMID: 30268121 PMCID: PMC6162934 DOI: 10.1186/s12910-018-0320-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 09/12/2018] [Indexed: 12/12/2022] Open
Abstract
Background The use of Next Generation Sequencing such as Whole Genome Sequencing (WGS) is a promising step towards a better understanding and treatment of neurological diseases. WGS can result into unexpected information (incidental findings, IFs), and information with uncertain clinical significance. In the context of a Genome Canada project on ‘Personalized Medicine in the Treatment of Epilepsy’, we intended to address these challenges surveying neurologists’ opinions about the type of results that should be returned, and their professional responsibility toward recontacting patients regarding new discovered mutations. Methods Potential participants were contacted through professional organizations or direct invitations. Results A total of 204 neurologists were recruited. Fifty nine percent indicated that to be conveyed, WGS results should have a demonstrated clinical utility for diagnosis, prognosis or treatment. Yet, 41% deemed appropriate to return results without clinical utility, when they could impact patients’ reproductive decisions, or on patients’ request. Current use of targeted genetic testing and age of patients influenced respondents’ answers. Respondents stated that analysis of genomics data resulting from WGS should be limited to the genes likely to be relevant for the patient’s specific medical condition (69%), so as to limit IFs. Respondents felt responsible to recontact patients and inform them about newly discovered mutations related to the medical condition that triggered the test (75%) for as long as they are following up on the patient (55%). Finally, 53.5% of the respondents felt responsible to recontact and inform patients of clinically significant, newly discovered IFs. Conclusion Our results show the importance of formulating professional guidelines sensitive to the various – and sometimes opposite – viewpoints that may prevail within a same community of practice, as well as flexible so as to be attuned to the characteristics of the neurological conditions that triggered a WGS.
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Affiliation(s)
- Thierry Hurlimann
- Institut de recherche en santé publique, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada.,Quebec Population Health Research Network, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada
| | - Iris Jaitovich Groisman
- Institut de recherche en santé publique, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada
| | - Béatrice Godard
- Institut de recherche en santé publique, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada. .,Department of Social and Preventive Medicine, Université de Montréal, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada. .,Quebec Population Health Research Network, PO Box 6128, Station Centre-ville, Montreal, Quebec, H3C 3J7, Canada.
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88
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Meeting Patients' Right to the Correct Diagnosis: Ongoing International Initiatives on Undiagnosed Rare Diseases and Ethical and Social Issues. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15102072. [PMID: 30248891 PMCID: PMC6210164 DOI: 10.3390/ijerph15102072] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 12/19/2022]
Abstract
The time required to reach a correct diagnosis is a key concern for rare disease (RD) patients. Diagnostic delay can be intolerably long, often described as an “odyssey” and, for some, a diagnosis may remain frustratingly elusive. The International Rare Disease Research Consortium proposed, as ultimate goal for 2017–2027, to enable all people with a suspected RD to be diagnosed within one year of presentation, if the disorder is known. Subsequently, unsolved cases would enter a globally coordinated diagnostic and research pipeline. In-depth analysis of the genotype through next generation sequencing, together with a standardized in-depth phenotype description and sophisticated high-throughput approaches, have been applied as diagnostic tools to increase the chance of a timely and accurate diagnosis. The success of this approach is evident in the Orphanet database. From 2010 to March 2017 over 600 new RDs and roughly 3600 linked genes have been described and identified. However, combination of -omics and phenotype data, as well as international sharing of this information, has raised ethical concerns. Values to be assessed include not only patient autonomy but also family implications, beneficence, non-maleficence, justice, solidarity and reciprocity, which must be respected and promoted and, at the same time, balanced among each other. In this work we suggest that, to maximize patients’ involvement in the search for a diagnosis and identification of new causative genes, undiagnosed patients should have the possibility to: (1) actively participate in the description of their phenotype; (2) choose the level of visibility of their profile in matchmaking databases; (3) express their preferences regarding return of new findings, in particular which level of Variant of Unknown Significance (VUS) significance should be considered relevant to them. The quality of the relationship between individual patients and physicians, and between the patient community and the scientific community, is critically important for optimizing the use of available data and enabling international collaboration in order to provide a diagnosis, and the attached support, to unsolved cases. The contribution of patients to collecting and coding data comprehensively is critical for efficient use of data downstream of data collection.
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SpainUDP: The Spanish Undiagnosed Rare Diseases Program. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15081746. [PMID: 30110963 PMCID: PMC6121381 DOI: 10.3390/ijerph15081746] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 11/24/2022]
Abstract
One of the IRDiRC goals for 2017–2027 is to achieve definitive diagnosis for rare undiagnosed diseases within one year, as delay in diagnosis remains one of the pending issues in the rare diseases field. The Spanish Undiagnosed Rare Diseases Program (SpainUDP) was created in response to this challenging scenario to cover patients’ needs and after seeing the success of the Undiagnosed Diseases Program (UDP) in the USA. SpainUDP offers a multidisciplinary approach to those patients who have long sought a diagnosis without any success. During the first phase of the protocol, undiagnosed cases are sent to SpainUDP by individual patients or families, patient organizations or hospitals. After careful analysis of phenotype, data from sequencing experiments (WES) is processed with a standard pipeline and detailed standardized phenotypic information (mapped to the Human Phenotype Ontology, HPO) is connected to genetic data. In addition, the participation of SpainUDP in international initiatives such as the European projects RD-Connect and Solve RD, the Undiagnosed Diseases Network International (UDNI), and the MatchMaker Exchange (MME) platform, allows the establishment of a global data sharing strategy across multiple projects submitting data to these international initiatives. From the official beginning of the program (at the end of 2015) until early 2018, 147 cases were accepted in SpainUDP. During this time, 37 cases (25%) dropped out the program due to several reasons. The remaining 110 cases are distributed as follows: phenotypic and genotypic (WES) characterization was finished in 30 cases, of which 20 (67%) were diagnosed; 21 cases are pending on variants’ validation by Sanger sequencing; in 25 cases, WES is ongoing and 34 cases are being studied for deep phenotypic characterization. In conclusion, SpainUDP aims to achieve a diagnosis following two recommendations of the IRDiRC: the patients’ diagnosis in as short a time as possible and the promotion of data sharing (especially genomic) at the international level.
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90
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An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. NPJ Genom Med 2018; 3:21. [PMID: 30131872 PMCID: PMC6089983 DOI: 10.1038/s41525-018-0060-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/06/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022] Open
Abstract
Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs.
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91
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Ferreira CR, Goorden SMI, Soldatos A, Byers HM, Ghauharali-van der Vlugt JMM, Beers-Stet FS, Groden C, van Karnebeek CD, Gahl WA, Vaz FM, Jiang X, Vernon HJ. Deoxysphingolipid precursors indicate abnormal sphingolipid metabolism in individuals with primary and secondary disturbances of serine availability. Mol Genet Metab 2018; 124:204-209. [PMID: 29789193 PMCID: PMC6057808 DOI: 10.1016/j.ymgme.2018.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 12/27/2022]
Abstract
Patients with primary serine biosynthetic defects manifest with intellectual disability, microcephaly, ichthyosis, seizures and peripheral neuropathy. The underlying pathogenesis of peripheral neuropathy in these patients has not been elucidated, but could be related to a decrease in the availability of certain classical sphingolipids, or to an increase in atypical sphingolipids. Here, we show that patients with primary serine deficiency have a statistically significant elevation in specific atypical sphingolipids, namely deoxydihydroceramides of 18-22 carbons in acyl length. We also show that patients with aberrant plasma serine and alanine levels secondary to mitochondrial disorders also display peripheral neuropathy along with similar elevations of atypical sphingolipids. We hypothesize that the etiology of peripheral neuropathy in patients with primary mitochondrial disorders is related to this elevation of deoxysphingolipids, in turn caused by increased availability of alanine and decreased availability of serine. These findings could have important therapeutic implications for the management of these patients.
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Affiliation(s)
- C R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Division of Genetics and Metabolism, Children's National Health System, Washington, DC, USA
| | - S M I Goorden
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - A Soldatos
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - H M Byers
- Division of Medical Genetics, Stanford University, Palo Alto, CA, USA
| | | | - F S Beers-Stet
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - C Groden
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - C D van Karnebeek
- Departments of Pediatrics and Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - W A Gahl
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - F M Vaz
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - X Jiang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - H J Vernon
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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92
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Munung NS, Mayosi BM, de Vries J. Genomics research in Africa and its impact on global health: insights from African researchers. Glob Health Epidemiol Genom 2018; 3:e12. [PMID: 30263136 PMCID: PMC6152488 DOI: 10.1017/gheg.2018.3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/19/2018] [Accepted: 03/01/2018] [Indexed: 12/27/2022] Open
Abstract
Africa may be heading for an era of genomics medicine. There are also expectations that genomics may play a role in reducing global health inequities. However, the near lack of genomics studies on African populations has led to concerns that genomics may widen, rather than close, the global health inequity gap. To prevent a possible genomics divide, the genomics 'revolution' has been extended to Africa. This is motivated, in part, by Africa's rich genetic diversity and high disease burden. What remains unclear, however, are the prospects of using genomics technology for healthcare in Africa. In this qualitative study, we explored the views of 17 genomics researchers in Africa on the prospects and challenges of genomics medicine in Africa. Interviewees were researchers in Africa who were involved in genomics research projects in Africa. Analysis of in-depth interviews suggest that genomics medicine may have an impact on disease surveillance, diagnosis, treatment and prevention. However, Africa's capacity for genomics medicine, current research priorities in genomics and the translation of research findings will be key defining factors impacting on the ability of genomics medicine to improve healthcare in Africa.
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Affiliation(s)
- N. S. Munung
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - B. M. Mayosi
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Dean's Office, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - J. de Vries
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
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93
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Fuller TD, Westfall TA, Das T, Dawson DV, Slusarski DC. High-throughput behavioral assay to investigate seizure sensitivity in zebrafish implicates ZFHX3 in epilepsy. J Neurogenet 2018; 32:92-105. [PMID: 29718741 DOI: 10.1080/01677063.2018.1445247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epilepsy, which affects ∼1% of the population, is caused by abnormal synchronous neural activity in the central nervous system (CNS). While there is a significant genetic contribution to epilepsy, the underlying causes for the majority of genetic cases remain unknown. The NIH Undiagnosed Diseases Project (UDP) utilized exome sequencing to identify genetic variants in patients affected by various conditions with undefined etiology, including epilepsy. Confirming the functional relevance of the candidate genes identified by exome sequencing in a timely manner is crucial to translating exome data into clinically useful information. To this end, we developed a high throughput version of a seizure-sensitivity assay in zebrafish (Danio rerio) to rapidly evaluate candidate genes found by exome sequencing. We developed open access software, Studying Epilepsy In Zebrafish using R (SEIZR), to efficiently analyze the data. SEIZR was validated by disrupting function of a known epilepsy gene, prickle 1. Next, using SEIZR, we analyzed a candidate gene from the UDP screen (Zinc Finger Homeobox 3, ZFHX3), and showed that reduced ZFHX3 function in zebrafish results in a significant hyperactive response to the convulsant drug pentylenetetrazol (PTZ). We find that ZFHX3 shows strong expression in the CNS during neurogenesis including in the pallium, thalamus, tegmentum, reticular formation, and medulla oblongata - all regions which have roles in motor control and coordination. Our findings in the zebrafish confirm human ZFHX3 is a strong candidate for further neurological studies. We offer SEIZR to other researchers as a tool to rapidly and efficiently analyze large behavioral data sets.
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Affiliation(s)
- Tyson D Fuller
- a Department of Biology , University of Iowa , Iowa City , IA , USA.,b Interdisciplinary Graduate Program in Genetics , University of Iowa , Iowa City , IA , USA
| | - Trudi A Westfall
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | - Tirthasree Das
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | - Deborah V Dawson
- b Interdisciplinary Graduate Program in Genetics , University of Iowa , Iowa City , IA , USA.,c Iowa Institute for Oral Health Research , University of Iowa , Iowa City , IA , USA.,d Department of Biostatistics , University of Iowa , Iowa City , IA , USA
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94
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Abstract
Conventional workup of rare neurological disease is frequently hampered by diagnostic delay or lack of diagnosis. While biomarkers have been established for many neurometabolic disorders, improved methods are required for diagnosis of previously unidentified or underreported causes of rare neurological disease. This would result in a higher diagnostic yield and increased patient numbers required for interventional studies. Recent studies using next-generation sequencing and metabolomics have led to identification of novel disease-causing genes and biomarkers. This combined approach can assist in overcoming challenges associated with analyzing and interpreting the large amount of data obtained from each technique. In particular, metabolomics can support the pathogenicity of sequence variants in genes encoding enzymes or transporters involved in metabolic pathways. Moreover, metabolomics can show the broader perturbation caused by inborn errors of metabolism and identify a metabolic fingerprint of metabolic disorders. As such, using "omics" has great potential to meet the current needs for improved diagnosis and elucidation of rare neurological disease.
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Affiliation(s)
- L M Crowther
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland
- CRC Clinical Research Center, University Children's Hospital Zurich, Zurich, Switzerland
- Radiz - Rare Disease Intiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland
| | - M Poms
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland
- CRC Clinical Research Center, University Children's Hospital Zurich, Zurich, Switzerland
- Radiz - Rare Disease Intiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland
| | - Barbara Plecko
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland.
- CRC Clinical Research Center, University Children's Hospital Zurich, Zurich, Switzerland.
- Radiz - Rare Disease Intiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland.
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, University Childrens' Hospital Graz, Auenbruggerplatz 34/2, 8036, Graz, Austria.
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95
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Nestler-Parr S, Korchagina D, Toumi M, Pashos CL, Blanchette C, Molsen E, Morel T, Simoens S, Kaló Z, Gatermann R, Redekop W. Challenges in Research and Health Technology Assessment of Rare Disease Technologies: Report of the ISPOR Rare Disease Special Interest Group. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2018; 21:493-500. [PMID: 29753344 DOI: 10.1016/j.jval.2018.03.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 02/18/2018] [Accepted: 03/05/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Successful development of new treatments for rare diseases (RDs) and their sustainable patient access require overcoming a series of challenges related to research and health technology assessment (HTA). These impediments, which may be unique to RDs or also apply to common diseases but are particularly pertinent in RDs, are diverse and interrelated. OBJECTIVE To develop for the first time a catalog of primary impediments to RD research and HTA, and to describe the cause and effect of individual challenges. METHODS Challenges were identified by an international 22-person expert working group and qualitative outreach to colleagues with relevant expertise. A broad range of stakeholder perspectives is represented. Draft results were presented at annual European and North American International Society for Pharmacoeconomics and Outcomes Research (ISPOR) congresses, and written comments were received by the 385-strong ISPOR Rare Disease Review Group from two rounds of review. Findings were refined and confirmed via targeted literature search. RESULTS Research-related challenges linked to the low prevalence of RDs were categorized into those pertaining to disease recognition and diagnosis, evaluation of treatment effect, and patient recruitment for clinical research. HTA-related challenges were classified into issues relating to the lack of a tailored HTA method for RD treatments and uncertainty for HTA agencies and health care payers. CONCLUSIONS Identifying and highlighting diverse, but interrelated, key challenges in RD research and HTA is an essential first step toward developing implementable and sustainable solutions. A collaborative multistakeholder effort is required to enable faster and less costly development of safe, efficacious, and appropriate new RD therapies that offer value for money.
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Affiliation(s)
| | - Daria Korchagina
- Mental Health and Public Health Unit (Inserm U669), University of Paris-Sud, Paris, France.
| | - Mondher Toumi
- Public Health and Chronic Disease Laboratory, Aix-Marseille University, Marseille, France
| | - Chris L Pashos
- Global Outcomes and Epidemiology Research, Takeda Pharmaceuticals International, Inc., Cambridge, MA, USA
| | - Christopher Blanchette
- College of Health and Human Services, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Elizabeth Molsen
- Scientific & Health Policy Initiatives, ISPOR, Lawrenceville, NJ, USA
| | - Thomas Morel
- KU Leuven Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium
| | - Steven Simoens
- KU Leuven Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium
| | - Zoltán Kaló
- Department of Health Policy and Health Economics, Eötvös Loránd University (ELTE), Budapest, Hungary; Syreon Research Institute, Budapest, Hungary
| | - Ruediger Gatermann
- Healthcare Policy and External Affairs Europe, CSL Behring, Biotherapies for Life, Marburg, Germany
| | - William Redekop
- Health Technology Assessment, Erasmus University, Rotterdam, The Netherlands
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96
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Toro C, Hori RT, Malicdan MCV, Tifft CJ, Goldstein A, Gahl WA, Adams DR, Fauni HB, Wolfe LA, Xiao J, Khan MM, Tian J, Hope KA, Reiter LT, Tremblay MG, Moss T, Franks AL, Balak C, LeDoux MS. A recurrent de novo missense mutation in UBTF causes developmental neuroregression. Hum Mol Genet 2018; 27:691-705. [PMID: 29300972 PMCID: PMC5886272 DOI: 10.1093/hmg/ddx435] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/29/2017] [Accepted: 12/19/2017] [Indexed: 12/17/2022] Open
Abstract
UBTF (upstream binding transcription factor) exists as two isoforms; UBTF1 regulates rRNA transcription by RNA polymerase 1, whereas UBTF2 regulates mRNA transcription by RNA polymerase 2. Herein, we describe 4 patients with very similar patterns of neuroregression due to recurrent de novo mutations in UBTF (GRCh37/hg19, NC_000017.10: g.42290219C > T, NM_014233.3: c.628G > A) resulting in the same amino acid change in both UBTF1 and UBTF2 (p.Glu210Lys [p.E210K]). Disease onset in our cohort was at 2.5 to 3 years and characterized by slow progression of global motor, cognitive and behavioral dysfunction. Notable early features included hypotonia with a floppy gait, high-pitched dysarthria and hyperactivity. Later features included aphasia, dystonia, and spasticity. Speech and ambulatory ability were lost by the early teens. Magnetic resonance imaging showed progressive generalized cerebral atrophy (supratentorial > infratentorial) with involvement of both gray and white matter. Patient fibroblasts showed normal levels of UBTF transcripts, increased expression of pre-rRNA and 18S rRNA, nucleolar abnormalities, markedly increased numbers of DNA breaks, defective cell-cycle progression, and apoptosis. Expression of mutant human UBTF1 in Drosophila neurons was lethal. Although no loss-of-function variants are reported in the Exome Aggregation Consortium (ExAC) database and Ubtf-/- is early embryonic lethal in mice, Ubtf+/- mice displayed only mild motor and behavioral dysfunction in adulthood. Our data underscore the importance of including UBTF E210K in the differential diagnosis of neuroregression and suggest that mainly gain-of-function mechanisms contribute to the pathogenesis of the UBTF E210K neuroregression syndrome.
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Affiliation(s)
- Camilo Toro
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Roderick T Hori
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - May Christine V Malicdan
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy Goldstein
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - William A Gahl
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David R Adams
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Harper B Fauni
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lynne A Wolfe
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianfeng Xiao
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mohammad M Khan
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Tian
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kevin A Hope
- Integrated Program in Biological Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lawrence T Reiter
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Michel G Tremblay
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, QC, Canada
| | - Tom Moss
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, QC, Canada
| | - Alexis L Franks
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Chris Balak
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - C4RCD Research Group
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Mark S LeDoux
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
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97
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Burke EA, Frucht SJ, Thompson K, Wolfe LA, Yokoyama T, Bertoni M, Huang Y, Sincan M, Adams DR, Taylor RW, Gahl WA, Toro C, Malicdan MCV. Biallelic mutations in mitochondrial tryptophanyl-tRNA synthetase cause Levodopa-responsive infantile-onset Parkinsonism. Clin Genet 2018; 93:712-718. [PMID: 29120065 PMCID: PMC5828974 DOI: 10.1111/cge.13172] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/30/2017] [Accepted: 11/05/2017] [Indexed: 12/30/2022]
Abstract
Mitochondrial aminoacyl‐tRNA synthetases (mtARSs) are essential, ubiquitously expressed enzymes that covalently attach amino acids to their corresponding tRNA molecules during translation of mitochondrial genes. Deleterious variants in the mtARS genes cause a diverse array of phenotypes, many of which involve the nervous system. Moreover, distinct mutations in mtARSs often cause different clinical manifestations. Recently, the gene encoding mitochondrial tryptophanyl tRNA synthetase (WARS2) was reported to cause 2 different neurological phenotypes, a form of autosomal recessive intellectual disability and a syndrome of severe infantile‐onset leukoencephalopathy. Here, we report the case of a 17‐year‐old boy with compound heterozygous mutations in WARS2 (p.Trp13Gly, p.Ser228Trp) who presented with infantile‐onset, Levodopa‐responsive Parkinsonism at the age of 2 years. Analysis of patient‐derived dermal fibroblasts revealed decreased steady‐state WARS2 protein and normal OXPHOS content. Muscle mitochondrial studies suggested mitochondrial proliferation without obvious respiratory chain deficiencies at the age of 9 years. This case expands the phenotypic spectrum of WARS2 deficiency and emphasizes the importance of mitochondrial protein synthesis in the pathogenesis of Parkinsonism.
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Affiliation(s)
- E A Burke
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland
| | - S J Frucht
- Movement Disorders Division, School of Medicine, New York University Langone, New York, New York
| | - K Thompson
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - L A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - T Yokoyama
- Section of Human Biochemical Genetics, Medical Genetics Branch, NHGRI, NIH, Bethesda, Maryland
| | - M Bertoni
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland
| | - Y Huang
- Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - M Sincan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland
| | - D R Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - R W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - W A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland.,Section of Human Biochemical Genetics, Medical Genetics Branch, NHGRI, NIH, Bethesda, Maryland
| | - C Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
| | - M C V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NHGRI, NIH, Bethesda, Maryland.,Office of the Clinical Director, NHGRI, NIH, Bethesda, Maryland
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98
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Zlatic SA, Vrailas-Mortimer A, Gokhale A, Carey LJ, Scott E, Burch R, McCall MM, Rudin-Rush S, Davis JB, Hartwig C, Werner E, Li L, Petris M, Faundez V. Rare Disease Mechanisms Identified by Genealogical Proteomics of Copper Homeostasis Mutant Pedigrees. Cell Syst 2018; 6:368-380.e6. [PMID: 29397366 DOI: 10.1016/j.cels.2018.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/28/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022]
Abstract
Rare neurological diseases shed light onto universal neurobiological processes. However, molecular mechanisms connecting genetic defects to their disease phenotypes are elusive. Here, we obtain mechanistic information by comparing proteomes of cells from individuals with rare disorders with proteomes from their disease-free consanguineous relatives. We use triple-SILAC mass spectrometry to quantify proteomes from human pedigrees affected by mutations in ATP7A, which cause Menkes disease, a rare neurodegenerative and neurodevelopmental disorder stemming from systemic copper depletion. We identified 214 proteins whose expression was altered in ATP7A-/y fibroblasts. Bioinformatic analysis of ATP7A-mutant proteomes identified known phenotypes and processes affected in rare genetic diseases causing copper dyshomeostasis, including altered mitochondrial function. We found connections between copper dyshomeostasis and the UCHL1/PARK5 pathway of Parkinson disease, which we validated with mitochondrial respiration and Drosophila genetics assays. We propose that our genealogical "omics" strategy can be broadly applied to identify mechanisms linking a genomic locus to its phenotypes.
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Affiliation(s)
| | - Alysia Vrailas-Mortimer
- School of Biological Sciences Illinois State University, Normal, IL 617901, USA; University of Denver, Department of Biological Sciences, Denver, CO 80208, USA
| | - Avanti Gokhale
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA
| | - Lucas J Carey
- School of Biological Sciences Illinois State University, Normal, IL 617901, USA
| | - Elizabeth Scott
- School of Biological Sciences Illinois State University, Normal, IL 617901, USA
| | - Reid Burch
- School of Biological Sciences Illinois State University, Normal, IL 617901, USA; University of Denver, Department of Biological Sciences, Denver, CO 80208, USA
| | - Morgan M McCall
- School of Biological Sciences Illinois State University, Normal, IL 617901, USA
| | | | | | - Cortnie Hartwig
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA; Department of Chemistry, Agnes Scott College, Decatur, GA 30030, USA
| | - Erica Werner
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Lian Li
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA
| | - Michael Petris
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Victor Faundez
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA.
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Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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García-Acero M, Acosta J. Whole-Exome Sequencing Identifies a de novo AHDC1 Mutation in a Colombian Patient with Xia-Gibbs Syndrome. Mol Syndromol 2017; 8:308-312. [PMID: 29230160 DOI: 10.1159/000479357] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2017] [Indexed: 12/11/2022] Open
Abstract
Xia-Gibbs syndrome is an autosomal dominant multisystem developmental disorder characterized by global developmental delay, hypotonia, obstructive sleep apnea, seizures, retrocerebellar cysts, delayed myelination, micrognathia, and mild dysmorphic features. Using whole-exome sequencing, we identified a de novo AHDC1 frameshift mutation c.2030_2030delG (p.G677Afs*52) in a Colombian patient, which was absent in both parents. Furthermore, we summarized the phenotypes of patients reported in the literature.
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Affiliation(s)
- Mary García-Acero
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Johanna Acosta
- Roosevelt Pediatric Orthopedic Institute, Bogotá, Colombia
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