51
|
Gauquelin L, Hartley T, Tarnopolsky M, Dyment DA, Brais B, Geraghty MT, Tétreault M, Ahmed S, Rojas S, Choquet K, Majewski J, Bernier F, Innes AM, Rouleau G, Suchowersky O, Boycott KM, Yoon G. Channelopathies Are a Frequent Cause of Genetic Ataxias Associated with Cerebellar Atrophy. Mov Disord Clin Pract 2020; 7:940-949. [PMID: 33163565 DOI: 10.1002/mdc3.13086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 11/08/2022] Open
Abstract
Background Cerebellar atrophy is a nonspecific imaging finding observed in a number of neurological disorders. Genetic ataxias associated with cerebellar atrophy are a heterogeneous group of conditions, rendering the approach to diagnosis challenging. Objectives To define the spectrum of genetic ataxias associated with cerebellar atrophy in a Canadian cohort and the diagnostic yield of exome sequencing for this group of conditions. Methods A total of 92 participants from 66 families with cerebellar atrophy were recruited for this multicenter prospective cohort study. Exome sequencing was performed for all participants between 2011 and 2017 as part of 1 of 2 national research programs, Finding of Rare Genetic Disease Genes or Enhanced Care for Rare Genetic Diseases in Canada. Results A genetic diagnosis was established in 53% of families (35/66). Pathogenic variants were found in 21 known genes, providing a diagnosis for 31/35 families (89%), and in 4 novel genes, accounting for 4/35 families (11%). Of the families, 31/66 (47%) remained without a genetic diagnosis. The most common diagnoses were channelopathies, which were established in 9/35 families (26%). Additional clinical findings provided useful clues to specific diagnoses. Conclusions We report on the high frequency of channelopathies as a cause of genetic ataxias associated with cerebellar atrophy and the utility of exome sequencing for this group of conditions.
Collapse
Affiliation(s)
- Laurence Gauquelin
- Division of Clinical and Metabolic Genetics, Department of Paediatrics The Hospital for Sick Children, University of Toronto Toronto Ontario Canada.,Division of Paediatric Neurology, Department of Paediatrics The Hospital for Sick Children, University of Toronto Toronto Ontario Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Mark Tarnopolsky
- Department of Paediatrics McMaster University Medical Centre Hamilton Ontario Canada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Bernard Brais
- Department of Neurology and Neurosurgery McGill University, Montreal Neurological Institute Montreal Qubec Canada.,Department of Human Genetics McGill University Montreal Qubec Canada
| | - Michael T Geraghty
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Martine Tétreault
- Department of Human Genetics McGill University Montreal Qubec Canada.,Department of Neuroscience Université de Montréal CHUM, Montreal Qubec Canada
| | - Sohnee Ahmed
- Division of Clinical and Metabolic Genetics, Department of Paediatrics The Hospital for Sick Children, University of Toronto Toronto Ontario Canada
| | - Samantha Rojas
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Karine Choquet
- Department of Neurology and Neurosurgery McGill University, Montreal Neurological Institute Montreal Qubec Canada
| | - Jacek Majewski
- Department of Human Genetics McGill University Montreal Qubec Canada
| | - François Bernier
- Department of Medical Genetics University of Calgary Calgary Alberta Canada
| | | | - Guy Rouleau
- Department of Neurology and Neurosurgery McGill University, Montreal Neurological Institute Montreal Qubec Canada
| | - Oksana Suchowersky
- Department of Medicine Division of Neurology, University of Alberta Edmonton Alberta Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Grace Yoon
- Division of Clinical and Metabolic Genetics, Department of Paediatrics The Hospital for Sick Children, University of Toronto Toronto Ontario Canada.,Division of Paediatric Neurology, Department of Paediatrics The Hospital for Sick Children, University of Toronto Toronto Ontario Canada
| |
Collapse
|
52
|
Link N, Bellen HJ. Using Drosophila to drive the diagnosis and understand the mechanisms of rare human diseases. Development 2020; 147:dev191411. [PMID: 32988995 PMCID: PMC7541339 DOI: 10.1242/dev.191411] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing has greatly accelerated the discovery of rare human genetic diseases. Nearly 45% of patients have variants associated with known diseases but the unsolved cases remain a conundrum. Moreover, causative mutations can be difficult to pinpoint because variants frequently map to genes with no previous disease associations and, often, only one or a few patients with variants in the same gene are identified. Model organisms, such as Drosophila, can help to identify and characterize these new disease-causing genes. Importantly, Drosophila allow quick and sophisticated genetic manipulations, permit functional testing of human variants, enable the characterization of pathogenic mechanisms and are amenable to drug tests. In this Spotlight, focusing on microcephaly as a case study, we highlight how studies of human genes in Drosophila have aided our understanding of human genetic disorders, allowing the identification of new genes in well-established signaling pathways.
Collapse
Affiliation(s)
- Nichole Link
- Howard Hughes Medical Institute, BCM, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics (MHG), BCM, Houston, TX, 77030, USA
- Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Hugo J Bellen
- Howard Hughes Medical Institute, BCM, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics (MHG), BCM, Houston, TX, 77030, USA
- Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| |
Collapse
|
53
|
Rahimzadeh V, Knoppers BM, Bartlett G. Ethical, Legal, and Social Issues (ELSI) of Responsible Data Sharing Involving Children in Genomics: A Systematic Literature Review of Reasons. AJOB Empir Bioeth 2020; 11:233-245. [PMID: 32975491 DOI: 10.1080/23294515.2020.1818875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Progress in precision medicine relies on the access to, use of, and exchange of genomic and associated clinical data, including from children. The ethical, legal, and social issues (ELSI) of such data access, use, and exchange may be accentuated in the pediatric context due in part to the highly sensitive nature of genomic data, children's consent-related vulnerabilities, and uncertain risks of reidentification. Systematic analyses of the ELSI and scientific reasons for why and how genomic data may be shared responsibly are, however, limited. Methods: We conducted a modified systematic review of reasons according to Sofaer and Strech to examine the ELSI and scientific reasons for "responsible" sharing of children's genomic and associated clinical data. Empirical articles, commentaries, and data-sharing policies indexed in Medline, Scopus, Web of Science, and BIOSIS were included in the analysis if they discussed ELSI and were published between 2003 and 2017 in English. Results: One hundred and fifty-one records met our inclusion criteria. We identified 11 unique reasons and 8 subreasons for why children's genomic data should or should not be shared. Enhancing the prospect of direct and indirect benefits and maximizing the utility of children's data were top reasons why data should be shared. Inadequate data privacy protection was the leading reason why it should not. We furthermore identified 8 reasons and 30 subreasons that support conditional data sharing, in which recontact for the continued use of children's data once they reach the age of majority was the most frequently endorsed condition. Conclusions: The complete list of ELSI reasons and responsible conditions provides an evidentiary basis upon which institutions can develop data-sharing policies. Institutions should encourage the sharing of children's data to advance genomic research, while heeding special reconsent and data protection mechanisms that may help mitigate uncertain longitudinal risks for children and families.
Collapse
Affiliation(s)
- Vasiliki Rahimzadeh
- Center for Biomedical Ethics, Stanford University, Stanford, California, USA
| | | | | |
Collapse
|
54
|
Uehara T, Yamada M, Umetsu S, Nittono H, Suzuki H, Fujisawa T, Takenouchi T, Inui A, Kosaki K. Biallelic Mutations in the LSR Gene Cause a Novel Type of Infantile Intrahepatic Cholestasis. J Pediatr 2020; 221:251-254. [PMID: 32303357 DOI: 10.1016/j.jpeds.2020.01.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/03/2020] [Accepted: 01/30/2020] [Indexed: 12/16/2022]
Abstract
We identified biallelic pathogenic mutations in the Lipolysis-stimulated lipoprotein receptor (LSR) gene in a patient with infantile intrahepatic cholestasis. We established that mutations in the LSR gene, which encodes a protein which is critical for the formation of tricellular tight junctions in the liver, are a novel cause of pediatric cholestasis.
Collapse
Affiliation(s)
- Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Shuichiro Umetsu
- Department of Pediatric Hepatology and Gastroenterology, Saiseikai Yokohama-shi Tobu Hospital, Kanagawa, Japan
| | | | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Tomoo Fujisawa
- Department of Pediatric Hepatology and Gastroenterology, Saiseikai Yokohama-shi Tobu Hospital, Kanagawa, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Ayano Inui
- Department of Pediatric Hepatology and Gastroenterology, Saiseikai Yokohama-shi Tobu Hospital, Kanagawa, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
| |
Collapse
|
55
|
Daneshjoo O, hosseini A, Garshasbi M, Pizzuti A. Evidence of involvement of a novel VUS variant in the CHKB gene to congenital muscular dystrophy affection. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
|
56
|
Lemire G, MacDonald SK, Boycott KM. SMG9-deficiency syndrome caused by a homozygous missense variant: Expanding the genotypic and phenotypic spectrum of this developmental disorder. Am J Med Genet A 2020; 182:1829-1831. [PMID: 32412169 DOI: 10.1002/ajmg.a.61616] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Gabrielle Lemire
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Stella K MacDonald
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| |
Collapse
|
57
|
The diagnostic utility of genome sequencing in a pediatric cohort with suspected mitochondrial disease. Genet Med 2020; 22:1254-1261. [DOI: 10.1038/s41436-020-0793-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/15/2022] Open
|
58
|
Eaton A, Hartley T, Kernohan K, Ito Y, Lamont R, Parboosingh J, Barrowman N, Innes AM, Boycott K. When to think outside the autozygome: Best practices for exome sequencing in "consanguineous" families. Clin Genet 2020; 97:835-843. [PMID: 32162313 DOI: 10.1111/cge.13736] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/15/2020] [Accepted: 03/09/2020] [Indexed: 12/14/2022]
Abstract
Exome sequencing (ES) is an effective diagnostic tool with a high yield in consanguineous families. However, how diagnostic yield and mode of inheritance relate to family structure has not been well delineated. We reviewed ES results from families enrolled in the Care4Rare Canada research consortium with various degrees of consanguinity. We contrasted the diagnostic yield in families with parents who are second cousins or closer ("close" consanguinity) vs those more distantly related or from isolated populations ("presumed" consanguinity). We further stratified by number of affected individuals (multiple affected ["multiplex"] vs single affected [simplex]). The overall yield in 116 families was 45.7% (n = 53) with no significant difference between subgroups. Homozygous variants accounted for 100% and 75% of diagnoses in close and presumed consanguineous multiplex families, respectively. In simplex presumed consanguineous families, a striking 46.2% of diagnoses were due to de novo variants, vs only 11.8% in simplex closely consanguineous families (88.2% homozygous). Our data underscores the high yield of ES in consanguineous families and highlights that while a singleton approach may frequently be reasonable and a responsible use of resources, trio sequencing should be strongly considered in simplex families in the absence of confirmed consanguinity given the proportion of de novo variants.
Collapse
Affiliation(s)
- Alison Eaton
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Ryan Lamont
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jillian Parboosingh
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nick Barrowman
- Clinical Research Unit, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | -
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
59
|
Gillespie MK, McMillan HJ, Kernohan KD, Pena IA, Meyer-Schuman R, Antonellis A, Boycott KM. A Novel Mutation in MARS in a Patient with Charcot-Marie-Tooth Disease, Axonal, Type 2U with Congenital Onset. J Neuromuscul Dis 2020; 6:333-339. [PMID: 31356216 PMCID: PMC6889022 DOI: 10.3233/jnd-190404] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Charcot-Marie-Tooth disease is a phenotypically and genetically heterogeneous group of disorders affecting both motor and sensory neurons. Exome sequencing has driven discovery of genes responsible for Charcot-Marie-Tooth disease with more than 70 genes now associated with this neuromuscular disease. The MARS gene was recently reported as the cause of Charcot-Marie-Tooth 2U, a slowly progressive axonal sensorimotor polyneuropathy with adult-onset reported in six patients. We report here a patient with a progressive, early childhood-onset, motor-predominant form of Charcot-Marie-Tooth disease. Exome sequencing identified a novel MARS variant (c.1189G>A; p.Ala397Thr) that was not present in her unaffected mother; her unaffected father was unavailable. Further studies using structural modeling and a yeast humanization assay support pathogenicity of the variant. Our study expands the phenotype of Charcot-Marie-Tooth 2U, while highlighting the utility of functional assays to evaluate variant pathogenicity.
Collapse
Affiliation(s)
- Meredith K Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Hugh J McMillan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Izabella A Pena
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | | | | | - Anthony Antonellis
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| |
Collapse
|
60
|
Boycott KM, Hartley T, Biesecker LG, Gibbs RA, Innes AM, Riess O, Belmont J, Dunwoodie SL, Jojic N, Lassmann T, Mackay D, Temple IK, Visel A, Baynam G. A Diagnosis for All Rare Genetic Diseases: The Horizon and the Next Frontiers. Cell 2020; 177:32-37. [PMID: 30901545 DOI: 10.1016/j.cell.2019.02.040] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The introduction of exome sequencing in the clinic has sparked tremendous optimism for the future of rare disease diagnosis, and there is exciting opportunity to further leverage these advances. To provide diagnostic clarity to all of these patients, however, there is a critical need for the field to develop and implement strategies to understand the mechanisms underlying all rare diseases and translate these to clinical care.
Collapse
Affiliation(s)
- Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - John Belmont
- Illumina, Madison, WI, USA; Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | | | - Timo Lassmann
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Deborah Mackay
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
| | - I Karen Temple
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, CA, USA; DOE Joint Genome Institute, CA, USA; The University of California at Merced, CA, USA
| | - Gareth Baynam
- Faculty of Health and Medical Sciences, University of Western Australia Medical School, Perth, WA, Australia; Western Australian Register of Developmental Anomalies, Genetic Services of Western Australia, Perth, WA, Australia; Office of Population Health Genomics, Western Australian Department of Health, Perth, WA, Australia
| |
Collapse
|
61
|
Boycott KM, Campeau PM, Howley HE, Pavlidis P, Rogic S, Oriel C, Berman JN, Hamilton RM, Hicks GG, Lipshitz HD, Masson JY, Shoubridge EA, Junker A, Leroux MR, McMaster CR, Michaud JL, Turvey SE, Dyment D, Innes AM, van Karnebeek CD, Lehman A, Cohn RD, MacDonald IM, Rachubinski RA, Frosk P, Vandersteen A, Wozniak RW, Pena IA, Wen XY, Lacaze-Masmonteil T, Rankin C, Hieter P. The Canadian Rare Diseases Models and Mechanisms (RDMM) Network: Connecting Understudied Genes to Model Organisms. Am J Hum Genet 2020; 106:143-152. [PMID: 32032513 DOI: 10.1016/j.ajhg.2020.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/10/2020] [Indexed: 01/14/2023] Open
Abstract
Advances in genomics have transformed our ability to identify the genetic causes of rare diseases (RDs), yet we have a limited understanding of the mechanistic roles of most genes in health and disease. When a novel RD gene is first discovered, there is minimal insight into its biological function, the pathogenic mechanisms of disease-causing variants, and how therapy might be approached. To address this gap, the Canadian Rare Diseases Models and Mechanisms (RDMM) Network was established to connect clinicians discovering new disease genes with Canadian scientists able to study equivalent genes and pathways in model organisms (MOs). The Network is built around a registry of more than 500 Canadian MO scientists, representing expertise for over 7,500 human genes. RDMM uses a committee process to identify and evaluate clinician-MO scientist collaborations and approve 25,000 Canadian dollars in catalyst funding. To date, we have made 85 clinician-MO scientist connections and funded 105 projects. These collaborations help confirm variant pathogenicity and unravel the molecular mechanisms of RD, and also test novel therapies and lead to long-term collaborations. To expand the impact and reach of this model, we made the RDMM Registry open-source, portable, and customizable, and we freely share our committee structures and processes. We are currently working with emerging networks in Europe, Australia, and Japan to link international RDMM networks and registries and enable matches across borders. We will continue to create meaningful collaborations, generate knowledge, and advance RD research locally and globally for the benefit of patients and families living with RD.
Collapse
Affiliation(s)
- Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
| | - Philippe M Campeau
- Centre de Recherche du CHU Ste-Justine, Department of Pediatrics, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Heather E Howley
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sanja Rogic
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Christine Oriel
- Maternal Infant Child and Youth Research Network (MICYRN), Vancouver, BC V5Z 4H4, Canada
| | - Jason N Berman
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Robert M Hamilton
- Labatt Family Heart Centre and Translational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Geoffrey G Hicks
- Regenerative Medicine Program, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada; Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jean-Yves Masson
- Oncology Division, CHU de Québec-Université Laval, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Eric A Shoubridge
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Anne Junker
- Department of Pediatrics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | - Jaques L Michaud
- Centre de Recherche du CHU Ste-Justine, Department of Pediatrics, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Stuart E Turvey
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - David Dyment
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Alberta Children's Hospital, Calgary, AB T2N 4N1, Canada
| | - Clara D van Karnebeek
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada; Department of Pediatrics, Amsterdam University Medical Centres, Amsterdam, the Netherlands; Department of Clinical Genetics, Amsterdam University Medical Centres, Amsterdam, the Netherlands
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Ronald D Cohn
- Genetics and Genome Biology Program, SickKids Research Institute, Department of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Ian M MacDonald
- Department of Ophthalmology and Visual Sciences, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R7, Canada
| | - Richard A Rachubinski
- Genetics and Genome Biology Program, SickKids Research Institute, Department of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Patrick Frosk
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Anthony Vandersteen
- Department of Pediatrics, Maritime Medical Genetics Service, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Richard W Wozniak
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Izabella A Pena
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Xiao-Yan Wen
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Centre for Biomedical Science, St Michael's Hospital, Unity Health Toronto, Department of Medicine, University of Toronto, Toronto, ON M5B 1T8
| | - Thierry Lacaze-Masmonteil
- Maternal Infant Child and Youth Research Network (MICYRN), Vancouver, BC V5Z 4H4, Canada; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Catharine Rankin
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| |
Collapse
|
62
|
Lee Y, Park S, Lee JS, Kim SY, Cho J, Yoo Y, Lee S, Yoo T, Lee M, Seo J, Lee J, Kneissl J, Lee J, Jeon H, Jeon EY, Hong SE, Kim E, Kim H, Kim WJ, Kim JS, Ko JM, Cho A, Lim BC, Kim WS, Choi M, Chae JH. Genomic profiling of 553 uncharacterized neurodevelopment patients reveals a high proportion of recessive pathogenic variant carriers in an outbred population. Sci Rep 2020; 10:1413. [PMID: 31996704 PMCID: PMC6989631 DOI: 10.1038/s41598-020-58101-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/10/2020] [Indexed: 11/22/2022] Open
Abstract
A substantial portion of Mendelian disease patients suffers from genetic variants that are inherited in a recessive manner. A precise understanding of pathogenic recessive variants in a population would assist in pre-screening births of such patients. However, a systematic understanding of the contribution of recessive variants to Mendelian diseases is still lacking. Therefore, genetic diagnosis and variant discovery of 553 undiagnosed Korean patients with complex neurodevelopmental problems (KND for Korean NeuroDevelopmental cohort) were performed using whole exome sequencing of patients and their parents. Disease-causing variants, including newly discovered variants, were identified in 57.5% of the probands of the KND cohort. Among the patients with the previous reported pathogenic variants, 35.1% inherited these variants in a recessive manner. Genes that cause recessive disorders in our cohort tend to be less constrained by loss-of-function variants and were enriched in lipid metabolism and mitochondrial functions. This observation was applied to an estimation that approximately 1 in 17 healthy Korean individuals carry at least one of these pathogenic variants that develop severe neurodevelopmental problems in a recessive manner. Furthermore, the feasibility of these genes for carrier screening was evaluated. Our results will serve as a foundation for recessive variant screening to reduce occurrences of rare Mendelian disease patients. Additionally, our results highlight the utility and necessity of whole exome sequencing-based diagnostics for improving patient care in a country with a centralized medical system.
Collapse
Affiliation(s)
- Youngha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Soojin Park
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jin Sook Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Pediatrics, Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, Republic of Korea
- Department of Genome Medicine and Science, Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, Republic of Korea
| | - Soo Yeon Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jaeso Cho
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Yongjin Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Sangmoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Taekyeong Yoo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Moses Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jieun Seo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jeongeun Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Interdisciplinary Program for Bioengineering, Graduate School, Seoul National Universty, Seoul, 03080, Republic of Korea
| | - Jana Kneissl
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jean Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Hyoungseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Eun Young Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Sung Eun Hong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Eunha Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Hyuna Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Woo Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jon Soo Kim
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju, 28644, Republic of Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Anna Cho
- Department of Pediatrics, Ewha Womans University School of Medicine, Seoul, 07804, Republic of Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Won Seop Kim
- Department of Pediatrics, College of Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| |
Collapse
|
63
|
Liu HY, Zhou L, Zheng MY, Huang J, Wan S, Zhu A, Zhang M, Dong A, Hou L, Li J, Xu H, Lu B, Lu W, Liu P, Lu Y. Diagnostic and clinical utility of whole genome sequencing in a cohort of undiagnosed Chinese families with rare diseases. Sci Rep 2019; 9:19365. [PMID: 31852928 PMCID: PMC6920370 DOI: 10.1038/s41598-019-55832-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 12/03/2019] [Indexed: 12/23/2022] Open
Abstract
Rare diseases are usually chronically debilitating or even life-threatening with diagnostic and therapeutic challenges in current clinical practice. It has been estimated that 80% of rare diseases are genetic in origin, and thus genome sequencing-based diagnosis offers a promising alternative for rare-disease management. In this study, 79 individuals from 16 independent families were performed for whole-genome sequencing (WGS) in an effort to identify the causative mutations for 16 distinct rare diseases that are largely clinically intractable. Comprehensive analysis of variations, including simple nucleotide variants (SNVs), copy-number variations (CNVs), and structural variations (SVs), was implemented using the WGS data. A flexible analysis pipeline that allowed a certain degree of misclassification of disease status was developed to facilitate the identification of causative variants. As a result, disease-causing variants were identified in 10 of the 16 investigated diseases, yielding a diagnostic rate of 62.5%. Additionally, new potentially pathogenic variants were discovered for two disorders, including IGF2/INS-IGF2 in mitochondrial disease and FBN3 in Klippel–Trenaunay–Weber syndrome. Our WGS analysis not only detected a CNV associated with 3p deletion syndrome but also captured a simple sequence repeat (SSR) variation associated with Machado–Joseph disease. To our knowledge, this is the first time the clinical WGS analysis of short-read sequences has been used successfully to identify a causative SSR variation that perfectly segregates with a repeat expansion disorder. After the WGS analysis, we confirmed the initial diagnosis for three of 10 established disorders and modified or corrected the initial diagnosis for the remaining seven disorders. In summary, clinical WGS is a powerful tool for the diagnosis of rare diseases, and its diagnostic clarity at molecular levels offers important benefits for the participating families.
Collapse
Affiliation(s)
- Hong-Yan Liu
- Department of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan, 450003, China
| | - Liyuan Zhou
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Meng-Yue Zheng
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
| | - Jia Huang
- Department of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan, 450003, China
| | - Shu Wan
- Department of Neurosurgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Aiying Zhu
- Department of Dermatology, People's Hospital of Lushi County, Lushi, Henan, 472200, China
| | - Mingjie Zhang
- Department of Medical Genetics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan, 450003, China
| | - Anliang Dong
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
| | - Ling Hou
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
| | - Jia Li
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Haiming Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Bingjian Lu
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
| | - Weiguo Lu
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China. .,Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
| | - Yan Lu
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China.
| |
Collapse
|
64
|
Hannah-Shmouni F, MacNeil L, Brady L, Nilsson MI, Tarnopolsky M. Expanding the Clinical Spectrum of LONP1-Related Mitochondrial Cytopathy. Front Neurol 2019; 10:981. [PMID: 31636596 PMCID: PMC6787162 DOI: 10.3389/fneur.2019.00981] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022] Open
Abstract
Pathogenic variants in the LONP1 gene have been associated with CODAS syndrome (Cerebral, Ocular, Dental, Auricular, and Skeletal Anomalies Syndrome). A recent report identified the first newborn case with LONP1-related mitochondrial cytopathy due to a compound heterozygous pathogenic variant in LONP1 without features of CODAS. The proband had manifested with severe congenital lactic acidosis and profound multiple respiratory chain complex activity deficiencies associated with the quantitative loss of mtDNA copy number in muscle. A subsequent report identified two siblings with regression during infancy, profound hypotonia and muscle weakness, severe intellectual disability, progressive cerebellar atrophy, where muscle biopsy showed an electron dense mitochondrial inclusions without ragged-red fibers and normal electron transport chain enzyme activities. Here, we report an additional case of autosomal recessive mitochondrial cytopathy due to a homozygous missense variant in LONP1 that was identified on whole exome sequencing (c.810G > A; p.D463N). The proband, a 20-year-old male born to consanguineous parents, presented with global developmental delay, emotional outbursts, speech and swallowing difficulties, hypotonia, and ataxia since childhood. Muscle biopsy showed massive granular bodies, increased oxidative stress, and autophagic block and reduced mitochondrial state 3 respiration. We have identified another case of LONP1-related mitochondrial cytopathy further confirming a neurological phenotype without CODAS features.
Collapse
Affiliation(s)
- Fady Hannah-Shmouni
- Clinical Biochemical Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.,Section on Endocrinology and Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Lauren MacNeil
- Division of Pediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Lauren Brady
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Mats I Nilsson
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| |
Collapse
|
65
|
Kernohan KD, McBride A, Hartley T, Rojas SK, Dyment DA, Boycott KM, Dyack S. p21 protein-activated kinase 1 is associated with severe regressive autism, and epilepsy. Clin Genet 2019; 96:449-455. [PMID: 31392718 DOI: 10.1111/cge.13618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/08/2019] [Indexed: 01/26/2023]
Abstract
The p21-activated kinase (PAK) family of proteins function as key effectors of RHO family GTPases in mammalian cells to regulate many pathways including Ras/Raf/MEK/ERK and Wnt/β-catenin, amongst others. Here we report an individual with a novel autosomal dominant disorder characterized by severe regressive autism, intellectual disability, and epilepsy. Exome sequencing of the proband and her parents revealed a de novo variant in the PAK1 gene ([NM_001128620] c.362C>T/p.Pro121Leu). Studies in patient cells showed a clear effect on PAK1 protein function, including altered phosphorylation of targets (JNK and ERK), decreased abundance of β-catenin, and concomitant altered expression downstream of these key regulators. Our findings add PAK1 to the list of PAK proteins and kinases which when mutated cause rare genetic diseases.
Collapse
Affiliation(s)
- Kristin D Kernohan
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Arran McBride
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Samantha K Rojas
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | -
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Sarah Dyack
- Department of Pediatrics, Dalhousie University and IWK Health Centre, Halifax, Nova Scotia, Canada
| |
Collapse
|
66
|
Jia J, An Z, Ming Y, Guo Y, Li W, Liang Y, Guo D, Li X, Tai J, Chen G, Jin Y, Liu Z, Ni X, Shi T. eRAM: encyclopedia of rare disease annotations for precision medicine. Nucleic Acids Res 2019; 46:D937-D943. [PMID: 29106618 PMCID: PMC5753383 DOI: 10.1093/nar/gkx1062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/24/2017] [Indexed: 01/12/2023] Open
Abstract
Rare diseases affect over a hundred million people worldwide, most of these patients are not accurately diagnosed and effectively treated. The limited knowledge of rare diseases forms the biggest obstacle for improving their treatment. Detailed clinical phenotyping is considered as a keystone of deciphering genes and realizing the precision medicine for rare diseases. Here, we preset a standardized system for various types of rare diseases, called encyclopedia of Rare disease Annotations for Precision Medicine (eRAM). eRAM was built by text-mining nearly 10 million scientific publications and electronic medical records, and integrating various data in existing recognized databases (such as Unified Medical Language System (UMLS), Human Phenotype Ontology, Orphanet, OMIM, GWAS). eRAM systematically incorporates currently available data on clinical manifestations and molecular mechanisms of rare diseases and uncovers many novel associations among diseases. eRAM provides enriched annotations for 15 942 rare diseases, yielding 6147 human disease related phenotype terms, 31 661 mammalians phenotype terms, 10,202 symptoms from UMLS, 18 815 genes and 92 580 genotypes. eRAM can not only provide information about rare disease mechanism but also facilitate clinicians to make accurate diagnostic and therapeutic decisions towards rare diseases. eRAM can be freely accessed at http://www.unimd.org/eram/.
Collapse
Affiliation(s)
- Jinmeng Jia
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Zhongxin An
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yue Ming
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, the Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, The Ministry of Education Key Laboratory of Major Diseases in Children, Center for Medical Genetics, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Yunxiang Liang
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Dongming Guo
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xin Li
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jun Tai
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, the Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Geng Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yaqiong Jin
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, the Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Zhimei Liu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, the Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Xin Ni
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, the Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| |
Collapse
|
67
|
Chelban V, Wilson MP, Warman Chardon J, Vandrovcova J, Zanetti MN, Zamba‐Papanicolaou E, Efthymiou S, Pope S, Conte MR, Abis G, Liu Y, Tribollet E, Haridy NA, Botía JA, Ryten M, Nicolaou P, Minaidou A, Christodoulou K, Kernohan KD, Eaton A, Osmond M, Ito Y, Bourque P, Jepson JEC, Bello O, Bremner F, Cordivari C, Reilly MM, Foiani M, Heslegrave A, Zetterberg H, Heales SJR, Wood NW, Rothman JE, Boycott KM, Mills PB, Clayton PT, Houlden H. PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation. Ann Neurol 2019; 86:225-240. [PMID: 31187503 PMCID: PMC6772106 DOI: 10.1002/ana.25524] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To identify disease-causing variants in autosomal recessive axonal polyneuropathy with optic atrophy and provide targeted replacement therapy. METHODS We performed genome-wide sequencing, homozygosity mapping, and segregation analysis for novel disease-causing gene discovery. We used circular dichroism to show secondary structure changes and isothermal titration calorimetry to investigate the impact of variants on adenosine triphosphate (ATP) binding. Pathogenicity was further supported by enzymatic assays and mass spectroscopy on recombinant protein, patient-derived fibroblasts, plasma, and erythrocytes. Response to supplementation was measured with clinical validated rating scales, electrophysiology, and biochemical quantification. RESULTS We identified biallelic mutations in PDXK in 5 individuals from 2 unrelated families with primary axonal polyneuropathy and optic atrophy. The natural history of this disorder suggests that untreated, affected individuals become wheelchair-bound and blind. We identified conformational rearrangement in the mutant enzyme around the ATP-binding pocket. Low PDXK ATP binding resulted in decreased erythrocyte PDXK activity and low pyridoxal 5'-phosphate (PLP) concentrations. We rescued the clinical and biochemical profile with PLP supplementation in 1 family, improvement in power, pain, and fatigue contributing to patients regaining their ability to walk independently during the first year of PLP normalization. INTERPRETATION We show that mutations in PDXK cause autosomal recessive axonal peripheral polyneuropathy leading to disease via reduced PDXK enzymatic activity and low PLP. We show that the biochemical profile can be rescued with PLP supplementation associated with clinical improvement. As B6 is a cofactor in diverse essential biological pathways, our findings may have direct implications for neuropathies of unknown etiology characterized by reduced PLP levels. ANN NEUROL 2019;86:225-240.
Collapse
Affiliation(s)
- Viorica Chelban
- Department of Neuromuscular DiseasesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
- Department of Neurology and NeurosurgeryInstitute of Emergency MedicineChisinauMoldova
| | - Matthew P. Wilson
- Genetics and Genomic MedicineUniversity College London Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Jodi Warman Chardon
- Department of Medicine (Neurology)University of OttawaOttawaOntarioCanada
- Ottawa Hospital Research InstituteOttawaOntarioCanada
- Children's Hospital of Eastern Ontario Research Institute, University of OttawaOttawaOntarioCanada
| | - Jana Vandrovcova
- Department of Neuromuscular DiseasesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - M. Natalia Zanetti
- Department of Clinical and Experimental EpilepsyUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Eleni Zamba‐Papanicolaou
- Cyprus Institute of Neurology and GeneticsNicosiaCyprus
- Cyprus School of Molecular MedicineNicosiaCyprus
| | - Stephanie Efthymiou
- Department of Neuromuscular DiseasesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Simon Pope
- Neurometabolic Unit, National Hospital for Neurology and NeurosurgeryLondonUnited Kingdom
| | - Maria R. Conte
- Randall Centre of Cell and Molecular Biophysics, School of Basic and Medical BiosciencesKing's College LondonLondonUnited Kingdom
| | - Giancarlo Abis
- Randall Centre of Cell and Molecular Biophysics, School of Basic and Medical BiosciencesKing's College LondonLondonUnited Kingdom
| | - Yo‐Tsen Liu
- Department of NeurologyNeurological Institute, Taipei Veterans General HospitalTaipeiTaiwan
- National Yang‐Ming University School of MedicineTaipeiTaiwan
- Institute of Brain Science, National Yang‐Ming UniversityTaipeiTaiwan
| | - Eloise Tribollet
- Department of Neuromuscular DiseasesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Nourelhoda A. Haridy
- Department of Neuromuscular DiseasesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
- Department of Neurology and PsychiatryAssiut University Hospital, Faculty of MedicineAsyutEgypt
| | - Juan A. Botía
- Reta Lila Weston Research LaboratoriesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
- Department of Information and Communications EngineeringUniversity of MurciaMurciaSpain
| | - Mina Ryten
- Reta Lila Weston Research LaboratoriesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
- Department of Medical & Molecular GeneticsKing's College London, Guy's HospitalLondonUnited Kingdom
| | - Paschalis Nicolaou
- Cyprus Institute of Neurology and GeneticsNicosiaCyprus
- Cyprus School of Molecular MedicineNicosiaCyprus
| | - Anna Minaidou
- Cyprus Institute of Neurology and GeneticsNicosiaCyprus
- Cyprus School of Molecular MedicineNicosiaCyprus
| | - Kyproula Christodoulou
- Cyprus Institute of Neurology and GeneticsNicosiaCyprus
- Cyprus School of Molecular MedicineNicosiaCyprus
| | - Kristin D. Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of OttawaOttawaOntarioCanada
- Newborn Screening Ontario, Children's Hospital of Eastern OntarioOttawaOntarioCanada
| | - Alison Eaton
- Children's Hospital of Eastern Ontario Research Institute, University of OttawaOttawaOntarioCanada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of OttawaOttawaOntarioCanada
| | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, University of OttawaOttawaOntarioCanada
| | - Pierre Bourque
- Department of Medicine (Neurology)University of OttawaOttawaOntarioCanada
- Ottawa Hospital Research InstituteOttawaOntarioCanada
| | - James E. C. Jepson
- Department of Clinical and Experimental EpilepsyUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Oscar Bello
- Department of Clinical and Experimental EpilepsyUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Fion Bremner
- Neuro‐ophthalmology DepartmentNational Hospital for Neurology and NeurosurgeryLondonUnited Kingdom
| | - Carla Cordivari
- Clinical Neurophysiology DepartmentNational Hospital for Neurology and NeurosurgeryLondonUnited Kingdom
| | - Mary M. Reilly
- Department of Neuromuscular DiseasesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Martha Foiani
- Clinical Neurophysiology DepartmentNational Hospital for Neurology and NeurosurgeryLondonUnited Kingdom
- Department of Neurodegenerative DiseaseUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
| | - Amanda Heslegrave
- Department of Neurodegenerative DiseaseUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
- UK Dementia Research Institute at University College LondonLondonUnited Kingdom
| | - Henrik Zetterberg
- Department of Neurodegenerative DiseaseUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
- UK Dementia Research Institute at University College LondonLondonUnited Kingdom
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
- Department of Psychiatry and NeurochemistryInstitute of Neuroscience and Physiology, Sahlgrenska Academy at University of GothenburgMölndalSweden
| | - Simon J. R. Heales
- Neurometabolic Unit, National Hospital for Neurology and NeurosurgeryLondonUnited Kingdom
| | - Nicholas W. Wood
- Department of Neuromuscular DiseasesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
- Neurogenetics LaboratoryNational Hospital for Neurology and NeurosurgeryLondonUnited Kingdom
| | - James E. Rothman
- Department of Clinical and Experimental EpilepsyUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
- Department of Cell BiologyYale School of MedicineNew HavenCT
| | - Kym M. Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of OttawaOttawaOntarioCanada
| | - Philippa B. Mills
- Genetics and Genomic MedicineUniversity College London Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Peter T. Clayton
- Genetics and Genomic MedicineUniversity College London Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Henry Houlden
- Department of Neuromuscular DiseasesUniversity College London Queen Square Institute of NeurologyLondonUnited Kingdom
- Neurogenetics LaboratoryNational Hospital for Neurology and NeurosurgeryLondonUnited Kingdom
| |
Collapse
|
68
|
Almutawa W, Smith C, Sabouny R, Smit RB, Zhao T, Wong R, Lee-Glover L, Desrochers-Goyette J, Ilamathi HS, Suchowersky O, Germain M, Mains PE, Parboosingh JS, Pfeffer G, Innes AM, Shutt TE. The R941L mutation in MYH14 disrupts mitochondrial fission and associates with peripheral neuropathy. EBioMedicine 2019; 45:379-392. [PMID: 31231018 PMCID: PMC6642256 DOI: 10.1016/j.ebiom.2019.06.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 11/25/2022] Open
Abstract
Background Peripheral neuropathies are often caused by disruption of genes responsible for myelination or axonal transport. In particular, impairment in mitochondrial fission and fusion are known causes of peripheral neuropathies. However, the causal mechanisms for peripheral neuropathy gene mutations are not always known. While loss of function mutations in MYH14 typically cause non-syndromic hearing loss, the recently described R941L mutation in MYH14, encoding the non-muscle myosin protein isoform NMIIC, leads to a complex clinical presentation with an unexplained peripheral neuropathy phenotype. Methods Confocal microscopy was used to examine mitochondrial dynamics in MYH14 patient fibroblast cells, as well as U2OS and M17 cells overexpressing NMIIC. The consequence of the R941L mutation on myosin activity was modeled in C. elegans. Findings We describe the third family carrying the R941L mutation in MYH14, and demonstrate that the R941L mutation impairs non-muscle myosin protein function. To better understand the molecular basis of the peripheral neuropathy phenotype associated with the R941L mutation, which has been hindered by the fact that NMIIC is largely uncharacterized, we have established a previously unrecognized biological role for NMIIC in mediating mitochondrial fission in human cells. Notably, the R941L mutation acts in a dominant-negative fashion to inhibit mitochondrial fission, especially in the cell periphery. In addition, we observed alterations to the organization of the mitochondrial genome. Interpretation As impairments in mitochondrial fission cause peripheral neuropathy, this insight into the function of NMIIC likely explains the peripheral neuropathy phenotype associated with the R941L mutation. Fund This study was supported by the Alberta Children's Hospital Research Institute, the Canadian Institutes of Health Research and the Care4Rare Canada Consortium.
Collapse
Affiliation(s)
- Walaa Almutawa
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Christopher Smith
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rasha Sabouny
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ryan B Smit
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Tian Zhao
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rachel Wong
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Laurie Lee-Glover
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Justine Desrochers-Goyette
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada; Centre de Recherche Biomed, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Hema Saranya Ilamathi
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada; Centre de Recherche Biomed, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Oksana Suchowersky
- Departments of Medicine (Neurology), Medical Genetics and Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Marc Germain
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada; Centre de Recherche Biomed, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Paul E Mains
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jillian S Parboosingh
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Gerald Pfeffer
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Timothy E Shutt
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
69
|
Brodehl A, Rezazadeh S, Williams T, Munsie NM, Liedtke D, Oh T, Ferrier R, Shen Y, Jones SJM, Stiegler AL, Boggon TJ, Duff HJ, Friedman JM, Gibson WT, Childs SJ, Gerull B. Mutations in ILK, encoding integrin-linked kinase, are associated with arrhythmogenic cardiomyopathy. Transl Res 2019; 208:15-29. [PMID: 30802431 PMCID: PMC7412573 DOI: 10.1016/j.trsl.2019.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/17/2019] [Accepted: 02/12/2019] [Indexed: 12/11/2022]
Abstract
Arrhythmogenic cardiomyopathy is a genetic heart muscle disorder characterized by fibro-fatty replacement of cardiomyocytes leading to life-threatening ventricular arrhythmias, heart failure, and sudden cardiac death. Mutations in genes encoding cardiac junctional proteins are known to cause about half of cases, while remaining genetic causes are unknown. Using exome sequencing, we identified 2 missense variants (p.H33N and p.H77Y) that were predicted to be damaging in the integrin-linked kinase (ILK) gene in 2 unrelated families. The p.H33N variant was found to be de novo. ILK links integrins and the actin cytoskeleton, and is essential for the maintenance of normal cardiac function. Both of the new variants are located in the ILK ankyrin repeat domain, which binds to the first LIM domain of the adaptor proteins PINCH1 and PINCH2. In silico binding studies proposed that the human variants disrupt the ILK-PINCH complex. Recombinant mutant ILK expressed in H9c2 rat myoblast cells shows aberrant prominent cytoplasmic localization compared to the wild-type. Expression of human wild-type and mutant ILK under the control of the cardiac-specific cmlc2 promotor in zebrafish shows that p.H77Y and p.P70L, a variant previously reported in a dilated cardiomyopathy family, cause cardiac dysfunction and death by about 2-3 weeks of age. Our findings provide genetic and functional evidence that ILK is a cardiomyopathy disease gene and highlight its relevance for diagnosis and genetic counseling of inherited cardiomyopathies.
Collapse
Affiliation(s)
- Andreas Brodehl
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Saman Rezazadeh
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Tatjana Williams
- Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Nicole M Munsie
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Daniel Liedtke
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Tracey Oh
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Raechel Ferrier
- Department of Medical Genetics, Alberta Health Services, Calgary, Alberta, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Amy L Stiegler
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Henry J Duff
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | | | - Sarah J Childs
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Brenda Gerull
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada; Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany.
| |
Collapse
|
70
|
Simons C, Dyment D, Bent SJ, Crawford J, D'Hooghe M, Kohlschütter A, Venkateswaran S, Helman G, Poll-The BT, Makowski CC, Ito Y, Kernohan K, Hartley T, Waisfisz Q, Taft RJ, van der Knaap MS, Wolf NI. A recurrent de novo mutation in TMEM106B causes hypomyelinating leukodystrophy. Brain 2019; 140:3105-3111. [PMID: 29186371 DOI: 10.1093/brain/awx314] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/05/2017] [Indexed: 12/28/2022] Open
Abstract
Hypomyelinating leukodystrophies are a heterogeneous group of disorders with a clinical presentation that often includes early-onset nystagmus, ataxia and spasticity and a wide range of severity. Using next-generation sequencing techniques and GeneMatcher, we identified four unrelated patients with brain hypomyelination, all with the same recurrent dominant mutation, c.754G>A p.(Asp252Asn), in TMEM106B. The mutation was confirmed as de novo in three of the cases, and the mildly affected father of the fourth affected individual was confirmed as mosaic for this variant. The protein encoded by TMEM106B is poorly characterized but is reported to have a role in regulation of lysosomal trafficking. Polymorphisms in TMEM106B are thought to modify disease onset in frontotemporal dementia, but its relation to myelination is not understood. Clinical presentation in three of the four patients is remarkably benign compared to other hypomyelinating disorders, with congenital nystagmus and mild motor delay. These findings add TMEM106B to the growing list of genes causing hypomyelinating disorders and emphasize the essential role lysosomes play in myelination.
Collapse
Affiliation(s)
- Cas Simons
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Stephen J Bent
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Marc D'Hooghe
- Department of Neurology, General Hospital Sint-Jan, Brugge, Belgium
| | - Alfried Kohlschütter
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Sunita Venkateswaran
- Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Guy Helman
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Bwee-Tien Poll-The
- Department of Child Neurology, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Quinten Waisfisz
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Ryan J Taft
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia.,Illumina Inc, San Diego, California, USA
| | | | - Marjo S van der Knaap
- Department of Child Neurology, VU University Medical Center, and Amsterdam Neuroscience, Amsterdam, The Netherlands.,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Nicole I Wolf
- Department of Child Neurology, VU University Medical Center, and Amsterdam Neuroscience, Amsterdam, The Netherlands
| |
Collapse
|
71
|
Kernohan KD, Hartley T, Naumenko S, Armour CM, Graham GE, Nikkel SM, Lines M, Geraghty MT, Richer J, Mears W, Boycott KM, Dyment DA. Diagnostic clarity of exome sequencing following negative comprehensive panel testing in the neonatal intensive care unit. Am J Med Genet A 2019; 176:1688-1691. [PMID: 30160830 DOI: 10.1002/ajmg.a.38838] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Sergey Naumenko
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christine M Armour
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gail E Graham
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - Sarah M Nikkel
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew Lines
- Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael T Geraghty
- Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - Julie Richer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - Wendy Mears
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
72
|
Pál E, Zima J, Hadzsiev K, Ito YA, Hartley T, Boycott KM, Melegh B. A novel pathogenic variant in TNPO3 in a Hungarian family with limb-girdle muscular dystrophy 1F. Eur J Med Genet 2019; 62:103662. [PMID: 31071488 DOI: 10.1016/j.ejmg.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 04/30/2019] [Accepted: 05/04/2019] [Indexed: 12/20/2022]
Abstract
Limb-girdle muscular dystrophies (LGMDs) are a group of genetically heterogeneous muscular diseases that predominantly affect the proximal muscles. Pathogenic variants in TNPO3 have been associated with a rare, autosomal dominant limb-girdle muscular dystrophy 1F (LGMD1F) in a large Italian-Spanish family and an isolated LGMD1F case. Here we present two individuals from a Hungarian family with an early-onset, slowly progressive muscular dystrophy. Both the female proband and her affected son had delayed early motor milestones including first walking at 14 months and 18 months, respectively. Both present with progressive weakness of facial, bulbar, axial, and distal muscles especially of the lower extremities. Electromyography indicated myogenic damage and muscle biopsy from the proband showed myopathic alterations with sarcoplasmic masses and signs of mitochondrial dysfunction. Exome sequencing of the female proband identified a novel c.2767delC p.(Arg923AspfsTer17) variant in TNPO3. Sanger sequencing confirmed the presence of the TNPO3 variant in the affected son; the unaffected son did not have the variant. The identification of the c.2767delC variant further supports the clinical significance of TNPO3 and expands the clinical spectrum of TNPO3-associated LGMD1F.
Collapse
Affiliation(s)
- Endre Pál
- Department of Neurology, University of Pécs, Medical School, Pécs, Hungary; Neuropathology Unit, Department of Pathology, University of Pécs, Medical School, Pécs, Hungary.
| | - Judith Zima
- Department of Medical Genetics, University of Pécs, Medical School, Pécs, Hungary; Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Kinga Hadzsiev
- Department of Medical Genetics, University of Pécs, Medical School, Pécs, Hungary; Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Yoko A Ito
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Canada
| | -
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Canada
| | - Béla Melegh
- Department of Medical Genetics, University of Pécs, Medical School, Pécs, Hungary; Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| |
Collapse
|
73
|
Intrafamilial variability of limb-girdle muscular dystrophy, LGMD1D type. Eur J Med Genet 2019; 63:103655. [PMID: 31034989 DOI: 10.1016/j.ejmg.2019.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 04/12/2019] [Accepted: 04/21/2019] [Indexed: 12/20/2022]
Abstract
LGMD1D is an autosomal dominant limb girdle muscular dystrophy caused by variants in the DNAJB6 gene. This is typically an adult-onset disorder characterized by moderately progressive proximal muscle weakness without respiratory or bulbar involvement; however phenotypic variability is often observed with some individuals having earlier onset and more severe symptoms. Here, we present a family with a novel NM_005494.2:c.271T > G p.(Phe91Val) variant in DNAJB6 with a late-onset, mild and slowly progressive form of the disease, including one individual, who in her 7th decade of life has subclinical LGMD1D with only mild features on muscle biopsy and MRI. Unlike previously reported cases where missense variants affecting the Phe91 amino acid residue are associated with a more severe form of the disease, this family represents the mild end of the LGMD1D clinical spectrum. Therefore, this family adds further complexity to the genotype-phenotype correlation in DNAJB6-associated muscular dystrophies.
Collapse
|
74
|
Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, Witmer PD, Boehm C, Sutton VR, Muzny DM, Boerwinkle E, Günel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR. Insights into genetics, human biology and disease gleaned from family based genomic studies. Genet Med 2019; 21:798-812. [PMID: 30655598 PMCID: PMC6691975 DOI: 10.1038/s41436-018-0408-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Identifying genes and variants contributing to rare disease phenotypes and Mendelian conditions informs biology and medicine, yet potential phenotypic consequences for variation of >75% of the ~20,000 annotated genes in the human genome are lacking. Technical advances to assess rare variation genome-wide, particularly exome sequencing (ES), enabled establishment in the United States of the National Institutes of Health (NIH)-supported Centers for Mendelian Genomics (CMGs) and have facilitated collaborative studies resulting in novel "disease gene" discoveries. Pedigree-based genomic studies and rare variant analyses in families with suspected Mendelian conditions have led to the elucidation of hundreds of novel disease genes and highlighted the impact of de novo mutational events, somatic variation underlying nononcologic traits, incompletely penetrant alleles, phenotypes with high locus heterogeneity, and multilocus pathogenic variation. Herein, we highlight CMG collaborative discoveries that have contributed to understanding both rare and common diseases and discuss opportunities for future discovery in single-locus Mendelian disorder genomics. Phenotypic annotation of all human genes; development of bioinformatic tools and analytic methods; exploration of non-Mendelian modes of inheritance including reduced penetrance, multilocus variation, and oligogenic inheritance; construction of allelic series at a locus; enhanced data sharing worldwide; and integration with clinical genomics are explored. Realizing the full contribution of rare disease research to functional annotation of the human genome, and further illuminating human biology and health, will lay the foundation for the Precision Medicine Initiative.
Collapse
Affiliation(s)
- Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Department of Statistics, Rutgers University, Piscataway, NJ, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sushant Kumar
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Dimitri Avramopoulos
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kimberly F Doheny
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Corinne Boehm
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Shrikant Mane
- Yale Center for Genome Analysis, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Richard P Lifton
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
75
|
Yip S, Christofides A, Banerji S, Downes MR, Izevbaye I, Lo B, MacMillan A, McCuaig J, Stockley T, Yousef GM, Spatz A. A Canadian guideline on the use of next-generation sequencing in oncology. Curr Oncol 2019; 26:e241-e254. [PMID: 31043833 PMCID: PMC6476432 DOI: 10.3747/co.26.4731] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rapid advancements in next-generation sequencing (ngs) technology have created an unprecedented opportunity to decipher the molecular profile of tumours to more effectively prevent, diagnose, and treat cancer. Oncologists now have the option to order molecular tests that can guide treatment decisions. However, to date, most oncologists have received limited training in genomics, and they are now faced with the challenge of understanding how such tests and their interpretation align with patient management. Guidance on how to effectively use ngs technology is therefore needed to aid oncologists in applying the results of genomic tests. The Canadian guideline presented here describes best practices and unmet needs related to ngs-based testing for somatic variants in oncology, including clinical application, assay and sample selection, bioinformatics and interpretation of reports performed by laboratories, patient communication, and clinical trials.
Collapse
Affiliation(s)
- S Yip
- Cancer Genetics and Genomics Lab, BC Cancer, Vancouver, BC
| | | | - S Banerji
- Department of Medical Oncology, CancerCare Manitoba, Winnipeg, MB
| | - M R Downes
- Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON
| | - I Izevbaye
- Division of Molecular Pathology, Laboratory Medicine and Pathology, University of Alberta Hospital, Edmonton, AB
| | - B Lo
- Molecular Diagnostics, The Ottawa Hospital, Ottawa, ON
| | - A MacMillan
- Provincial Medical Genetics Program, St. John's, NL
| | - J McCuaig
- Princess Margaret Cancer Centre, Toronto, ON
| | - T Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto and University Health Network, Toronto, ON
| | - G M Yousef
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON
| | - A Spatz
- Departments of Pathology and Oncology, McGill University, McGill University Health Centre and Lady Davis Institute, Montreal, QC
| |
Collapse
|
76
|
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.
Collapse
|
77
|
Carter MT, Venkateswaran S, Shapira-Zaltsberg G, Davila J, Humphreys P, Kernohan KD, Boycott KM. Clinical delineation of GTPBP2-associated neuro-ectodermal syndrome: Report of two new families and review of the literature. Clin Genet 2019; 95:601-606. [PMID: 30790272 DOI: 10.1111/cge.13523] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/30/2019] [Accepted: 02/11/2019] [Indexed: 12/01/2022]
Abstract
The GTPBP2 gene encodes a guanosine triphosphate (GTP)-binding protein of unknown function. Biallelic loss-of-function variants in the GTPBP2 gene have been previously reported in association with a neuro-ectodermal clinical presentation in six individuals from four unrelated families. Here, we provide detailed descriptions of three additional individuals from two unrelated families in the context of the previous literature. Both families carry nonsense variants in GTPBP2: homozygous p.(Arg470*) and compound heterozygous p.(Arg432*)/p.(Arg131*). Key features of this clinically recognizable condition include prenatal onset microcephaly, tone abnormalities, and movement disorders, epilepsy, dysmorphic features, retinal dysfunction, ectodermal dysplasia, and brain iron accumulation. Our findings suggest that some aspects of the clinical presentation appear to be age-related; brain iron accumulation may appear only after childhood, and the ectodermal findings and peripheral neuropathy are most prominent in older individuals. In addition, we present prenatal and neonatal findings as well as the first Caucasian and black African families with GTPBP2 biallelic variants. The individuals described herein provide valuable additional phenotypic information about this rare, novel, and progressive neuroectodermal condition.
Collapse
Affiliation(s)
- Melissa T Carter
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Sunita Venkateswaran
- Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Gali Shapira-Zaltsberg
- Department of Medical Imaging, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Jorge Davila
- Department of Medical Imaging, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Peter Humphreys
- Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
78
|
Zhao T, Goedhart CM, Sam PN, Sabouny R, Lingrell S, Cornish AJ, Lamont RE, Bernier FP, Sinasac D, Parboosingh JS, Vance JE, Claypool SM, Innes AM, Shutt TE. PISD is a mitochondrial disease gene causing skeletal dysplasia, cataracts, and white matter changes. Life Sci Alliance 2019; 2:2/2/e201900353. [PMID: 30858161 PMCID: PMC6412922 DOI: 10.26508/lsa.201900353] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/18/2022] Open
Abstract
This work demonstrates that pathogenic variants in PISD cause mitochondrial disease and suggests a novel mechanistic link whereby impaired lipid content in the inner mitochondrial membrane alters the activity of inner mitochondrial membrane proteases. Exome sequencing of two sisters with congenital cataracts, short stature, and white matter changes identified compound heterozygous variants in the PISD gene, encoding the phosphatidylserine decarboxylase enzyme that converts phosphatidylserine to phosphatidylethanolamine (PE) in the inner mitochondrial membrane (IMM). Decreased conversion of phosphatidylserine to PE in patient fibroblasts is consistent with impaired phosphatidylserine decarboxylase (PISD) enzyme activity. Meanwhile, as evidence for mitochondrial dysfunction, patient fibroblasts exhibited more fragmented mitochondrial networks, enlarged lysosomes, decreased maximal oxygen consumption rates, and increased sensitivity to 2-deoxyglucose. Moreover, treatment with lyso-PE, which can replenish the mitochondrial pool of PE, and genetic complementation restored mitochondrial and lysosome morphology in patient fibroblasts. Functional characterization of the PISD variants demonstrates that the maternal variant causes an alternative splice product. Meanwhile, the paternal variant impairs autocatalytic self-processing of the PISD protein required for its activity. Finally, evidence for impaired activity of mitochondrial IMM proteases suggests an explanation as to why the phenotypes of these PISD patients resemble recently described “mitochondrial chaperonopathies.” Collectively, these findings demonstrate that PISD is a novel mitochondrial disease gene.
Collapse
Affiliation(s)
- Tian Zhao
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Caitlin M Goedhart
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Pingdewinde N Sam
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rasha Sabouny
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Susanne Lingrell
- Department of Medicine and Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, Alberta, Canada
| | - Adam J Cornish
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan E Lamont
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Francois P Bernier
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - David Sinasac
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jillian S Parboosingh
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Jean E Vance
- Department of Medicine and Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, Alberta, Canada
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada .,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Timothy E Shutt
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada .,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
79
|
Harries LW. RNA Biology Provides New Therapeutic Targets for Human Disease. Front Genet 2019; 10:205. [PMID: 30906315 PMCID: PMC6418379 DOI: 10.3389/fgene.2019.00205] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/26/2019] [Indexed: 12/11/2022] Open
Abstract
RNA is the messenger molecule that conveys information from the genome and allows the production of biomolecules required for life in a responsive and regulated way. Most genes are able to produce multiple mRNA products in response to different internal or external environmental signals, in different tissues and organs, and at specific times in development or later life. This fine tuning of gene expression is dependent on the coordinated effects of a large and intricate set of regulatory machinery, which together orchestrate the genomic output at each locus and ensure that each gene is expressed at the right amount, at the right time and in the correct location. This complexity of control, and the requirement for both sequence elements and the entities that bind them, results in multiple points at which errors may occur. Errors of RNA biology are common and found in association with both rare, single gene disorders, but also more common, chronic diseases. Fortunately, complexity also brings opportunity. The existence of many regulatory steps also offers multiple levels of potential therapeutic intervention which can be exploited. In this review, I will outline the specific points at which coding RNAs may be regulated, indicate potential means of intervention at each stage, and outline with examples some of the progress that has been made in this area. Finally, I will outline some of the remaining challenges with the delivery of RNA-based therapeutics but indicate why there are reasons for optimism.
Collapse
Affiliation(s)
- Lorna W. Harries
- RNA-Mediated Mechanisms of Disease, College of Medicine and Health, The Institute of Biomedical and Clinical Science, Medical School, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
80
|
McNiven V, Ito YA, Hartley T, Kernohan K, Miller E, Armour CM. NID1 variant associated with occipital cephaloceles in a family expressing a spectrum of phenotypes. Am J Med Genet A 2019; 179:837-841. [PMID: 30773799 DOI: 10.1002/ajmg.a.61095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Autosomal dominant Dandy-Walker malformation and occipital cephalocele (ADDWOC) is a rare, congenital, and incompletely penetrant malformation that is considered to be part of the Dandy-Walker spectrum of disorders. Affected individuals often present with an occipital cephalocele with a bony skull defect, but typically have normal neurological development. Here, we report on a three-generation family in which individuals have variable phenotypes that are consistent with the ADDWOC spectrum: arachnoid cysts in the proband and his maternal grandfather, an occipital cephalocele in the proband and his brother, and a small bony defect in the proband's mother. Whole exome sequencing identified a rare heterozygous variant in NID1 (NM_002508.2:c.1162C>T, (p.Gln388Ter)) in the proband, his brother, and his mother. Sanger sequencing confirmed the presence of this variant in the maternal grandfather. The identical c.1162C>T variant was previously identified in variably affected members of a three-generation family with ADDWOC. This case report provides further evidence that variants in NID1 may be clinically relevant for the development of a phenotype that is consistent with ADDWOC, and extends the phenotype of NID1-associated ADDWOC to include arachnoid cysts. Given that the Dandy-Walker malformation itself is not a pre-requisite to this spectrum of phenotypes, we also suggest a novel term for the NID1-associated disorder in order to give emphasis to this phenotypic variability: "Autosomal Dominant Posterior Fossa Anomalies with Occipital Cephaloceles."
Collapse
Affiliation(s)
- Vanda McNiven
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yoko A Ito
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Elka Miller
- Department of Medical Imaging, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Christine M Armour
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Regional Genetics Unit, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| |
Collapse
|
81
|
Accogli A, Guerrero K, D'Agostino MD, Tran L, Cieuta-Walti C, Thiffault I, Chénier S, Schwartzentruber J, Majewski J, Bernard G. Biallelic Loss-of-Function Variants in AIMP1 Cause a Rare Neurodegenerative Disease. J Child Neurol 2019; 34:74-80. [PMID: 30486714 DOI: 10.1177/0883073818811223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
AIMP1/p43, is a noncatalytic component of the mammalian multi-tRNA synthetase complex that catalyzes the ligation of amino acids to their cognate tRNAs. AIMP1 is largely expressed in the central nervous system, where it is part of the regulatory machine of the neurofilament assembly, playing a crucial role in neuronal development and function. To date, nonsense mutations in AIMP1 have been associated with a primary neurodegenerative disorder consisting of cerebral atrophy, hypomyelination, microcephaly and epilepsy, whereas missense mutations have recently been linked to intellectual disability without neurodegeneration. Here, we report the first French-Canadian patient with a novel frameshift AIMP1 homozygous mutation (c.191_192delAA, p.Gln64Argfs*25), resulting in a severe neurodegenerative phenotype. We review and discuss the phenotypic spectrum associated with AIMP1 pathogenic variants.
Collapse
Affiliation(s)
- Andrea Accogli
- 1 Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, Canada.,2 UOC Neurochirurgia, Istituto Giannina Gaslini, Genova, Italy.,3 Università degli Studi di Genova, Genoa, Italy
| | - Kether Guerrero
- 1 Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, Canada.,4 Department of Internal Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, Canada.,5 Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Maria Daniela D'Agostino
- 4 Department of Internal Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, Canada.,6 Department of Human Genetics, McGill University, Montreal, Canada
| | - Luan Tran
- 1 Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, Canada.,4 Department of Internal Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, Canada.,5 Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Cécile Cieuta-Walti
- 7 Service de Neuropédiatre, Université de Sherbrooke, Quebec, Canada.,8 Institut Lejeune, Paris, France
| | - Isabelle Thiffault
- 9 Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,10 University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Sébastien Chénier
- 11 Department of Pediatrics, Division of Medical Genetics, Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada
| | | | - Jacek Majewski
- 6 Department of Human Genetics, McGill University, Montreal, Canada
| | | | - Geneviève Bernard
- 1 Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, Canada.,4 Department of Internal Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, Canada.,5 Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Canada
| |
Collapse
|
82
|
Gennarino VA, Palmer EE, McDonell LM, Wang L, Adamski CJ, Koire A, See L, Chen CA, Schaaf CP, Rosenfeld JA, Panzer JA, Moog U, Hao S, Bye A, Kirk EP, Stankiewicz P, Breman AM, McBride A, Kandula T, Dubbs HA, Macintosh R, Cardamone M, Zhu Y, Ying K, Dias KR, Cho MT, Henderson LB, Baskin B, Morris P, Tao J, Cowley MJ, Dinger ME, Roscioli T, Caluseriu O, Suchowersky O, Sachdev RK, Lichtarge O, Tang J, Boycott KM, Holder JL, Zoghbi HY. A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures. Cell 2019; 172:924-936.e11. [PMID: 29474920 DOI: 10.1016/j.cell.2018.02.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/23/2017] [Accepted: 02/01/2018] [Indexed: 02/06/2023]
Abstract
Certain mutations can cause proteins to accumulate in neurons, leading to neurodegeneration. We recently showed, however, that upregulation of a wild-type protein, Ataxin1, caused by haploinsufficiency of its repressor, the RNA-binding protein Pumilio1 (PUM1), also causes neurodegeneration in mice. We therefore searched for human patients with PUM1 mutations. We identified eleven individuals with either PUM1 deletions or de novo missense variants who suffer a developmental syndrome (Pumilio1-associated developmental disability, ataxia, and seizure; PADDAS). We also identified a milder missense mutation in a family with adult-onset ataxia with incomplete penetrance (Pumilio1-related cerebellar ataxia, PRCA). Studies in patient-derived cells revealed that the missense mutations reduced PUM1 protein levels by ∼25% in the adult-onset cases and by ∼50% in the infantile-onset cases; levels of known PUM1 targets increased accordingly. Changes in protein levels thus track with phenotypic severity, and identifying posttranscriptional modulators of protein expression should identify new candidate disease genes.
Collapse
Affiliation(s)
- Vincenzo A Gennarino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
| | - Elizabeth E Palmer
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia; Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Laura M McDonell
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Li Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Carolyn J Adamski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda Koire
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lauren See
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jessica A Panzer
- Department of Pediatrics, Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany
| | - Shuang Hao
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ann Bye
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Edwin P Kirk
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia; Genetics Laboratory, NSW Health Pathology East Randwick, Sydney, NSW, Australia
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arran McBride
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Tejaswi Kandula
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Michael Cardamone
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Ying Zhu
- Genetics Laboratory, NSW Health Pathology East Randwick, Sydney, NSW, Australia
| | - Kevin Ying
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Kerith-Rae Dias
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Megan T Cho
- GeneDx, 207 Perry Pkwy Gaithersburg, MD 20877, USA
| | | | | | - Paula Morris
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Jiang Tao
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Tony Roscioli
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; Genetics Laboratory, NSW Health Pathology East Randwick, Sydney, NSW, Australia; Neuroscience Research Australia and Prince of Wales Clinical School, University of New South Wales, Randwick, NSW 2031, Australia
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, AB T6G 2H7, Canada
| | - Oksana Suchowersky
- Department of Medical Genetics, University of Alberta, AB T6G 2H7, Canada; Departments of Medicine (Neurology) and Pediatrics, University of Alberta, AB, Canada
| | - Rani K Sachdev
- Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, NSW 2031, Australia
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianrong Tang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - J Lloyd Holder
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
83
|
Adachi T, Imanishi N, Ogawa Y, Furusawa Y, Izumida Y, Izumi Y, Suematsu M. Survey on patients with undiagnosed diseases in Japan: potential patient numbers benefiting from Japan's initiative on rare and undiagnosed diseases (IRUD). Orphanet J Rare Dis 2018; 13:208. [PMID: 30458817 PMCID: PMC6245805 DOI: 10.1186/s13023-018-0943-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 10/24/2018] [Indexed: 12/31/2022] Open
Abstract
Background There is now an international partnership to establish global programs for patients with rare and undiagnosed diseases, involving interdisciplinary expert panels and phenotype-driven genetic analyses utilizing next-generation sequencing and analytics. Whereas it is crucial to have data such as the actual number of undiagnosed patients, to help inform the implementation plan with such programs, there have been no systematic studies to quantitate the numbers of patients principally because of the inherent difficulty in most health systems to identify patients whose condition has not yet been diagnosed and coded. Our national experience with a rare disease program, Nan-Byo which was established in 1972, and the more recently expanded Initiative on Rare and Undiagnosed Diseases (IRUD), provided a unique opportunity to design a cross-sectional study to ascertain the undiagnosed patients in Japan based on the IRUD referral criteria. Results Two rounds of online surveys were performed: one survey targeting physicians affiliated with general hospitals (GH) and family clinics (FC) (the response rate: 30.6% (242/792)) and one nationwide survey targeting university hospitals (UH) in Japan (47.1% (839/1781)). A high percentage of doctors needing IRUD was seen in pediatrics at GH, FC, while there was a clear demand for IRUD in most departments at UH. We calculated the number of undiagnosed patients in Japan, as the “percentage of doctors needing IRUD” × “number of patients who would be referred to IRUD per doctor needing IRUD (cases/person)” × “total number of doctors in the relevant facilities in Japan (persons)”, resulting in 3681 cases in pediatrics/pediatric surgery and 33,703 cases in other departments, for a total of 37,384 cases. Conclusions Our study revealed the extant demand for IRUD in most departments and 37,000+ potential patients with undiagnosed diseases in the Japanese health system. These data inform the establishment of an equitable, sustainable, efficient and effective outpatient-based IRUD. These findings would serve as a valuable reference for undiagnosed diseases programs in different international jurisdictions and for countries and regions who also share vision(s) for societal implementation that help to advance international efforts to support patients with rare diseases who are direly waiting for diagnosis, subsequent treatment and care.
Collapse
Affiliation(s)
- Takeya Adachi
- Japan Agency for Medical Research and Development (AMED), 22F Yomiuri Shimbun Bldg., 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.
| | - Noriaki Imanishi
- Japan Agency for Medical Research and Development (AMED), 22F Yomiuri Shimbun Bldg., 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yasushi Ogawa
- Japan Agency for Medical Research and Development (AMED), 22F Yomiuri Shimbun Bldg., 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yoshihiko Furusawa
- Japan Agency for Medical Research and Development (AMED), 22F Yomiuri Shimbun Bldg., 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yoshihiko Izumida
- Japan Agency for Medical Research and Development (AMED), 22F Yomiuri Shimbun Bldg., 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yoko Izumi
- Japan Agency for Medical Research and Development (AMED), 22F Yomiuri Shimbun Bldg., 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Makoto Suematsu
- Japan Agency for Medical Research and Development (AMED), 22F Yomiuri Shimbun Bldg., 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| |
Collapse
|
84
|
Osinalde N, Duarri A, Ramirez J, Barrio R, Perez de Nanclares G, Mayor U. Impaired proteostasis in rare neurological diseases. Semin Cell Dev Biol 2018; 93:164-177. [PMID: 30355526 DOI: 10.1016/j.semcdb.2018.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/09/2018] [Accepted: 10/16/2018] [Indexed: 12/19/2022]
Abstract
Rare diseases are classified as such when their prevalence is 1:2000 or lower, but even if each of them is so infrequent, altogether more than 300 million people in the world suffer one of the ∼7000 diseases considered as rare. Over 1200 of these disorders are known to affect the brain or other parts of our nervous system, and their symptoms can affect cognition, motor function and/or social interaction of the patients; we refer collectively to them as rare neurological disorders or RNDs. We have focused this review on RNDs known to have compromised protein homeostasis pathways. Proteostasis can be regulated and/or altered by a chain of cellular mechanisms, from protein synthesis and folding, to aggregation and degradation. Overall, we provide a list comprised of above 215 genes responsible for causing more than 170 distinct RNDs, deepening on some representative diseases, including as well a clinical view of how those diseases are diagnosed and dealt with. Additionally, we review existing methodologies for diagnosis and treatment, discussing the potential of specific deubiquitinating enzyme inhibition as a future therapeutic avenue for RNDs.
Collapse
Affiliation(s)
- Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Anna Duarri
- Barcelona Stem Cell Bank, Center of Regenerative Medicine in Barcelona, 08908 Hospitalet de Llobregat, Barcelona, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Rosa Barrio
- Functional Genomics Unit, CIC bioGUNE, 48160 Derio, Spain
| | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetics Laboratory, BioAraba National Health Institute, Hospital Universitario Araba-Txagorritxu, Vitoria-Gasteiz, Alava, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
| |
Collapse
|
85
|
Bonnefoy S, Watson CM, Kernohan KD, Lemos M, Hutchinson S, Poulter JA, Crinnion LA, Berry I, Simmonds J, Vasudevan P, O'Callaghan C, Hirst RA, Rutman A, Huang L, Hartley T, Grynspan D, Moya E, Li C, Carr IM, Bonthron DT, Leroux M, Boycott KM, Bastin P, Sheridan EG. Biallelic Mutations in LRRC56, Encoding a Protein Associated with Intraflagellar Transport, Cause Mucociliary Clearance and Laterality Defects. Am J Hum Genet 2018; 103:727-739. [PMID: 30388400 PMCID: PMC6218757 DOI: 10.1016/j.ajhg.2018.10.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023] Open
Abstract
Primary defects in motile cilia result in dysfunction of the apparatus responsible for generating fluid flows. Defects in these mechanisms underlie disorders characterized by poor mucus clearance, resulting in susceptibility to chronic recurrent respiratory infections, often associated with infertility; laterality defects occur in about 50% of such individuals. Here we report biallelic variants in LRRC56 (known as oda8 in Chlamydomonas) identified in three unrelated families. The phenotype comprises laterality defects and chronic pulmonary infections. High-speed video microscopy of cultured epithelial cells from an affected individual showed severely dyskinetic cilia but no obvious ultra-structural abnormalities on routine transmission electron microscopy (TEM). Further investigation revealed that LRRC56 interacts with the intraflagellar transport (IFT) protein IFT88. The link with IFT was interrogated in Trypanosoma brucei. In this protist, LRRC56 is recruited to the cilium during axoneme construction, where it co-localizes with IFT trains and is required for the addition of dynein arms to the distal end of the flagellum. In T. brucei carrying LRRC56-null mutations, or a variant resulting in the p.Leu259Pro substitution corresponding to the p.Leu140Pro variant seen in one of the affected families, we observed abnormal ciliary beat patterns and an absence of outer dynein arms restricted to the distal portion of the axoneme. Together, our findings confirm that deleterious variants in LRRC56 result in a human disease and suggest that this protein has a likely role in dynein transport during cilia assembly that is evolutionarily important for cilia motility.
Collapse
Affiliation(s)
- Serge Bonnefoy
- Trypanosome Cell Biology Unit & INSERM U1201, Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France
| | - Christopher M Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK; School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Moara Lemos
- Trypanosome Cell Biology Unit & INSERM U1201, Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France
| | - Sebastian Hutchinson
- Trypanosome Cell Biology Unit & INSERM U1201, Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France
| | - James A Poulter
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Laura A Crinnion
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK; School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Ian Berry
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Jennifer Simmonds
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Pradeep Vasudevan
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester LE2 7LX, UK
| | - Chris O'Callaghan
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester LE2 7LX, UK; Respiratory, Critical Care & Anaesthesia, Institute of Child Health, University College London & Great Ormond Street Children's Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Robert A Hirst
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester LE2 7LX, UK
| | - Andrew Rutman
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester LE2 7LX, UK
| | - Lijia Huang
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - David Grynspan
- Department of Pathology, Children's Hospital of Eastern Ontario, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
| | - Eduardo Moya
- Bradford Royal Infirmary, Bradford, West Yorkshire BD9 6R, UK
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Ian M Carr
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK
| | - David T Bonthron
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK; School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Michel Leroux
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Philippe Bastin
- Trypanosome Cell Biology Unit & INSERM U1201, Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France.
| | - Eamonn G Sheridan
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK; School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK.
| |
Collapse
|
86
|
Lin PC, Chiou SS, Lin CY, Wang SC, Huang HY, Chang YS, Tseng YH, Kan TM, Liao YM, Tsai SP, Peng CT, Chang JG. Whole-exome sequencing for the genetic diagnosis of congenital red blood cell membrane disorders in Taiwan. Clin Chim Acta 2018; 487:311-317. [PMID: 30317022 DOI: 10.1016/j.cca.2018.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/21/2018] [Accepted: 10/10/2018] [Indexed: 12/16/2022]
Abstract
PURPOSE Congenital hemolytic anemia caused by red blood cell (RBC) membrane defects is a heterogeneous group of disorders. The present study aimed to search the causative gene mutations in patients with RBC membrane disorders in Taiwan. MATERIALS AND METHODS Next-generation sequencing approach using whole-exome sequencing (WES) was performed. Sanger sequencing was performed for confirmation of variants detected in WES in patients and their family members. RESULTS Five causative variants, including two ANK1, two SPTA and one SPTB variants, were detected in four patients. All these variants, except one SPTA1 variant c.83G > A (p.R28H), are novel variants. Their pedigree analysis showed one de novo SPTA1 mutation c.83G > A (p.R28H) combined with αLELY, one de novo ANK1 mutation c.1034C > A (p.A345E), one autosomal dominant combined SPTA1 c.4604A > C (p.Q1535P) and SPTB c.6203 T > C (p.L2068P) mutations and one autosomal dominant ANK1 c.4462C > T (p.R1488X) mutation. CONCLUSIONS Our data demonstrated that WES is an efficient tool for determining genetic etiologies of RBC membrane disorders and can facilitate accurate diagnosis and genetic counseling. Additional studies should be conducted on larger cohorts to investigate the distribution of gene mutations in patients with RBC membrane disorders in Taiwan.
Collapse
Affiliation(s)
- Pei-Chin Lin
- Division of Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shyh-Shin Chiou
- Division of Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chien-Yu Lin
- Department of Laboratory Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Shu-Chen Wang
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hsi-Yuan Huang
- Department of Laboratory Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Ya-Sian Chang
- Department of Laboratory Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan
| | - Yu-Hsin Tseng
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Tzu-Min Kan
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yu-Mei Liao
- Division of Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shih-Pien Tsai
- Department of Nursing, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ching-Tien Peng
- Department of Pediatrics, China Medical University Children's Hospital, Taichung, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan.
| | - Jan-Gowth Chang
- Department of Laboratory Medicine, China Medical University Hospital, China Medical University, Taichung, Taiwan; Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan; Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan; Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan.
| |
Collapse
|
87
|
ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants. Am J Hum Genet 2018; 103:474-483. [PMID: 30220433 DOI: 10.1016/j.ajhg.2018.08.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/08/2018] [Indexed: 02/08/2023] Open
Abstract
Advances in high-throughput DNA sequencing have revolutionized the discovery of variants in the human genome; however, interpreting the phenotypic effects of those variants is still a challenge. While several computational approaches to predict variant impact are available, their accuracy is limited and further improvement is needed. Here, we introduce ClinPred, an efficient tool for identifying disease-relevant nonsynonymous variants. Our predictor incorporates two machine learning algorithms that use existing pathogenicity scores and, notably, benefits from inclusion of normal population allele frequency from the gnomAD database as an input feature. Another major strength of our approach is the use of ClinVar-a rapidly growing database that allows selection of confidently annotated disease-causing variants-as a training set. Compared to other methods, ClinPred showed superior accuracy for predicting pathogenicity, achieving the highest area under the curve (AUC) score and increasing both the specificity and sensitivity in different test datasets. It also obtained the best performance according to various other metrics. Moreover, ClinPred performance remained robust with respect to disease type (cancer or rare disease) and mechanism (gain or loss of function). Importantly, we observed that adding allele frequency as a predictive feature-as opposed to setting fixed allele frequency cutoffs-boosts the performance of prediction. We provide pre-computed ClinPred scores for all possible human missense variants in the exome to facilitate its use by the community.
Collapse
|
88
|
Is PNPT1
-related hearing loss ever non-syndromic? Whole exome sequencing of adult siblings expands the natural history of PNPT1
-related disorders. Am J Med Genet A 2018; 176:2487-2493. [DOI: 10.1002/ajmg.a.40516] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/27/2018] [Accepted: 07/27/2018] [Indexed: 11/07/2022]
|
89
|
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.
Collapse
|
90
|
Baumbusch J, Mayer S, Sloan-Yip I. Alone in a Crowd? Parents of Children with Rare Diseases' Experiences of Navigating the Healthcare System. J Genet Couns 2018; 28:10.1007/s10897-018-0294-9. [PMID: 30128673 DOI: 10.1007/s10897-018-0294-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/12/2018] [Indexed: 11/26/2022]
Abstract
A disorder is considered a rare disease if it affects 1 in 2000, hence, while independently unique, collectively, these conditions are quite common. Many rare diseases are diagnosed during childhood, and therefore parents become primary caregivers in addition to their parental role. Despite the prevalence of rare diseases among children, there has been little research focused on parents' experiences of navigating the healthcare system, a gap we begin to address in this study. Guided by an interpretive description methodology, participants were recruited through online listservs and posting flyers at a pediatric hospital in Western Canada. Sixteen parents (15 mothers and 1 father) participated in in-depth, semi-structured interviews between April 2013 and March 2014. Data were analyzed inductively, generating the main study themes. Findings illuminated the challenges parents' experienced on their child's diagnostic journey-from seeking, to receiving, to adjusting to the rare disease diagnosis. Following diagnosis, gaps, and barriers to services resulted in parents pursuing services that could support their child's unique care needs, which often resulted in out-of-pocket payments and changes to employment. Parents found peer support, both online and in person, to be an effective resource. This study illustrates the common challenges experienced by parents of children with rare diseases as they navigate the healthcare system. Parents' role as "expert caregiver" was rarely acknowledged by healthcare providers, pointing to the need to foster more egalitarian relationships. As well, parents were burdened with the additional role of care coordinator, a role that could be filled formally by a healthcare provider. Lastly, peer support was a key resource in terms of information and emotional support for parents who often begin their journey feeling isolated and alone. Policies and programs are needed that validate the invisible care work of parents and ensure adequate formal supports are in place to mitigate potential sources of inequity for these families. Furthermore, genetic counselors can play a key role in ensuring parents' informational needs are addressed at the time of diagnosis and in connecting families who share common experiences regardless of the rare disease diagnosis.
Collapse
Affiliation(s)
- Jennifer Baumbusch
- School of Nursing, University of British Columbia, T201 - 2211 Wesbrook Mall, Vancouver, BC, V6T 2B5, Canada.
| | - Samara Mayer
- School of Nursing, University of British Columbia, T201 - 2211 Wesbrook Mall, Vancouver, BC, V6T 2B5, Canada
| | - Isabel Sloan-Yip
- School of Nursing, University of British Columbia, T201 - 2211 Wesbrook Mall, Vancouver, BC, V6T 2B5, Canada
| |
Collapse
|
91
|
Adamson KI, Sheridan E, Grierson AJ. Use of zebrafish models to investigate rare human disease. J Med Genet 2018; 55:641-649. [PMID: 30065072 DOI: 10.1136/jmedgenet-2018-105358] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 01/07/2023]
Abstract
Rare diseases are collectively common and often extremely debilitating. Following the emergence of next-generation sequencing (NGS) technologies, the variants underpinning rare genetic disorders are being unearthed at an accelerating rate. However, many rare conditions lack effective treatments due to their poorly understood pathophysiology. There is therefore a growing demand for the development of novel experimental models of rare genetic diseases, so that potentially causative variants can be validated, pathogenic mechanisms can be investigated and therapeutic targets can be identified. Animal models of rare diseases need to be genetically and physiologically similar to humans, and well-suited to large-scale experimental manipulation, considering the vast number of novel variants that are being identified through NGS. The zebrafish has emerged as a popular model system for investigating these variants, combining conserved vertebrate characteristics with a capacity for large-scale phenotypic and therapeutic screening. In this review, we aim to highlight the unique advantages of the zebrafish over other in vivo model systems for the large-scale study of rare genetic variants. We will also consider the generation of zebrafish disease models from a practical standpoint, by discussing how genome editing technologies, particularly the recently developed clustered regularly interspaced repeat (CRISPR)/CRISPR-associated protein 9 system, can be used to model rare pathogenic variants in zebrafish. Finally, we will review examples in the literature where zebrafish models have played a pivotal role in confirming variant causality and revealing the underlying mechanisms of rare diseases, often with wider implications for our understanding of human biology.
Collapse
Affiliation(s)
- Kathryn Isabel Adamson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Andrew James Grierson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK.,Department of Neuroscience, University of Sheffield, Sheffield, UK
| |
Collapse
|
92
|
Mestek-Boukhibar L, Clement E, Jones WD, Drury S, Ocaka L, Gagunashvili A, Le Quesne Stabej P, Bacchelli C, Jani N, Rahman S, Jenkins L, Hurst JA, Bitner-Glindzicz M, Peters M, Beales PL, Williams HJ. Rapid Paediatric Sequencing (RaPS): comprehensive real-life workflow for rapid diagnosis of critically ill children. J Med Genet 2018; 55:721-728. [PMID: 30049826 PMCID: PMC6252361 DOI: 10.1136/jmedgenet-2018-105396] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/22/2018] [Accepted: 06/10/2018] [Indexed: 11/13/2022]
Abstract
Background Rare genetic conditions are frequent risk factors for, or direct causes of, paediatric intensive care unit (PICU) admission. Such conditions are frequently suspected but unidentified at PICU admission. Compassionate and effective care is greatly assisted by definitive diagnostic information. There is therefore a need to provide a rapid genetic diagnosis to inform clinical management. To date, whole genome sequencing (WGS) approaches have proved successful in diagnosing a proportion of children with rare diseases, but results may take months to report. Our aim was to develop an end-to-end workflow for the use of rapid WGS for diagnosis in critically ill children in a UK National Health Service (NHS) diagnostic setting. Methods We sought to establish a multidisciplinary Rapid Paediatric Sequencing team for case selection, trio WGS, rapid bioinformatics sequence analysis and a phased analysis and reporting system to prioritise genes with a high likelihood of being causal. Results Trio WGS in 24 critically ill children led to a molecular diagnosis in 10 (42%) through the identification of causative genetic variants. In 3 of these 10 individuals (30%), the diagnostic result had an immediate impact on the individual’s clinical management. For the last 14 trios, the shortest time taken to reach a provisional diagnosis was 4 days (median 8.5 days). Conclusion Rapid WGS can be used to diagnose and inform management of critically ill children within the constraints of an NHS clinical diagnostic setting. We provide a robust workflow that will inform and facilitate the rollout of rapid genome sequencing in the NHS and other healthcare systems globally.
Collapse
Affiliation(s)
- Lamia Mestek-Boukhibar
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Emma Clement
- Department of Clinical Genetics, North East Thames RegionalGenetics Service, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Wendy D Jones
- Department of Clinical Genetics, North East Thames RegionalGenetics Service, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Suzanne Drury
- Congenica Ltd, Bioinnovation Data Centre, Wellcome Genome Campus, Cambridge, UK
| | - Louise Ocaka
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Andrey Gagunashvili
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Polona Le Quesne Stabej
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Chiara Bacchelli
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Nital Jani
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Shamima Rahman
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Lucy Jenkins
- NE Thames Regional Genetics Laboratory, Great Ormond Street Hospital, London, UK
| | - Jane A Hurst
- Department of Clinical Genetics, North East Thames RegionalGenetics Service, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Maria Bitner-Glindzicz
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Mark Peters
- Respiratory, Critical Care and Anaesthesia Unit, UCL Great Ormond Street Institute of Child Health and Great Ormond Street NHS Foundation Trust, London, UK
| | - Philip L Beales
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Hywel J Williams
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| |
Collapse
|
93
|
Ito Y, Carss KJ, Duarte ST, Hartley T, Keren B, Kurian MA, Marey I, Charles P, Mendonça C, Nava C, Pfundt R, Sanchis-Juan A, van Bokhoven H, van Essen A, van Ravenswaaij-Arts C, Boycott KM, Kernohan KD, Dyack S, Raymond FL, Aitman T, Bennett D, Caulfield M, Chinnery P, Gale D, Koziell A, Kuijpers TW, Laffan MA, Maher E, Markus HS, Morrell NW, Ouwehand WH, Perry DJ, Raymond FL, Roberts I, Smith KG, Thrasher A, Watkins H, Williamson C, Woods G, Ashford S, Bradley JR, Fletcher D, Hammerton T, James R, Kingston N, Penkett CJ, Stirrups K, Veltman M, Young T, Brown M, Clements-Brod N, Davis J, Dewhurst E, Dolling H, Erwood M, Frary A, Linger R, Martin JM, Papadia S, Rehnstrom K, Stark H, Allsup D, Austin S, Bakchoul T, Bariana TK, Bolton-Maggs P, Chalmers E, Collins J, Collins P, Erber WN, Everington T, Favier R, Freson K, Furie B, Gattens M, Gebhart J, Gomez K, Greene D, Greinacher A, Gresele P, Hart D, Heemskerk JW, Henskens Y, Kazmi R, Keeling D, Kelly AM, Lambert MP, Lentaigne C, Liesner R, Makris M, Mangles S, Mathias M, Millar CM, Mumford A, Nurden P, Payne J, Pasi J, Peerlinck K, Revel-Vilk S, Richards M, Rondina M, Roughley C, Schulman S, Schulze H, Scully M, Sivapalaratnam S, Stubbs M, Tait RC, Talks K, Thachil J, Toh CH, Turro E, Van Geet C, De Vries M, Warner TQ, Watson H, Westbury S, Furnell A, Mapeta R, Rayner-Matthews P, Simeoni I, Staines S, Stephens J, Watt C, Whitehorn D, Attwood A, Daugherty L, Deevi SV, Halmagyi C, Hu F, Matser V, Meacham S, Megy K, Shamardina O, Titterton C, Tuna S, Yu P, von Ziegenweldt J, Astle W, Bleda M, Carss KJ, Gräf S, Haimel M, Lango-Allen H, Richardson S, Calleja P, Rankin S, Turek W, Anderson J, Bryson C, Carmichael J, McJannet C, Stock S, Allen L, Ambegaonkar G, Armstrong R, Arno G, Bitner-Glindzicz M, Brady A, Canham N, Chitre M, Clement E, Clowes V, Deegan P, Deshpande C, Doffinger R, Firth H, Flinter F, French C, Gardham A, Ghali N, Gissen P, Grozeva D, Henderson R, Hensiek A, Holden S, Holder M, Holder S, Hurst J, Josifova D, Krishnakumar D, Kurian MA, Lees M, MacLaren R, Maw A, Mehta S, Michaelides M, Moore A, Murphy E, Park SM, Parker A, Patch C, Paterson J, Rankin J, Reid E, Rosser E, Sanchis-Juan A, Sandford R, Santra S, Scott R, Sohal A, Stein P, Thomas E, Thompson D, Tischkowitz M, Vogt J, Wakeling E, Wassmer E, Webster A, Ali S, Ali S, Boggard HJ, Church C, Coghlan G, Cookson V, Corris PA, Creaser-Myers A, DaCosta R, Dormand N, Eyries M, Gall H, Ghataorhe PK, Ghio S, Ghofrani A, Gibbs JSR, Girerd B, Greenhalgh A, Hadinnapola C, Houweling AC, Humbert M, in’t Veld AH, Kennedy F, Kiely DG, Kovacs G, Lawrie A, Ross RVM, Machado R, Masati L, Meehan S, Moledina S, Montani D, Othman S, Peacock AJ, Pepke-Zaba J, Pollock V, Polwarth G, Ranganathan L, Rhodes CJ, Rue-Albrecht K, Schotte G, Shipley D, Soubrier F, Southgate L, Scelsi L, Suntharalingam J, Tan Y, Toshner M, Treacy CM, Trembath R, Vonk Noordegraaf A, Walker S, Wanjiku I, Wharton J, Wilkins M, Wort SJ, Yates K, Alachkar H, Antrobus R, Arumugakani G, Bacchelli C, Baxendale H, Bethune C, Bibi S, Booth C, Browning M, Burns S, Chandra A, Cooper N, Davies S, Devlin L, Drewe E, Edgar D, Egner W, Ghurye R, Gilmour K, Goddard S, Gordins P, Grigoriadou S, Hackett S, Hague R, Harper L, Hayman G, Herwadkar A, Huissoon A, Jolles S, Kelleher P, Kumararatne D, Lear S, Longhurst H, Lorenzo L, Maimaris J, Manson A, McDermott E, Murng S, Nejentsev S, Noorani S, Oksenhendler E, Ponsford M, Qasim W, Quinti I, Richter A, Samarghitean C, Sargur R, Savic S, Seneviratne S, Sewell C, Staples E, Stauss H, Thaventhiran J, Thomas M, Welch S, Willcocks L, Yeatman N, Yong P, Ancliff P, Babbs C, Layton M, Louka E, McGowan S, Mead A, Roy N, Chambers J, Dixon P, Estiu C, Hague B, Marschall HU, Simpson M, Chong S, Emmerson I, Ginsberg L, Gosal D, Hadden R, Horvath R, Mahdi-Rogers M, Manzur A, Marshall A, Matthews E, McCarthy M, Reilly M, Renton T, Rice A, Themistocleous A, Vale T, Van Zuydam N, Walker S, Ormondroyd L, Hudson G, Wei W, Yu Wai Man P, Whitworth J, Afzal M, Colby E, Saleem M, Alavijeh OS, Cook HT, Johnson S, Levine AP, Wong EK, Tan R, Boycott KM, MacKenzie A, Majewski J, Brudno M, Bulman D, Dyment D. De Novo Truncating Mutations in WASF1 Cause Intellectual Disability with Seizures. Am J Hum Genet 2018; 103:144-153. [PMID: 29961568 PMCID: PMC6037130 DOI: 10.1016/j.ajhg.2018.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/04/2018] [Indexed: 10/28/2022] Open
Abstract
Next-generation sequencing has been invaluable in the elucidation of the genetic etiology of many subtypes of intellectual disability in recent years. Here, using exome sequencing and whole-genome sequencing, we identified three de novo truncating mutations in WAS protein family member 1 (WASF1) in five unrelated individuals with moderate to profound intellectual disability with autistic features and seizures. WASF1, also known as WAVE1, is part of the WAVE complex and acts as a mediator between Rac-GTPase and actin to induce actin polymerization. The three mutations connected by Matchmaker Exchange were c.1516C>T (p.Arg506Ter), which occurs in three unrelated individuals, c.1558C>T (p.Gln520Ter), and c.1482delinsGCCAGG (p.Ile494MetfsTer23). All three variants are predicted to partially or fully disrupt the C-terminal actin-binding WCA domain. Functional studies using fibroblast cells from two affected individuals with the c.1516C>T mutation showed a truncated WASF1 and a defect in actin remodeling. This study provides evidence that de novo heterozygous mutations in WASF1 cause a rare form of intellectual disability.
Collapse
|
94
|
Bourque DK, Dyment DA, MacLusky I, Kernohan KD, McMillan HJ. Periodic breathing in patients with NALCN mutations. J Hum Genet 2018; 63:1093-1096. [PMID: 29968795 DOI: 10.1038/s10038-018-0484-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 01/10/2023]
Abstract
Biallelic mutations in NALCN are responsible for infantile hypotonia with psychomotor retardation and characteristic facies 1 (IHPRF1). Common features of this condition include severe neonatal-onset hypotonia and profound global developmental delay. Given the rarity of this condition, long-term natural history studies are limited. Here, we present a 9-year-old male with a homozygous nonsense mutation in NALCN (c.3910C>T, p.Arg1304X) leading to profound intellectual disability, seizures, feeding difficulties, and significant periodic breathing. Breathing irregularity was also reported in three previous patients; similar to our patient, those children demonstrated periodic breathing that was characterized by alternating apneic periods with deep, rapid breathing. As the phenotype associated with NALCN mutations continues to be delineated, attention should be given to abnormal respiratory patterns, which may be an important distinguishing feature of this condition.
Collapse
Affiliation(s)
- Danielle K Bourque
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - David A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Ian MacLusky
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Division of Respirology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | | | - Hugh J McMillan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada. .,Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.
| |
Collapse
|
95
|
Smith AC, Ito Y, Ahmed A, Schwartzentruber JA, Beaulieu CL, Aberg E, Majewski J, Bulman DE, Horsting-Wethly K, Koning DVD, Rodenburg RJ, Boycott KM, Penney LS. A family segregating lethal neonatal coenzyme Q 10 deficiency caused by mutations in COQ9. J Inherit Metab Dis 2018; 41:719-729. [PMID: 29560582 DOI: 10.1007/s10545-017-0122-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/12/2017] [Accepted: 11/30/2017] [Indexed: 11/27/2022]
Abstract
Primary CoQ10 deficiency is a clinically and genetically heterogeneous, autosomal recessive disorder resulting from mutations in genes involved in the synthesis of coenzyme Q10 (CoQ10). To date, mutations in nine proteins required for the biosynthesis of CoQ10 cause CoQ10 deficiency with varying clinical presentations. In 2009 the first patient with mutations in COQ9 was reported in an infant with a neonatal-onset, primary CoQ10 deficiency with multi-system disease. Here we describe four siblings with a previously undiagnosed lethal disorder characterized by oligohydramnios and intrauterine growth restriction, variable cardiomyopathy, anemia, and renal anomalies. The first and third pregnancy resulted in live born babies with abnormal tone who developed severe, treatment unresponsive lactic acidosis after birth and died hours later. Autopsy on one of the siblings demonstrated brain changes suggestive of the subacute necrotizing encephalopathy of Leigh disease. Whole-exome sequencing (WES) revealed the siblings shared compound heterozygous mutations in the COQ9 gene with both variants predicted to affect splicing. RT-PCR on RNA from patient fibroblasts revealed that the c.521 + 2 T > C variant resulted in splicing out of exons 4-5 and the c.711 + 3G > C variant spliced out exon 6, resulting in undetectable levels of COQ9 protein in patient fibroblasts. The biochemical profile of patient fibroblasts demonstrated a drastic reduction in CoQ10 levels. An additional peak on the chromatogram may represent accumulation of demethoxy coenzyme Q (DMQ), which was shown previously to accumulate as a result of a defect in COQ9. This family expands our understanding of this rare metabolic disease and highlights the prenatal onset, clinical variability, severity, and biochemical profile associated with COQ9-related CoQ10 deficiencies.
Collapse
Affiliation(s)
- Amanda C Smith
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Afsana Ahmed
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Jeremy A Schwartzentruber
- McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Chandree L Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Erika Aberg
- Maritime Medical Genetics Service, IWK Health Centre, 5850 University Avenue, P.O. Box 9700, Halifax, NS, B3K 6R8, Canada
| | - Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Dennis E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Karina Horsting-Wethly
- Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Diana Vermunt-de Koning
- Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richard J Rodenburg
- Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Lynette S Penney
- Maritime Medical Genetics Service, IWK Health Centre, 5850 University Avenue, P.O. Box 9700, Halifax, NS, B3K 6R8, Canada.
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada.
| |
Collapse
|
96
|
Ito YA, Smith AC, Kernohan KD, Pena IA, Ahmed A, McDonell LM, Beaulieu C, Bulman DE, Smidt A, Sawyer SL, Dyment DA, Boycott KM, Clericuzio CL. A ZPR1 mutation is associated with a novel syndrome of growth restriction, distinct craniofacial features, alopecia, and hypoplastic kidneys. Clin Genet 2018; 94:303-312. [PMID: 29851065 DOI: 10.1111/cge.13388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/24/2018] [Accepted: 05/27/2018] [Indexed: 12/24/2022]
Abstract
A novel autosomal recessive disorder characterized by pre- and postnatal growth restriction with microcephaly, distinctive craniofacial features, congenital alopecia, hypoplastic kidneys with renal insufficiency, global developmental delay, severe congenital sensorineural hearing loss, early mortality, hydrocephalus, and genital hypoplasia was observed in 4 children from 3 families of New Mexican Hispanic heritage. Three of the children died before 3 years of age from uremia and/or sepsis. Exome sequencing of the surviving individual identified a homozygous c.587T>C (p.Ile196Thr) mutation in ZPR1 Zinc Finger (ZPR1) that segregated appropriately in her family. In a second family, the identical variant was shown to be heterozygous in the affected individual's parents and not homozygous in any of her unaffected siblings. ZPR1 is a ubiquitously expressed, highly conserved protein postulated to transmit proliferative signals from the cell membrane to the nucleus. Structural modeling reveals that p.Ile196Thr disrupts the hydrophobic core of ZPR1. Patient fibroblast cells showed no detectable levels of ZPR1 and the cells showed a defect in cell cycle progression where a significant number of cells remained arrested in the G1 phase. We provide genetic and molecular evidence that a homozygous missense mutation in ZPR1 is associated with a rare and recognizable multisystem syndrome.
Collapse
Affiliation(s)
- Y A Ito
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - A C Smith
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - K D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - I A Pena
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - A Ahmed
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - L M McDonell
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - C Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - A Smidt
- Division of Genetics/Dysmorphology, Department of Pediatrics, University of New Mexico School of Medicine, Albuquerque, New Mexico.,Department of Dermatology, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - S L Sawyer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | -
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - C L Clericuzio
- Division of Genetics/Dysmorphology, Department of Pediatrics, University of New Mexico School of Medicine, Albuquerque, New Mexico
| |
Collapse
|
97
|
Li J, Yang S, Pu Z, Dai J, Jiang T, Du F, Jiang Z, Cheng Y, Dai G, Wang J, Qi J, Cao L, Cheng X, Ren C, Li X, Qin Y. Whole-exome sequencing identifies SGCD and ACVRL1 mutations associated with total anomalous pulmonary venous return (TAPVR) in Chinese population. Oncotarget 2018; 8:27812-27819. [PMID: 28412737 PMCID: PMC5438610 DOI: 10.18632/oncotarget.15434] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/06/2017] [Indexed: 12/30/2022] Open
Abstract
As a rare type of Congenital Heart Defects (CHD), the genetic mechanism of Total Anomalous Pulmonary Venous Return (TAPVR) remains unknown, although previous studies have revealed potential disease-driving regions/genes. Blood samples collected from the 6 sporadic TAPVR cases and 81 non-TAPVR controls were subjected to whole exome sequencing. All detected variations were confirmed by direct Sanger sequencing. Here, we identified 2 non-synonymous missense mutations: c.C652T, p.R218W in activin A receptor type II-like 1 (ACVRL1), c.C717G, p.D239E in sarcoglycan delta (SGCD). Our results offered the landscape of mutations for TAPVR in Chinese population firstly and are valuable in the mutation-based pre- and post-natal screening and genetic diagnosis for TAPVR.
Collapse
Affiliation(s)
- Jun Li
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Shiwei Yang
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Zhening Pu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Tao Jiang
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Fangzhi Du
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhu Jiang
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yue Cheng
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Genyin Dai
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Jun Wang
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Jirong Qi
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Liming Cao
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Xueying Cheng
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Cong Ren
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Xinli Li
- Department of Cardiology, The First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Yuming Qin
- Department of Cardiology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| |
Collapse
|
98
|
Saklatvala JR, Dand N, Simpson MA. Text-mined phenotype annotation and vector-based similarity to improve identification of similar phenotypes and causative genes in monogenic disease patients. Hum Mutat 2018; 39:643-652. [PMID: 29460986 DOI: 10.1002/humu.23413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/25/2018] [Accepted: 02/16/2018] [Indexed: 11/07/2022]
Abstract
The genetic diagnosis of rare monogenic diseases using exome/genome sequencing requires the true causal variant(s) to be identified from tens of thousands of observed variants. Typically a virtual gene panel approach is taken whereby only variants in genes known to cause phenotypes resembling the patient under investigation are considered. With the number of known monogenic gene-disease pairs exceeding 5,000, manual curation of personalized virtual panels using exhaustive knowledge of the genetic basis of the human monogenic phenotypic spectrum is challenging. We present improved probabilistic methods for estimating phenotypic similarity based on Human Phenotype Ontology annotation. A limitation of existing methods for evaluating a disease's similarity to a reference set is that reference diseases are typically represented as a series of binary (present/absent) observations of phenotypic terms. We evaluate a quantified disease reference set, using term frequency in phenotypic text descriptions to approximate term relevance. We demonstrate an improved ability to identify related diseases through the use of a quantified reference set, and that vector space similarity measures perform better than established information content-based measures. These improvements enable the generation of bespoke virtual gene panels, facilitating more accurate and efficient interpretation of genomic variant profiles from individuals with rare Mendelian disorders. These methods are available online at https://atlas.genetics.kcl.ac.uk/~jake/cgi-bin/patient_sim.py.
Collapse
Affiliation(s)
- Jake R Saklatvala
- Department of Medical & Molecular Genetics, King's College London, London, United Kingdom
| | - Nick Dand
- Department of Medical & Molecular Genetics, King's College London, London, United Kingdom
| | - Michael A Simpson
- Department of Medical & Molecular Genetics, King's College London, London, United Kingdom
| |
Collapse
|
99
|
Savarese M, Sarparanta J, Vihola A, Udd B, Hackman P. Increasing Role of Titin Mutations in Neuromuscular Disorders. J Neuromuscul Dis 2018; 3:293-308. [PMID: 27854229 PMCID: PMC5123623 DOI: 10.3233/jnd-160158] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The TTN gene with 363 coding exons encodes titin, a giant muscle protein spanning from the Z-disk to the M-band within the sarcomere. Mutations in the TTN gene have been associated with different genetic disorders, including hypertrophic and dilated cardiomyopathy and several skeletal muscle diseases. Before the introduction of next generation sequencing (NGS) methods, the molecular analysis of TTN has been laborious, expensive and not widely used, resulting in a limited number of mutations identified. Recent studies however, based on the use of NGS strategies, give evidence of an increasing number of rare and unique TTN variants. The interpretation of these rare variants of uncertain significance (VOUS) represents a challenge for clinicians and researchers. The main aim of this review is to describe the wide spectrum of muscle diseases caused by TTN mutations so far determined, summarizing the molecular findings as well as the clinical data, and to highlight the importance of joint efforts to respond to the challenges arising from the use of NGS. An international collaboration through a clinical and research consortium and the development of a single accessible database listing variants in the TTN gene, identified by high throughput approaches, may be the key to a better assessment of titinopathies and to systematic genotype– phenotype correlation studies.
Collapse
Affiliation(s)
- Marco Savarese
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Jaakko Sarparanta
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland.,Albert Einstein College of Medicine, Departments of Medicine- Endocrinology and Molecular Pharmacology, Bronx, NY, USA
| | - Anna Vihola
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland.,Neuromuscular Research Center, University of Tampere and Tampere University Hospital, Tampere, Finland.,Department of Neurology, Vaasa Central Hospital, Vaasa, Finland
| | - Peter Hackman
- Folkhälsan Institute of Genetics and Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| |
Collapse
|
100
|
Hocking JC, Famulski JK, Yoon KH, Widen SA, Bernstein CS, Koch S, Weiss O, Agarwala S, Inbal A, Lehmann OJ, Waskiewicz AJ. Morphogenetic defects underlie Superior Coloboma, a newly identified closure disorder of the dorsal eye. PLoS Genet 2018. [PMID: 29522511 PMCID: PMC5862500 DOI: 10.1371/journal.pgen.1007246] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The eye primordium arises as a lateral outgrowth of the forebrain, with a transient fissure on the inferior side of the optic cup providing an entry point for developing blood vessels. Incomplete closure of the inferior ocular fissure results in coloboma, a disease characterized by gaps in the inferior eye and recognized as a significant cause of pediatric blindness. Here, we identify eight patients with defects in tissues of the superior eye, a congenital disorder that we term superior coloboma. The embryonic origin of superior coloboma could not be explained by conventional models of eye development, leading us to reanalyze morphogenesis of the dorsal eye. Our studies revealed the presence of the superior ocular sulcus (SOS), a transient division of the dorsal eye conserved across fish, chick, and mouse. Exome sequencing of superior coloboma patients identified rare variants in a Bone Morphogenetic Protein (Bmp) receptor (BMPR1A) and T-box transcription factor (TBX2). Consistent with this, we find sulcus closure defects in zebrafish lacking Bmp signaling or Tbx2b. In addition, loss of dorsal ocular Bmp is rescued by concomitant suppression of the ventral-specific Hedgehog pathway, arguing that sulcus closure is dependent on dorsal-ventral eye patterning cues. The superior ocular sulcus acts as a conduit for blood vessels, with altered sulcus closure resulting in inappropriate connections between the hyaloid and superficial vascular systems. Together, our findings explain the existence of superior coloboma, a congenital ocular anomaly resulting from aberrant morphogenesis of a developmental structure. Ocular coloboma is a disease characterized by gaps in the lower portion of the eye and can affect the iris, lens, or retina, and cause loss of vision. Coloboma arises from incomplete closure of a transient fissure on the underside of the developing eye. Therefore, our identification of patients with similar tissue defects, but restricted to the superior half of eye, was surprising. Here, we describe an ocular developmental structure, the superior ocular sulcus, as a potential origin for the congenital disorder superior coloboma. Formation and closure of the sulcus are directed by dorsal-ventral eye patterning, and altered patterning interferes with the role of the sulcus as a pathway for blood vessel growth onto the eye.
Collapse
Affiliation(s)
- Jennifer C Hocking
- Division of Anatomy, Department of Surgery, University of Alberta, Edmonton, Canada.,Women & Children's Health Research Institute, University of Alberta, Edmonton, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Canada
| | - Jakub K Famulski
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Department of Biology, University of Kentucky, Lexington, Unites States of America
| | - Kevin H Yoon
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Sonya A Widen
- Women & Children's Health Research Institute, University of Alberta, Edmonton, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Cassidy S Bernstein
- Department of Molecular Biosciences, University of Texas at Austin,Unites States of America
| | - Sophie Koch
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Omri Weiss
- Department of Medical Neurobiology, Institute for Medical Research-Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | | | - Seema Agarwala
- Department of Molecular Biosciences, University of Texas at Austin,Unites States of America.,Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Unites States of America.,Institute for Neuroscience, University of Texas at Austin, Austin, Unites States of America
| | - Adi Inbal
- Department of Medical Neurobiology, Institute for Medical Research-Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ordan J Lehmann
- Women & Children's Health Research Institute, University of Alberta, Edmonton, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Canada.,Department of Ophthalmology, University of Alberta, Edmonton, Canada.,Neuroscience and Mental Health Research Institute, University of Alberta, Edmonton, Canada
| | - Andrew J Waskiewicz
- Women & Children's Health Research Institute, University of Alberta, Edmonton, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Neuroscience and Mental Health Research Institute, University of Alberta, Edmonton, Canada
| |
Collapse
|