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Puscas M, Martineau G, Bhella G, Bonnen PE, Carr P, Lim R, Mitchell J, Osmond M, Urquieta E, Flamenbaum J, Iaria G, Joly Y, Richer É, Saary J, Saint-Jacques D, Buckley N, Low-Decarie E. Rare diseases and space health: optimizing synergies from scientific questions to care. NPJ Microgravity 2022; 8:58. [PMID: 36550172 PMCID: PMC9780351 DOI: 10.1038/s41526-022-00224-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
Knowledge transfer among research disciplines can lead to substantial research progress. At first glance, astronaut health and rare diseases may be seen as having little common ground for such an exchange. However, deleterious health conditions linked to human space exploration may well be considered as a narrow sub-category of rare diseases. Here, we compare and contrast research and healthcare in the contexts of rare diseases and space health and identify common barriers and avenues of improvement. The prevalent genetic basis of most rare disorders contrasts sharply with the occupational considerations required to sustain human health in space. Nevertheless small sample sizes and large knowledge gaps in natural history are examples of the parallel challenges for research and clinical care in the context of both rare diseases and space health. The two areas also face the simultaneous challenges of evidence scarcity and the pressure to deliver therapeutic solutions, mandating expeditious translation of research knowledge into clinical care. Sharing best practices between these fields, including increasing participant involvement in all stages of research and ethical sharing of standardized data, has the potential to contribute to humankind's efforts to explore ever further into space while caring for people on Earth in a more inclusive fashion.
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Affiliation(s)
- Maria Puscas
- Astronauts, Life Sciences and Space Medicine Canadian Space Agency, Government of Canada, Longueil, Canada
- The School of Health Sciences, University of Western Ontario, London, Canada
| | - Gabrielle Martineau
- Astronauts, Life Sciences and Space Medicine Canadian Space Agency, Government of Canada, Longueil, Canada
- Hawaii Institute of Marine Biology (HIMB), Kaneohe, HI, USA
| | - Gurjot Bhella
- Astronauts, Life Sciences and Space Medicine Canadian Space Agency, Government of Canada, Longueil, Canada
- University of Waterloo, Waterloo, Canada
| | - Penelope E Bonnen
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Phil Carr
- The Strategic Review Group Inc., Ottawa, Canada
| | - Robyn Lim
- Legislative and Regulatory Modernization, Health Canada, Ottawa, Canada
| | - John Mitchell
- Pediatric Endocrinology and Biochemical Genetics, Montreal Children's Hospital-McGill University, Human Genetics and Pediatrics, McGill University, Montreal, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Emmanuel Urquieta
- Translational Research Institute for Space Health (TRISH) and Department of Emergency Medicine and Center for Space Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jaime Flamenbaum
- Canadian Institutes of Health Research Ethics Office, Ottawa, Canada
| | - Giuseppe Iaria
- Department of Psychology, Hotchkiss Brain Institute, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Yann Joly
- Centre of Genomics and Policy, Faculty of Medicine, Human Genetics, McGill University, Montreal, Canada
| | - Étienne Richer
- Canadian Institutes of Health Research Institute of Genetics, Ottawa, Canada
| | - Joan Saary
- Department of Medicine, Division of Occupational Medicine, University of Toronto, Toronto, Canada
| | - David Saint-Jacques
- Astronauts, Life Sciences and Space Medicine Canadian Space Agency, Government of Canada, Longueil, Canada
- Astronauts, Life Sciences and Space Medicine Canadian Space Agency, Government of Canada, Longueil, Canada
| | - Nicole Buckley
- Astronauts, Life Sciences and Space Medicine Canadian Space Agency, Government of Canada, Longueil, Canada.
- Directorate of Human Spaceflight and Robotic Exploration, European Space Agency, Noordwijk, Holland.
| | - Etienne Low-Decarie
- Astronauts, Life Sciences and Space Medicine Canadian Space Agency, Government of Canada, Longueil, Canada.
- Agriculture and Agri-Food Canada, Government of Canada, Montreal, Canada.
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Boycott KM, Azzariti DR, Hamosh A, Rehm HL. Seven years since the launch of the Matchmaker Exchange: The evolution of genomic matchmaking. Hum Mutat 2022; 43:659-667. [PMID: 35537081 PMCID: PMC9133175 DOI: 10.1002/humu.24373] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022]
Abstract
The Matchmaker Exchange (MME) was launched in 2015 to provide a robust mechanism to discover novel disease-gene relationships. It operates as a federated network connecting databases holding relevant data using a common application programming interface, where two or more users are looking for a match for the same gene (two-sided matchmaking). Seven years from its launch, it is clear that the MME is making outstanding contributions to understanding the morbid anatomy of the genome. The number of unique genes present across the MME has steadily increased over time; there are currently >13,520 unique genes (~68% of all protein-coding genes) connected across the MME's eight genomic matchmaking nodes, GeneMatcher, DECIPHER, PhenomeCentral, MyGene2, seqr, Initiative on Rare and Undiagnosed Disease, PatientMatcher, and the RD-Connect Genome-Phenome Analysis Platform. The collective data set accessible across the MME currently includes more than 120,000 cases from over 12,000 contributors in 98 countries. The discovery of potential new disease-gene relationships is happening daily and international collaborative teams are moving these advances forward to publication, now numbering well over 500. Expansion of data sharing into routine clinical practice by clinicians, genetic counselors, and clinical laboratories has ensured access to discovery for even more individuals with undiagnosed rare genetic diseases. Tens of thousands of patients and their family members have been directly or indirectly impacted by the discoveries facilitated by two-sided genomic matchmaking. MME supports further connections to the literature (PubCaseFinder) and to human and model organism resources (Monarch Initiative) and scientists (ModelMatcher). Efforts are now underway to explore additional approaches to matchmaking at the gene or variant level where there is only one querier (one-sided matchmaking). Genomic matchmaking has proven its utility over the past 7 years and will continue to facilitate discoveries in the years to come.
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Affiliation(s)
- Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Danielle R. Azzariti
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Clinical and Genetic Characteristics of COL2A1-Associated Skeletal Dysplasias in 60 Russian Patients: Part I. Genes (Basel) 2022; 13:genes13010137. [PMID: 35052477 PMCID: PMC8775336 DOI: 10.3390/genes13010137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
The significant variability in the clinical manifestations of COL2A1-associated skeletal dysplasias makes it necessary to conduct a clinical and genetic analysis of individual nosological variants, which will contribute to improving our understanding of the pathogenetic mechanisms and prognosis. We presented the clinical and genetic characteristics of 60 Russian pediatric patients with type II collagenopathies caused by previously described and newly identified variants in the COL2A1 gene. Diagnosis confirmation was carried out by new generation sequencing of the target panel with subsequent validation of the identified variants using automated Sanger sequencing. It has been shown that clinical forms of spondyloepiphyseal dysplasias predominate in childhood, both with more severe clinical manifestations (58%) and with unusual phenotypes of mild forms with normal growth (25%). However, Stickler syndrome, type I was less common (17%). In the COL2A1 gene, 28 novel variants were identified, and a total of 63% of the variants were found in the triple helix region resulted in glycine substitution in Gly-XY repeats, which were identified in patients with clinical manifestations of congenital spondyloepiphyseal dysplasia with varying severity, and were not found in Stickler syndrome, type I and Kniest dysplasia. In the C-propeptide region, five novel variants leading to the development of unusual phenotypes of spondyloepiphyseal dysplasia have been identified.
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Zhang T, Sun X, Li M, Huang H. De novo mutation in COL2A1 leads to lethal foetal skeletal dysplasia. Bone 2021; 153:116169. [PMID: 34492360 DOI: 10.1016/j.bone.2021.116169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Skeletal dysplasia caused by genetic mutations places a heavy burden on families and society. This study was performed to precise diagnosis of variants of unknown significance and to expand the genotypic spectrum of lethal skeletal dysplasia. METHODS According to the ultrasonic phenotype of the proband and whole-exome sequencing results, variation sites or genes that may be related to the disease were screened out. We verified the accuracy of the variation site through Sanger sequencing. Using bioinformatics, zebrafish models, and assisted reproduction technology (ART) combined with preimplantation genetic testing for monogenic diseases, the disease-causing mutation was verified. RESULTS A missense mutation (c.3944G>A, p.Cys1315Tyr) was found in the coding region of COL2A1. Although the mutation is a variant of unknown significance, it is highly conserved and was predicted to be harmful by the SIFT and PolyPhen-2 software. In contrast to the control group, col2a1a mutation-expressing zebrafish larvae showed significant spinal curvature. Through preimplantation genetic testing for monogenic diseases excluding the missense mutation, a child conceived by ART was birthed with normal bone development. CONCLUSION We identified a de novo mutation in human COL2A1 related to lethal skeletal dysplasia and expanded the mutation spectrum of type II collagenopathies. In addition, we provided a new strategy based on a zebrafish model and ART for patients who harbour variants of unknown significance to have a healthy baby without genetic disease similar to the proband.
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Affiliation(s)
- Ting Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China; Department of Obstetrics and Gynecology, Nanjing GaoChun People's Hospital, Nanjing 211300, Jiangsu Province, China
| | - Xueping Sun
- Clinical Center of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Mei Li
- Clinical Center of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Huan Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China; Clinical Center of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China.
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Drtikolová Kaupová S, Velemínský P, Cvrček J, Džupa V, Kuželka V, Laboš M, Němečková A, Tomková K, Zazvonilová E, Kacki S. Multiple occurrence of premature polyarticular osteoarthritis in an early medieval Bohemian cemetery (Prague, Czech Republic). INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2020; 30:35-46. [PMID: 32417673 DOI: 10.1016/j.ijpp.2020.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVES To highlight conditions that may cause early-onset degenerative joint disease, and to assess the possible impact of such diseases upon everyday life. MATERIAL Four adults aged under 50 years from a medieval skeletal collection of Prague (Czechia). METHODS Visual, osteometric, X-ray, and histological examinations, stable isotope analysis of bone collagen. RESULTS All four individuals showed multiple symmetrical degenerative changes, affecting the majority of joints of the postcranial skeleton. Associated dysplastic deformities were observed in all individuals, including bilateral hip dysplasia (n = 1), flattening of the femoral condyles (n = 3), and substantial deformation of the elbows (n = 3). The diet of the affected individuals differed from the contemporary population sample. CONCLUSIONS We propose the diagnosis of a mild form of skeletal dysplasia in these four individuals, with multiple epiphyseal dysplasia or type-II collagenopathy linked to premature osteoarthritis as the most probable causes. SIGNIFICANCE Combining the skeletal findings with information from the medical literature, this paper defines several characteristic traits which may assist with the diagnosis of skeletal dysplasia in the archaeological record. LIMITATIONS As no genetic analysis was performed to confirm the possible kinship of the individuals, it is not possible to definitively assess whether the individuals suffered from the same hereditary condition or from different forms of skeletal dysplasia. SUGGESTIONS FOR FURTHER RESEARCH Further studies on premature osteoarthritis in archaeological skeletal series are needed to correct the underrepresentation of these mild forms of dysplasia in past populations.
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Affiliation(s)
- Sylva Drtikolová Kaupová
- Department of Anthropology, National Museum, Václavské Náměstí 68, 11579 Praha 1, Czech Republic.
| | - Petr Velemínský
- Department of Anthropology, National Museum, Václavské Náměstí 68, 11579 Praha 1, Czech Republic.
| | - Jan Cvrček
- Department of Anthropology, National Museum, Václavské Náměstí 68, 11579 Praha 1, Czech Republic; Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Viničná 7, 128 43, Praha 2, Czech Republic.
| | - Valér Džupa
- Deparment of Orthopaedics and Traumatology, Third Faculty of Medicine, Charles University, and University Hospital Kralovske Vinohrady, Srobarova 50, 100 34, Praha 10, Czech Republic.
| | - Vítězslav Kuželka
- Department of Anthropology, National Museum, Václavské Náměstí 68, 11579 Praha 1, Czech Republic.
| | - Marek Laboš
- Deparment of Radiodiagnostics, Third Faculty of Medicine, Charles University, and University Hospital Kralovske Vinohrady, Srobarova 50, 100 34, Praha 10, Czech Republic.
| | - Alena Němečková
- Department of Histology and Embryology, Medical Faculty in Pilsen, Charles University, Karlovarská 48, 301 00, Pilsen, Czech Republic.
| | - Kateřina Tomková
- Institute of Archaeology of the Czech Academy of Sciences, Prague, v.v.i., Letenská 4, 118 01 Praha 1, Czech Republic.
| | - Eliška Zazvonilová
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Viničná 7, 128 43, Praha 2, Czech Republic; Institute of Archaeology of the Czech Academy of Sciences, Prague, v.v.i., Letenská 4, 118 01 Praha 1, Czech Republic.
| | - Sacha Kacki
- CNRS, UMR 5199 PACEA, Université de Bordeaux, Bât. B8, Allée Geoffroy St Hilaire, CS 50023, 33615 Pessac Cedex, France; Department of Archaeology, Durham University, South Road, Durham, DH1 3LE, United Kingdom.
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Travessa AM, Díaz-González F, Mirco T, Oliveira-Ramos F, Parrón-Pajares M, Heath KE, Sousa AB. Spondyloepiphyseal dysplasia type Stanescu: Expanding the clinical and molecular spectrum of a very rare type II collagenopathy. Am J Med Genet A 2020; 182:2715-2721. [PMID: 32856782 DOI: 10.1002/ajmg.a.61817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 07/01/2020] [Accepted: 07/18/2020] [Indexed: 12/25/2022]
Abstract
Spondyloepiphyseal dysplasia type Stanescu (SED-S) is a very rare type II collagenopathy. We describe an 8-year-old boy who presented with short trunk, C2-C3 vertebral fusion, hand, foot, leg and thigh pain, stiffness and limited joint mobility, and waddling gait. Radiographs showed platyspondyly with anterior wedging and endplate irregularities, broad femoral necks, and large epiphyses and epiphyseal equivalents. Differential diagnosis included progressive pseudorheumatoid dysplasia and SED-S. A skeletal dysplasia custom-designed NGS panel was performed and the heterozygous pathogenic variant c.620G>A; p.(Gly207Glu) in COL2A1 was detected, establishing the diagnosis of SED-S. Vertebral fusions, observed in our patient, have not been previously described in this dysplasia. This variant has not been previously associated with SED-S, but was reported in two other families with spondyloepiphyseal dysplasia. Thus, this case expands the clinical and mutational spectrum of SED-S and demonstrates that SED-S significantly overlaps with other skeletal dysplasias.
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Affiliation(s)
- André M Travessa
- Department of Medical Genetics, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal.,Institute of Histology and Developmental Biology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Francisca Díaz-González
- Institute of Medical & Molecular Genetics (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autonóma de Madrid (UAM), and CIBERER, ISCIII, Madrid, Spain.,Skeletal Dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, UAM, Madrid, Spain
| | - Teresa Mirco
- Department of Physical Therapy and Rehabilitation, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Filipa Oliveira-Ramos
- Department of Rheumatology, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Manuel Parrón-Pajares
- Skeletal Dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, UAM, Madrid, Spain.,Department of Radiology, Hospital Universitario La Paz, UAM, Madrid, Spain
| | - Karen E Heath
- Institute of Medical & Molecular Genetics (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autonóma de Madrid (UAM), and CIBERER, ISCIII, Madrid, Spain.,Skeletal Dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, UAM, Madrid, Spain
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal.,Laboratory of Basic Immunology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
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Wang Y, Xiao K, Yang Y, Wu Z, Jin J, Qiu G, Weng X, Zhao X. CCN6 mutation detection in Chinese patients with progressive pseudo-rheumatoid dysplasia and identification of four novel mutations. Mol Genet Genomic Med 2020; 8:e1261. [PMID: 32351055 PMCID: PMC7336755 DOI: 10.1002/mgg3.1261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/20/2020] [Accepted: 03/27/2020] [Indexed: 02/05/2023] Open
Abstract
Background No formal diagnostic criteria for progressive pseudo‐rheumatoid dysplasia (PPD) are available because of insufficient clinical data, which results in that PPD is often misdiagnosed with other diseases. Whole exome sequencing (WES) and Sanger sequencing were employed to reveal the novel mutations on CCN6 of five patients with PPD from China in order to increase the clinical data of PPD. Methods Four suspected PPD pedigrees containing five patients in total were collected from 1998 to 2018 in our medical center. The phenotypes of each suspected PPD case were recorded in detail, and peripheral blood samples were collected for subsequent sequencing. Genomic DNA was extracted from peripheral blood samples, and Agilent liquid phase chip capture system was utilized for efficient enrichment of whole exome region DNA. After acquiring raw sequenced reads of whole exome region, bioinformatics analysis was completed in conjunction with reference or genome sequence (GRCh37/hg19). Sanger sequencing was performed to identify the results of WES. Results In total, four novel PPD‐related mutation sites in CCN6 gene were identified including (CCN6):c.643 + 2T>C, (CCN6):c.1064_1065dupGT(p.Gln356ValfsTer33), (CCN6):c.1064G > A), and exon4:c.670dupA:p.W223fs. Conclusion Our findings increase the clinical data of PPD including the CCN6 mutation spectrum, the clinical symptoms and signs. Moreover, the study highlights the utility of WES in reaching definitive diagnoses for PPD.
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Affiliation(s)
- Yingjie Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing, China
| | - Ke Xiao
- Department of Orthopedic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yuemei Yang
- Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing, China
| | - Zhihong Wu
- Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing, China
| | - Jin Jin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing, China
| | - Xisheng Weng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing, China
| | - Xiuli Zhao
- Department of Medical Genetics, School of Basic Medicine, Peking Union Medical College, Beijing, China
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Rolvien T, Yorgan TA, Kornak U, Hermans-Borgmeyer I, Mundlos S, Schmidt T, Niemeier A, Schinke T, Amling M, Oheim R. Skeletal deterioration in COL2A1-related spondyloepiphyseal dysplasia occurs prior to osteoarthritis. Osteoarthritis Cartilage 2020; 28:334-343. [PMID: 31958497 DOI: 10.1016/j.joca.2019.12.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/05/2019] [Accepted: 12/31/2019] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Spondyloepiphyseal dysplasia, a combination of progressive arthropathy with variable signs of skeletal dysplasia, can be a result of mutations in the collagen, type II, alpha 1 (COL2A1) gene. However, the bone involvement (e.g., density, microstructure) in this disorder has hitherto not been studied. DESIGN A 50-year-old female patient and her 8-year-old son with flattening of vertebral bodies and early-onset osteoarthritis were genetically tested using a custom designed gene bone panel including 386 genes. Bone microstructure and turnover were assessed using high-resolution peripheral quantitative computed tomography (HR-pQCT) and serum bone turnover markers, respectively. Furthermore, the bone and cartilage phenotype of male mice heterozygous for the loss-of-function mutation of Col2a1 (Col2a1+/d) was analyzed compared to wildtype littermates using μ-CT and histomorphometry. RESULTS We identified a dominant COL2A1 mutation (c.620G > A p.(Gly207Glu)) indicating spondyloepiphyseal dysplasia in the female patient and her son, both being severely affected by skeletal deterioration. Although there was no osteoarthritis detectable at first visit, the son was affected by trabecular osteopenia, which progressed over time. In an iliac crest biopsy obtained from the mother, osteoclast indices were remarkably increased. Col2a1+/d mice developed a moderate skeletal phenotype expressed by reduced cortical and trabecular parameters at 4 weeks. Importantly, no articular defects could be observed in the knee joints at 4 weeks, while osteoarthritis was only detectable in 12-week-old mice. CONCLUSIONS Our results indicate that collagen type II deficiency in spondyloepiphyseal dysplasia leads to skeletal deterioration with early-onset in humans and mice that occurs prior to the development of osteoarthritis.
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Affiliation(s)
- T Rolvien
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529, Hamburg, Germany; Department of Orthopedics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - T A Yorgan
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529, Hamburg, Germany
| | - U Kornak
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - I Hermans-Borgmeyer
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - S Mundlos
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - T Schmidt
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529, Hamburg, Germany
| | - A Niemeier
- Department of Orthopedics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - T Schinke
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529, Hamburg, Germany
| | - M Amling
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529, Hamburg, Germany
| | - R Oheim
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529, Hamburg, Germany
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Zhang B, Zhang Y, Wu N, Li J, Liu H, Wang J. Integrated analysis of COL2A1 variant data and classification of type II collagenopathies. Clin Genet 2019; 97:383-395. [PMID: 31758797 DOI: 10.1111/cge.13680] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 11/29/2022]
Abstract
The COL2A1 gene encodes the alpha-1 chain of type II procollagen. Type II collagen, comprised of three identical alpha-1 chains, is the major component of cartilage. COL2A1 gene variants are the etiologies of genetic diseases, termed type II collagenopathies, with a wide spectrum of clinical presentations. To date, at least 460 distinct COL2A1 mutations, identified in 663 independent probands, and 21 definite disorders have been reported. Nevertheless, a well-defined genotype-phenotype correlation has not been established, and few hot spots of mutation have been reported. In this study, we analyzed data of COL2A1 variants and clinical information of patients obtained from the Leiden Open Variation Database 3.0, as well as the currently available relevant literature. We determined the characteristics of the COL2A1 variants and distributions of the clinical manifestations in patients, and identified four likely genotype-phenotype correlations. Moreover, we classified 21 COL2A1-related disorders into five categories, which may assist clinicians in understanding the essence of these complex phenotypes and prompt genetic screening in clinical practice.
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Affiliation(s)
- Boyan Zhang
- Orthopedic Medical Center, The Second Hospital of Jilin University, Changchun, China
| | - Yue Zhang
- Department of Radiation Oncology, First Bethune Hospital of Jilin University, Changchun, China
| | - Naichao Wu
- Orthopedic Medical Center, The Second Hospital of Jilin University, Changchun, China
| | - Jianing Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, China
| | - He Liu
- Orthopedic Medical Center, The Second Hospital of Jilin University, Changchun, China
| | - Jincheng Wang
- Orthopedic Medical Center, The Second Hospital of Jilin University, Changchun, China
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Riggs ER, Azzariti DR, Niehaus A, Goehringer SR, Ramos EM, Rodriguez LL, Knoppers B, Rehm HL, Martin CL. Development of a consent resource for genomic data sharing in the clinical setting. Genet Med 2019; 21:81-88. [PMID: 29899502 PMCID: PMC6292744 DOI: 10.1038/s41436-018-0017-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/20/2018] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Data sharing between clinicians, laboratories, and patients is essential for improvements in genomic medicine, but obtaining consent for individual-level data sharing is often hindered by a lack of time and resources. To address this issue, the Clinical Genome Resource (ClinGen) developed tools to facilitate consent, including a one-page consent form and online supplemental video with information on key topics, such as risks and benefits of data sharing. METHODS To determine whether the consent form and video accurately conveyed key data sharing concepts, we surveyed 5,162 members of the general public. We measured comprehension at baseline, after reading the form and watching the video. Additionally, we assessed participants' attitudes toward genomic data sharing. RESULTS Participants' performance on comprehension questions significantly improved over baseline after reading the form and continued to improve after watching the video. CONCLUSION Results suggest reading the form alone provided participants with important knowledge regarding broad data sharing, and watching the video allowed for broader comprehension. These materials are now available at http://www.clinicalgenome.org/share . These resources will provide patients a straightforward way to share their genetic and health information, and improve the scientific community's access to data generated through routine healthcare.
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Affiliation(s)
- Erin Rooney Riggs
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA.
| | - Danielle R Azzariti
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Annie Niehaus
- National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA
| | - Scott R Goehringer
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA
| | - Laura Lyman Rodriguez
- National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA
| | - Bartha Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
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11
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Torreggiani S, Torcoletti M, Campos-Xavier B, Baldo F, Agostoni C, Superti-Furga A, Filocamo G. Progressive pseudorheumatoid dysplasia: a rare childhood disease. Rheumatol Int 2018; 39:441-452. [PMID: 30327864 DOI: 10.1007/s00296-018-4170-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/04/2018] [Indexed: 01/13/2023]
Abstract
Progressive pseudorheumatoid dysplasia (PPRD) is a genetic bone disorder characterised by the progressive degeneration of articular cartilage that leads to pain, stiffness and joint enlargement. As PPRD is a rare disease, available literature is mainly represented by single case reports and only a few larger case series. Our aim is to review the literature concerning clinical, laboratory and radiological features of PPRD. PPRD is due to a mutation in Wnt1-inducible signalling protein 3 (WISP3) gene, which encodes a signalling factor involved in cartilage homeostasis. The disease onset in childhood and skeletal changes progresses over time leading to significant disability. PPRD is a rare condition that should be suspected if a child develops symmetrical polyarticular involvement without systemic inflammation, knobbly interphalangeal joints of the hands, and gait abnormalities. A full skeletal survey, or at least a lateral radiograph of the spine, can direct towards a correct diagnosis that can be confirmed molecularly. More than 70 WISP3 mutations have so far been reported. Genetic testing should start with the study of genomic DNA extracted from blood leucocytes, but intronic mutations in WISP3 causing splicing aberrations can only be detected by analysing WISP3 mRNA, which can be extracted from cultured skin fibroblasts. A skin biopsy is, therefore, indicated in patients with typical PPRD findings and negative mutation screening of genomic DNA.
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Affiliation(s)
- Sofia Torreggiani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via della Commenda 9, 20122, Milan, Italy.
| | - Marta Torcoletti
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via della Commenda 9, 20122, Milan, Italy
| | - Belinda Campos-Xavier
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois, Rue du Bugnon 21, 1011, Lausanne, Switzerland
| | - Francesco Baldo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via della Commenda 9, 20122, Milan, Italy
| | - Carlo Agostoni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via della Commenda 9, 20122, Milan, Italy
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois, Rue du Bugnon 21, 1011, Lausanne, Switzerland
| | - Giovanni Filocamo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via della Commenda 9, 20122, Milan, Italy
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12
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Fidler AL, Boudko SP, Rokas A, Hudson BG. The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution. J Cell Sci 2018; 131:jcs203950. [PMID: 29632050 PMCID: PMC5963836 DOI: 10.1242/jcs.203950] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The cellular microenvironment, characterized by an extracellular matrix (ECM), played an essential role in the transition from unicellularity to multicellularity in animals (metazoans), and in the subsequent evolution of diverse animal tissues and organs. A major ECM component are members of the collagen superfamily -comprising 28 types in vertebrates - that exist in diverse supramolecular assemblies ranging from networks to fibrils. Each assembly is characterized by a hallmark feature, a protein structure called a triple helix. A current gap in knowledge is understanding the mechanisms of how the triple helix encodes and utilizes information in building scaffolds on the outside of cells. Type IV collagen, recently revealed as the evolutionarily most ancient member of the collagen superfamily, serves as an archetype for a fresh view of fundamental structural features of a triple helix that underlie the diversity of biological activities of collagens. In this Opinion, we argue that the triple helix is a protein structure of fundamental importance in building the extracellular matrix, which enabled animal multicellularity and tissue evolution.
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Affiliation(s)
- Aaron L Fidler
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sergei P Boudko
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Billy G Hudson
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Medical Education and Administration, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
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13
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Xiao B, Qiu W, Ji X, Liu X, Huang Z, Liu H, Fan Y, Xu Y, Liu Y, Yie H, Wei W, Yan H, Gong Z, Shen L, Sun Y. Marked yield of re-evaluating phenotype and exome/target sequencing data in 33 individuals with intellectual disabilities. Am J Med Genet A 2017; 176:107-115. [PMID: 29159939 DOI: 10.1002/ajmg.a.38542] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/12/2017] [Accepted: 10/20/2017] [Indexed: 12/17/2022]
Abstract
The diagnosis of intellectual disability/developmental delay (ID/DD) benefits from the clinical application of target/exome sequencing. The yield in Mendelian diseases varies from 25% to 68%. The aim of the present study was to identify the genetic causes of 33 ID/DD patients using target/exome sequencing. Recent studies have demonstrated that reanalyzing undiagnosed exomes could yield additional diagnosis. Therefore, in addition to the normal data analysis, in this study, re-evaluation was performed prior to manuscript preparation after updating OMIM annotations, calling copy number variations (CNVs) and reviewing the current literature. Molecular diagnosis was obtained for 19/33 patients in the first round of analysis. Notably, five patients were diagnosed during the re-evaluation of the geno/phenotypic data. This study confirmed the utility of exome sequencing in the diagnosis of ID/DD. Furthermore, re-evaluation leads to a 15% improvement in diagnostic yield. Thus, to maximize the diagnostic yield of next-generation sequencing (NGS), periodical re-evaluation of the geno/phenotypic data of undiagnosed individuals is recommended by updating the OMIM annotation, applying new algorithms, reviewing the literature, sharing pheno/genotypic data, and re-contacting patients.
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Affiliation(s)
- Bing Xiao
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xing Ji
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xiaoqing Liu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Zhuo Huang
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Huili Liu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yanjie Fan
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yan Xu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yu Liu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Hui Yie
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wei Wei
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Hui Yan
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Zhuwen Gong
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Lixiao Shen
- Department of Children's Healthcare, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Sun
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University,, Shanghai, China.,Molecular Genetics Group, Shanghai Institute for Pediatric Research, Shanghai, China
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14
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Boycott KM, Rath A, Chong JX, Hartley T, Alkuraya FS, Baynam G, Brookes AJ, Brudno M, Carracedo A, den Dunnen JT, Dyke SOM, Estivill X, Goldblatt J, Gonthier C, Groft SC, Gut I, Hamosh A, Hieter P, Höhn S, Hurles ME, Kaufmann P, Knoppers BM, Krischer JP, Macek M, Matthijs G, Olry A, Parker S, Paschall J, Philippakis AA, Rehm HL, Robinson PN, Sham PC, Stefanov R, Taruscio D, Unni D, Vanstone MR, Zhang F, Brunner H, Bamshad MJ, Lochmüller H. International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. Am J Hum Genet 2017; 100:695-705. [PMID: 28475856 PMCID: PMC5420351 DOI: 10.1016/j.ajhg.2017.04.003] [Citation(s) in RCA: 247] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Provision of a molecularly confirmed diagnosis in a timely manner for children and adults with rare genetic diseases shortens their "diagnostic odyssey," improves disease management, and fosters genetic counseling with respect to recurrence risks while assuring reproductive choices. In a general clinical genetics setting, the current diagnostic rate is approximately 50%, but for those who do not receive a molecular diagnosis after the initial genetics evaluation, that rate is much lower. Diagnostic success for these more challenging affected individuals depends to a large extent on progress in the discovery of genes associated with, and mechanisms underlying, rare diseases. Thus, continued research is required for moving toward a more complete catalog of disease-related genes and variants. The International Rare Diseases Research Consortium (IRDiRC) was established in 2011 to bring together researchers and organizations invested in rare disease research to develop a means of achieving molecular diagnosis for all rare diseases. Here, we review the current and future bottlenecks to gene discovery and suggest strategies for enabling progress in this regard. Each successful discovery will define potential diagnostic, preventive, and therapeutic opportunities for the corresponding rare disease, enabling precision medicine for this patient population.
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Affiliation(s)
- Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
| | - Ana Rath
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Research Center, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Gareth Baynam
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Anthony J Brookes
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto M5S 1A1, Canada
| | - Angel Carracedo
- Genomic Medicine Group, Galician Foundation of Genomic Medicine and University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Johan T den Dunnen
- Departments of Human Genetics and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Stephanie O M Dyke
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Xavier Estivill
- Experimental Division, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar; Genetics Unit, Dexeus Woman's Health, 08028 Barcelona, Spain
| | - Jack Goldblatt
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Catherine Gonthier
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Stephen C Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Ivo Gut
- Centre Nacional d'Anàlisi Genòmica, Center for Genomic Regulation, Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, 08028 Barcelona, Spain
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21286, USA
| | - Philip Hieter
- Michael Smith Laboratories, Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sophie Höhn
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Petra Kaufmann
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Jeffrey P Krischer
- University of South Florida Health Informatics Institute, Tampa, FL 33620, USA
| | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, 150 06 Prague 5, Czech Republic
| | - Gert Matthijs
- Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Annie Olry
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | | | - Justin Paschall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité Universitätsmdizin Berlin, 13353 Berlin, Germany; Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, China
| | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv 4002, Bulgaria
| | - Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome 299-00161, Italy
| | - Divya Unni
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Megan R Vanstone
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Feng Zhang
- WuXi AppTec, Waigaoqiao Free Trade Zone, Shanghai 200131, China; WuXi NextCODE, Cambridge, MA 02142, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, 6229 GT Maastricht, the Netherlands
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
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15
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Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat 2015; 36:915-21. [PMID: 26295439 PMCID: PMC4610002 DOI: 10.1002/humu.22858] [Citation(s) in RCA: 351] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022]
Abstract
There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. Three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.
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Affiliation(s)
- Anthony A. Philippakis
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cardiology, Brigham & Women's Hospital,
Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Danielle R. Azzariti
- Laboratory for Molecular Medicine, Partners Personalized
Medicine, Boston, MA USA
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico, Barcelona,
Spain
| | | | - Catherine A. Brownstein
- Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and the Manton Center for
Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Genetics and Genome Biology Program, The Hospital for Sick
Children, Toronto, Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | - Han G. Brunner
- Radboud University Medical Center,Department of Human
Genetics, PO Box 9101, 6500HB Nijmegen, The Netherlands
- Maastricht University Medical Center, Department of Clinical
Genetics,PO Box 5800, 6202AZ Maastricht, The Netherlands
| | - Orion J. Buske
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Genetics and Genome Biology Program, The Hospital for Sick
Children, Toronto, Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | - Stephanie O.M. Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill
University, Canada
| | - Johan T. den Dunnen
- Human and Clinical Genetics, Leiden University Medical Center,
Leiden, Nederland
| | - Helen V. Firth
- East Anglian Medical Genetics Service, Box 134, Cambridge
University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ,
UK
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Tx 77030, U.S.A
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | - Melissa A. Haendel
- Department of Medical Informatics and Clinical Epidemiology,
Oregon Health & Science University, Portland, OR, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University, Baltimore, MD, USA
| | - Ingrid A. Holm
- Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and the Manton Center for
Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Lijia Huang
- The Children's Hospital of Eastern Ontario Research Institute,
Ottawa, ON, Canada
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Ben Hutton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Joel B. Krier
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA 02115, USA
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | - Justin Paschall
- European Molecular Biology Laboratory - European
Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD,
UK
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, 1156 High Street, Santa
Cruz, CA, USA
| | - Peter N. Robinson
- Institute for Medical Genetics and Human Genetics,
Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin,
Germany
- Institute for Bioinformatics, Department of Mathematics and
Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin Brandenburg Center for Regenerative Therapies, 13353
Berlin, Germany
| | | | - Nara L. Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University, Baltimore, MD, USA
| | - Ganesh J. Swaminathan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Peter E. Taschner
- Department of Medical Informatics and Clinical Epidemiology,
Oregon Health & Science University, Portland, OR, USA
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA 02115, USA
| | | | | | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics
and John P. Hussman Institute for Human Genomics, University of Miami Miller School of
Medicine, Miami, FL, USA
| | - Kym M. Boycott
- Department of Genetics, Children's Hospital of Eastern
Ontario, Ottawa, Ontario, Canada
| | - Heidi L. Rehm
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Laboratory for Molecular Medicine, Partners Personalized
Medicine, Boston, MA USA
- Department of Pathology, Brigham & Women's Hospital, Boston,
MA, USA
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