1
|
Jeffries L, Mis EK, McWalter K, Donkervoort S, Brodsky NN, Carpier JM, Ji W, Ionita C, Roy B, Morrow JS, Darbinyan A, Iyer K, Aul RB, Banka S, Chao KR, Cobbold L, Cohen S, Custodio HM, Drummond-Borg M, Elmslie F, Finanger E, Hainline BE, Helbig I, Hewson S, Hu Y, Jackson A, Josifova D, Konstantino M, Leach ME, Mak B, McCormick D, McGee E, Nelson S, Nguyen J, Nugent K, Ortega L, Goodkin HP, Roeder E, Roy S, Sapp K, Saade D, Sisodiya SM, Stals K, Towner S, Wilson W, Khokha MK, Bönnemann CG, Lucas CL, Lakhani SA. Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections. Genet Med 2024; 26:101023. [PMID: 37947183 PMCID: PMC10932913 DOI: 10.1016/j.gim.2023.101023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
PURPOSE We sought to delineate a multisystem disorder caused by recessive cysteine-rich with epidermal growth factor-like domains 1 (CRELD1) gene variants. METHODS The impact of CRELD1 variants was characterized through an international collaboration utilizing next-generation DNA sequencing, gene knockdown, and protein overexpression in Xenopus tropicalis, and in vitro analysis of patient immune cells. RESULTS Biallelic variants in CRELD1 were found in 18 participants from 14 families. Affected individuals displayed an array of phenotypes involving developmental delay, early-onset epilepsy, and hypotonia, with about half demonstrating cardiac arrhythmias and some experiencing recurrent infections. Most harbored a frameshift in trans with a missense allele, with 1 recurrent variant, p.(Cys192Tyr), identified in 10 families. X tropicalis tadpoles with creld1 knockdown displayed developmental defects along with increased susceptibility to induced seizures compared with controls. Additionally, human CRELD1 harboring missense variants from affected individuals had reduced protein function, indicated by a diminished ability to induce craniofacial defects when overexpressed in X tropicalis. Finally, baseline analyses of peripheral blood mononuclear cells showed similar proportions of immune cell subtypes in patients compared with healthy donors. CONCLUSION This patient cohort, combined with experimental data, provide evidence of a multisystem clinical syndrome mediated by recessive variants in CRELD1.
Collapse
Affiliation(s)
- Lauren Jeffries
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT
| | - Emily K Mis
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT
| | | | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Nina N Brodsky
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT; Yale University School of Medicine, Department of Immunobiology, New Haven, CT
| | - Jean-Marie Carpier
- Yale University School of Medicine, Department of Immunobiology, New Haven, CT
| | - Weizhen Ji
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT
| | - Cristian Ionita
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT
| | - Bhaskar Roy
- Yale University School of Medicine, Department of Neurology, New Haven, CT
| | - Jon S Morrow
- Yale University School of Medicine, Department of Pathology, New Haven, CT
| | - Armine Darbinyan
- Yale University School of Medicine, Department of Pathology, New Haven, CT
| | - Krishna Iyer
- Yale University School of Medicine, Department of Pathology, New Haven, CT
| | - Ritu B Aul
- Hospital for Sick Children, Division of Clinical and Metabolic Genetics, Toronto, Ontario, Canada
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Katherine R Chao
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Laura Cobbold
- South West Thames Regional Genetics Service, St George's, University of London, London, United Kingdom
| | - Stacey Cohen
- Children's Hospital of Philadelphia, Division of Neurology, Philadelphia, PA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA; University of Pennsylvania Perelman School of Medicine, Department of Neurology, Philadelphia, PA
| | - Helena M Custodio
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, WC1N 3BG, United Kingdom; Chalfont Centre for Epilepsy, Buckinghamshire, United Kingdom
| | | | - Frances Elmslie
- South West Thames Regional Genetics Service, St George's, University of London, London, United Kingdom
| | | | - Bryan E Hainline
- Indiana University School of Medicine, Indiana University Health Physicians, Indianapolis, IN
| | - Ingo Helbig
- Children's Hospital of Philadelphia, Division of Neurology, Philadelphia, PA; University of Pennsylvania Perelman School of Medicine, Department of Neurology, Philadelphia, PA
| | - Stacy Hewson
- Hospital for Sick Children, Division of Clinical and Metabolic Genetics, Toronto, Ontario, Canada
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Dragana Josifova
- Guys and St Thomas NHS Trust, Clinical Genetics, London, United Kingdom
| | | | | | - Bryan Mak
- University of California Los Angeles, David Geffen School of Medicine, Department of Human Genetics, Los Angeles, CA; Current affiliation: Genome Medical, South San Francisco, CA
| | - David McCormick
- King's College Hospital, Paediatric Neurosciences, London, United Kingdom
| | - Elisabeth McGee
- University of California Los Angeles, David Geffen School of Medicine, Department of Human Genetics, Los Angeles, CA; University of California Los Angeles, Clinical Genomics Center, Los Angeles, CA; University of California Los Angeles, Center for Duchenne Muscular Dystrophy, Los Angeles, CA
| | - Stanley Nelson
- University of California Los Angeles, David Geffen School of Medicine, Department of Human Genetics, Los Angeles, CA; University of California Los Angeles, Clinical Genomics Center, Los Angeles, CA; University of California Los Angeles, Center for Duchenne Muscular Dystrophy, Los Angeles, CA
| | - Joanne Nguyen
- Cook Children's Medical Center, Division of Genetics, Fort Worth, TX
| | - Kimberly Nugent
- Baylor College of Medicine, Department of Pediatrics, Houston, TX; Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX; Current affiliation: Cooper Surgical, Trumbull, CT
| | - Lucy Ortega
- Cook Children's Medical Center, Division of Genetics, Fort Worth, TX
| | | | - Elizabeth Roeder
- Baylor College of Medicine, Department of Pediatrics, Houston, TX; Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX
| | - Sani Roy
- Cook Children's Medical Center, Division of Endocrinology and Diabetes, Fort Worth, TX
| | - Katie Sapp
- Indiana University School of Medicine, Indiana University Health Physicians, Indianapolis, IN
| | - Dimah Saade
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD; Current affiliation: University of Iowa Carver College of Medicine, Iowa City, IA
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, WC1N 3BG, United Kingdom; Chalfont Centre for Epilepsy, Buckinghamshire, United Kingdom
| | - Karen Stals
- Royal Devon & Exeter NHS Foundation Trust, Exeter Genomics Laboratory, Exeter, United Kingdom
| | - Shelley Towner
- University of Virginia School of Medicine, Charlottesville, VA
| | - William Wilson
- University of Virginia School of Medicine, Charlottesville, VA
| | - Mustafa K Khokha
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT; Yale University School of Medicine, Department of Genetics, New Haven, CT
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Carrie L Lucas
- Yale Pediatric Genomics Discovery Program, New Haven, CT; Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Saquib A Lakhani
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT.
| |
Collapse
|
2
|
Sullivan JA, Spillmann RC, Schoch K, Walley N, Alkelai A, Stong N, Shea PR, Petrovski S, Jobanputra V, McConkie-Rosell A, Shashi V. The best of both worlds: Blending cutting-edge research with clinical processes for a productive exome clinic. Clin Genet 2024; 105:62-71. [PMID: 37853563 DOI: 10.1111/cge.14437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Genomic medicine has been transformed by next-generation sequencing (NGS), inclusive of exome sequencing (ES) and genome sequencing (GS). Currently, ES is offered widely in clinical settings, with a less prevalent alternative model consisting of hybrid programs that incorporate research ES along with clinical patient workflows. We were among the earliest to implement a hybrid ES clinic, have provided diagnoses to 45% of probands, and have identified several novel candidate genes. Our program is enabled by a cost-effective investment by the health system and is unique in encompassing all the processes that have been variably included in other hybrid/clinical programs. These include careful patient selection, utilization of a phenotype-agnostic bioinformatics pipeline followed by manual curation of variants and phenotype integration by clinicians, close collaborations between the clinicians and the bioinformatician, pursuit of interesting variants, communication of results to patients in categories that are predicated upon the certainty of a diagnosis, and tracking changes in results over time and the underlying mechanisms for such changes. Due to its effectiveness, scalability to GS and its resource efficiency, specific elements of our paradigm can be incorporated into existing clinical settings, or the entire hybrid model can be implemented within health systems that have genomic medicine programs, to provide NGS in a scientifically rigorous, yet pragmatic setting.
Collapse
Affiliation(s)
- Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Nicole Walley
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, USA
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Genomics and Bioinformatics Analysis Resource, Columbia University, New York, New York, USA
| | - Slavè Petrovski
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| |
Collapse
|