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Chao KR, Wang L, Panchal R, Liao C, Abderrazzaq H, Ye R, Schultz P, Compitello J, Grant RH, Kosmicki JA, Weisburd B, Phu W, Wilson MW, Laricchia KM, Goodrich JK, Goldstein D, Goldstein JI, Vittal C, Poterba T, Baxter S, Watts NA, Solomonson M, Tiao G, Rehm HL, Neale BM, Talkowski ME, MacArthur DG, O'Donnell-Luria A, Karczewski KJ, Radivojac P, Daly MJ, Samocha KE. The landscape of regional missense mutational intolerance quantified from 125,748 exomes. bioRxiv 2024:2024.04.11.588920. [PMID: 38645134 PMCID: PMC11030311 DOI: 10.1101/2024.04.11.588920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Missense variants can have a range of functional impacts depending on factors such as the specific amino acid substitution and location within the gene. To interpret their deleteriousness, studies have sought to identify regions within genes that are specifically intolerant of missense variation 1-12 . Here, we leverage the patterns of rare missense variation in 125,748 individuals in the Genome Aggregation Database (gnomAD) 13 against a null mutational model to identify transcripts that display regional differences in missense constraint. Missense-depleted regions are enriched for ClinVar 14 pathogenic variants, de novo missense variants from individuals with neurodevelopmental disorders (NDDs) 15,16 , and complex trait heritability. Following ClinGen calibration recommendations for the ACMG/AMP guidelines, we establish that regions with less than 20% of their expected missense variation achieve moderate support for pathogenicity. We create a missense deleteriousness metric (MPC) that incorporates regional constraint and outperforms other deleteriousness scores at stratifying case and control de novo missense variation, with a strong enrichment in NDDs. These results provide additional tools to aid in missense variant interpretation.
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2
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Lemire G, Sanchis-Juan A, Russell K, Baxter S, Chao KR, Singer-Berk M, Groopman E, Wong I, England E, Goodrich J, Pais L, Austin-Tse C, DiTroia S, O'Heir E, Ganesh VS, Wojcik MH, Evangelista E, Snow H, Osei-Owusu I, Fu J, Singh M, Mostovoy Y, Huang S, Garimella K, Kirkham SL, Neil JE, Shao DD, Walsh CA, Argilli E, Le C, Sherr EH, Gleeson JG, Shril S, Schneider R, Hildebrandt F, Sankaran VG, Madden JA, Genetti CA, Beggs AH, Agrawal PB, Bujakowska KM, Place E, Pierce EA, Donkervoort S, Bönnemann CG, Gallacher L, Stark Z, Tan TY, White SM, Töpf A, Straub V, Fleming MD, Pollak MR, Õunap K, Pajusalu S, Donald KA, Bruwer Z, Ravenscroft G, Laing NG, MacArthur DG, Rehm HL, Talkowski ME, Brand H, O'Donnell-Luria A. Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease. Am J Hum Genet 2024; 111:863-876. [PMID: 38565148 PMCID: PMC11080278 DOI: 10.1016/j.ajhg.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and, with new innovative methods, can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the Genomics Research to Elucidate the Genetics of Rare Diseases consortium and analyzed using the seqr platform. The addition of CNV detection to exome analysis identified causal CNVs for 171 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb. The causal CNVs consisted of 140 deletions, 15 duplications, 3 suspected complex structural variants (SVs), 3 insertions, and 10 complex SVs, the latter two groups being identified by orthogonal confirmation methods. To classify CNV variant pathogenicity, we used the 2020 American College of Medical Genetics and Genomics/ClinGen CNV interpretation standards and developed additional criteria to evaluate allelic and functional data as well as variants on the X chromosome to further advance the framework. We interpreted 151 CNVs as likely pathogenic/pathogenic and 20 CNVs as high-interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher-resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.
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Affiliation(s)
- Gabrielle Lemire
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Alba Sanchis-Juan
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn Russell
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha Baxter
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine R Chao
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moriel Singer-Berk
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily Groopman
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Isaac Wong
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eleina England
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Julia Goodrich
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lynn Pais
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christina Austin-Tse
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Stephanie DiTroia
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily O'Heir
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Vijay S Ganesh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Monica H Wojcik
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Emily Evangelista
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hana Snow
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack Fu
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mugdha Singh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yulia Mostovoy
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steve Huang
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kiran Garimella
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha L Kirkham
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Jennifer E Neil
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Diane D Shao
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Emanuela Argilli
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Carolyn Le
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Shirlee Shril
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Ronen Schneider
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Alan H Beggs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Pankaj B Agrawal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Kinga M Bujakowska
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Emily Place
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Eric A Pierce
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Tiong Yang Tan
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Mark D Fleming
- Harvard Medical School, Boston, MA, USA; Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Martin R Pollak
- Harvard Medical School, Boston, MA, USA; Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Genetics and Personalized Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Department of Genetics and Personalized Medicine, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Zandre Bruwer
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Gianina Ravenscroft
- University of Western Australia Centre for Medical Research, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Nigel G Laing
- University of Western Australia Centre for Medical Research, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Daniel G MacArthur
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Heidi L Rehm
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E Talkowski
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Harrison Brand
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
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3
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Silverstein S, Orbach R, Syeda S, Foley AR, Gorokhova S, Meilleur KG, Leach ME, Uapinyoying P, Chao KR, Donkervoort S, Bönnemann CG. Differential inclusion of NEB exons 143 and 144 provides insight into NEB-related myopathy variant interpretation and disease manifestation. medRxiv 2024:2024.03.25.24304535. [PMID: 38585796 PMCID: PMC10996755 DOI: 10.1101/2024.03.25.24304535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Biallelic pathogenic variants in the gene encoding nebulin (NEB) are a known cause of congenital myopathy. We present two individuals with congenital myopathy and compound heterozygous variants (NM_001271208.2: c.2079C>A; p.(Cys693Ter) and c.21522+3A>G ) in NEB. Transcriptomic sequencing on patient muscle revealed that the extended splice variant c.21522+3A>G causes exon 144 skipping. Nebulin isoforms containing exon 144 are known to be mutually exclusive with isoforms containing exon 143, and these isoforms are differentially expressed during development and in adult skeletal muscles. Patients MRIs were compared to the known pattern of relative abundance of these two isoforms in muscle. We propose that the pattern of muscle involvement in these patients better fits the distribution of exon 144-containing isoforms in muscle than with previously published MRI findings in NEB-related disease due to other variants. To our knowledge this is the first report hypothesizing disease pathogenesis through the alteration of isoform distributions in muscle.
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Affiliation(s)
- Sarah Silverstein
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
- Rutgers New Jersey School of Medicine, 185 S Orange Ave Newark NJ 07103 USA
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland 20892, USA
| | - Rotem Orbach
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Safoora Syeda
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Svetlana Gorokhova
- Aix Marseille Univ, INSERM, MMG, U 1251, Marseille, France
- Department of Medical Genetics, Timone Children’s Hospital, APHM, Marseille, France
| | - Katherine G. Meilleur
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
- Biogen, Boston MA
| | - Meganne E. Leach
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
- Division of Neurology, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd, Portland, OR
| | - Prech Uapinyoying
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
- Research Center for Genetic Medicine, Children’s National Research Institute, Children’s National Medical Center, Washington DC 20010
| | - Katherine R Chao
- Broad Institute of MIT and Harvard, 415 Main St. Cambridge MA 02142
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Carsten G. Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
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4
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Koenig Z, Yohannes MT, Nkambule LL, Zhao X, Goodrich JK, Kim HA, Wilson MW, Tiao G, Hao SP, Sahakian N, Chao KR, Walker MA, Lyu Y, Rehm HL, Neale BM, Talkowski ME, Daly MJ, Brand H, Karczewski KJ, Atkinson EG, Martin AR. A harmonized public resource of deeply sequenced diverse human genomes. bioRxiv 2024:2023.01.23.525248. [PMID: 36747613 PMCID: PMC9900804 DOI: 10.1101/2023.01.23.525248] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Underrepresented populations are often excluded from genomic studies due in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequenced to high coverage, are valuable genomic resources because of the global diversity they capture and their open data sharing policies. Here, we harmonized a high quality set of 4,094 whole genomes from HGDP and 1kGP with data from the Genome Aggregation Database (gnomAD) and identified over 153 million high-quality SNVs, indels, and SVs. We performed a detailed ancestry analysis of this cohort, characterizing population structure and patterns of admixture across populations, analyzing site frequency spectra, and measuring variant counts at global and subcontinental levels. We also demonstrate substantial added value from this dataset compared to the prior versions of the component resources, typically combined via liftover and variant intersection; for example, we catalog millions of new genetic variants, mostly rare, compared to previous releases. In addition to unrestricted individual-level public release, we provide detailed tutorials for conducting many of the most common quality control steps and analyses with these data in a scalable cloud-computing environment and publicly release this new phased joint callset for use as a haplotype resource in phasing and imputation pipelines. This jointly called reference panel will serve as a key resource to support research of diverse ancestry populations.
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Affiliation(s)
- Zan Koenig
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary T. Yohannes
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lethukuthula L. Nkambule
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Julia K. Goodrich
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heesu Ally Kim
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael W. Wilson
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Grace Tiao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stephanie P. Hao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Nareh Sahakian
- Broad Genomics, The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA
| | - Katherine R. Chao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark A. Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yunfei Lyu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Heidi L. Rehm
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin M. Neale
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael E. Talkowski
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Mark J. Daly
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Harrison Brand
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Konrad J. Karczewski
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Elizabeth G. Atkinson
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alicia R. Martin
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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6
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Syeda SB, Lone MA, Mohassel P, Donkervoort S, Munot P, França MC, Galarza-Brito JE, Eckenweiler M, Asamoah A, Gable K, Majumdar A, Schumann A, Gupta SD, Lakhotia A, Shieh PB, Foley AR, Jackson KE, Chao KR, Winder TL, Catapano F, Feng L, Kirschner J, Muntoni F, Dunn TM, Hornemann T, Bönnemann CG. Recurrent de novo SPTLC2 variant causes childhood-onset amyotrophic lateral sclerosis (ALS) by excess sphingolipid synthesis. J Neurol Neurosurg Psychiatry 2024; 95:103-113. [PMID: 38041679 PMCID: PMC10850718 DOI: 10.1136/jnnp-2023-332132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/27/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of the upper and lower motor neurons with varying ages of onset, progression and pathomechanisms. Monogenic childhood-onset ALS, although rare, forms an important subgroup of ALS. We recently reported specific SPTLC1 variants resulting in sphingolipid overproduction as a cause for juvenile ALS. Here, we report six patients from six independent families with a recurrent, de novo, heterozygous variant in SPTLC2 c.778G>A [p.Glu260Lys] manifesting with juvenile ALS. METHODS Clinical examination of the patients along with ancillary and genetic testing, followed by biochemical investigation of patients' blood and fibroblasts, was performed. RESULTS All patients presented with early-childhood-onset progressive weakness, with signs and symptoms of upper and lower motor neuron degeneration in multiple myotomes, without sensory neuropathy. These findings were supported on ancillary testing including nerve conduction studies and electromyography, muscle biopsies and muscle ultrasound studies. Biochemical investigations in plasma and fibroblasts showed elevated levels of ceramides and unrestrained de novo sphingolipid synthesis. Our studies indicate that SPTLC2 variant [c.778G>A, p.Glu260Lys] acts distinctly from hereditary sensory and autonomic neuropathy (HSAN)-causing SPTLC2 variants by causing excess canonical sphingolipid biosynthesis, similar to the recently reported SPTLC1 ALS associated pathogenic variants. Our studies also indicate that serine supplementation, which is a therapeutic in SPTLC1 and SPTCL2-associated HSAN, is expected to exacerbate the excess sphingolipid synthesis in serine palmitoyltransferase (SPT)-associated ALS. CONCLUSIONS SPTLC2 is the second SPT-associated gene that underlies monogenic, juvenile ALS and further establishes alterations of sphingolipid metabolism in motor neuron disease pathogenesis. Our findings also have important therapeutic implications: serine supplementation must be avoided in SPT-associated ALS, as it is expected to drive pathogenesis further.
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Affiliation(s)
- Safoora B Syeda
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Museer A Lone
- Institute of Clinical Chemistry, University Hospital Zürich, Zürich, Switzerland
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Pinki Munot
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Marcondes C França
- Department of Neurology, University of Campinas, Campinas, Sao Paulo, Brazil
| | | | - Matthias Eckenweiler
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Alexander Asamoah
- Norton Children's Medical Group, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, Maryland, USA
| | - Anirban Majumdar
- Department of Paediatric Neurology, Bristol Children's Hospital, Bristol, UK
| | - Anke Schumann
- Department of Paediatrics and Adolescent Medicine, Faculty of Medicine, Medical Centre, University of Freiburg, Baden-Württemberg, Germany
| | - Sita D Gupta
- Department of Biochemistry and Molecular Biology, Uniformed Services University, Bethesda, Maryland, USA
| | - Arpita Lakhotia
- Norton Children's Medical Group, University of Louisville School of Medicine, Louisville, KY, USA
- University of Louisville, Louisville, Kentucky, USA
| | - Perry B Shieh
- Department of Neurology and Pediatrics, University of California Los Angeles, Los Angeles, CA, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kelly E Jackson
- Norton Children's Medical Group, University of Louisville School of Medicine, Louisville, KY, USA
| | - Katherine R Chao
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Francesco Catapano
- Dubowitz Neuromuscular Centre, CL Great Ormond Street Institute of Child Health and Great Ormond Street Hospital, London, UK
| | - Lucy Feng
- Dubowitz Neuromuscular Centre, CL Great Ormond Street Institute of Child Health and Great Ormond Street Hospital, London, UK
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Francesco Muntoni
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- Dubowitz Neuromuscular Centre, CL Great Ormond Street Institute of Child Health and Great Ormond Street Hospital, London, UK
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, USA
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital Zürich, Zürich, Switzerland
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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7
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Lemire G, Sanchis-Juan A, Russell K, Baxter S, Chao KR, Singer-Berk M, Groopman E, Wong I, England E, Goodrich J, Pais L, Austin-Tse C, DiTroia S, O’Heir E, Ganesh VS, Wojcik MH, Evangelista E, Snow H, Osei-Owusu I, Fu J, Singh M, Mostovoy Y, Huang S, Garimella K, Kirkham SL, Neil JE, Shao DD, Walsh CA, Argili E, Le C, Sherr EH, Gleeson J, Shril S, Schneider R, Hildebrandt F, Sankaran VG, Madden JA, Genetti CA, Beggs AH, Agrawal PB, Bujakowska KM, Place E, Pierce EA, Donkervoort S, Bönnemann CG, Gallacher L, Stark Z, Tan T, White SM, Töpf A, Straub V, Fleming MD, Pollak MR, Õunap K, Pajusalu S, Donald KA, Bruwer Z, Ravenscroft G, Laing NG, MacArthur DG, Rehm HL, Talkowski ME, Brand H, O’Donnell-Luria A. Exome copy number variant detection, analysis and classification in a large cohort of families with undiagnosed rare genetic disease. medRxiv 2023:2023.10.05.23296595. [PMID: 37873196 PMCID: PMC10593084 DOI: 10.1101/2023.10.05.23296595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and with new innovative methods can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the GREGoR consortium. Each family's CNV data was analyzed using the seqr platform and candidate CNVs classified using the 2020 ACMG/ClinGen CNV interpretation standards. We developed additional evidence criteria to address situations not covered by the current standards. The addition of CNV calling to exome analysis identified causal CNVs for 173 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb with estimates that 44% would not have been detected by standard chromosomal microarrays. The causal CNVs consisted of 141 deletions, 15 duplications, 4 suspected complex structural variants (SVs), 3 insertions and 10 complex SVs, the latter two groups being identified by orthogonal validation methods. We interpreted 153 CNVs as likely pathogenic/pathogenic and 20 CNVs as high interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.
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Affiliation(s)
- Gabrielle Lemire
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- These authors contributed equally
| | - Alba Sanchis-Juan
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- These authors contributed equally
| | - Kathryn Russell
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha Baxter
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine R. Chao
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Moriel Singer-Berk
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily Groopman
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eleina England
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Goodrich
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lynn Pais
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christina Austin-Tse
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Stephanie DiTroia
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emily O’Heir
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Vijay S. Ganesh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Monica H. Wojcik
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Emily Evangelista
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hana Snow
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ikeoluwa Osei-Owusu
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jack Fu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mugdha Singh
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yulia Mostovoy
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steve Huang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kiran Garimella
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha L. Kirkham
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
| | - Jennifer E. Neil
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
| | - Diane D. Shao
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Christopher A. Walsh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
| | - Emanuela Argili
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Carolyn Le
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Elliott H. Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | - Shirlee Shril
- Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
| | - Ronen Schneider
- Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
| | - Vijay G. Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jill A. Madden
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
| | - Casie A. Genetti
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
| | - Alan H. Beggs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
| | - Pankaj B. Agrawal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, USA
| | - Kinga M. Bujakowska
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Emily Place
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Eric A. Pierce
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carsten G. Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Tiong Tan
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Susan M. White
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Mark D. Fleming
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Boston Children’s Hospital, Boston, MA, USA
| | - Martin R. Pollak
- Harvard Medical School, Boston, MA, USA
- Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kirsten A. Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- University of Cape Town, Cape Town, South Africa
| | - Zandre Bruwer
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- University of Cape Town, Cape Town, South Africa
| | - Gianina Ravenscroft
- University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Australia
| | - Nigel G. Laing
- University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Australia
| | - Daniel G. MacArthur
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute, Sydney, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Heidi L. Rehm
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael E. Talkowski
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Harrison Brand
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Senior authors
| | - Anne O’Donnell-Luria
- Broad Institute Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Senior authors
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8
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Wojcik MH, Lemire G, Zaki MS, Wissman M, Win W, White S, Weisburd B, Waddell LB, Verboon JM, VanNoy GE, Töpf A, Tan TY, Straub V, Stenton SL, Snow H, Singer-Berk M, Silver J, Shril S, Seaby EG, Schneider R, Sankaran VG, Sanchis-Juan A, Russell KA, Reinson K, Ravenscroft G, Pierce EA, Place EM, Pajusalu S, Pais L, Õunap K, Osei-Owusu I, Okur V, Oja KT, O'Leary M, O'Heir E, Morel C, Marchant RG, Mangilog BE, Madden JA, MacArthur D, Lovgren A, Lerner-Ellis JP, Lin J, Laing N, Hildebrandt F, Groopman E, Goodrich J, Gleeson JG, Ghaoui R, Genetti CA, Gazda HT, Ganesh VS, Ganapathy M, Gallacher L, Fu J, Evangelista E, England E, Donkervoort S, DiTroia S, Cooper ST, Chung WK, Christodoulou J, Chao KR, Cato LD, Bujakowska KM, Bryen SJ, Brand H, Bonnemann C, Beggs AH, Baxter SM, Agrawal PB, Talkowski M, Austin-Tse C, Rehm HL, O'Donnell-Luria A. Unique Capabilities of Genome Sequencing for Rare Disease Diagnosis. medRxiv 2023:2023.08.08.23293829. [PMID: 38328047 PMCID: PMC10849673 DOI: 10.1101/2023.08.08.23293829] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Background Causal variants underlying rare disorders may remain elusive even after expansive gene panels or exome sequencing (ES). Clinicians and researchers may then turn to genome sequencing (GS), though the added value of this technique and its optimal use remain poorly defined. We therefore investigated the advantages of GS within a phenotypically diverse cohort. Methods GS was performed for 744 individuals with rare disease who were genetically undiagnosed. Analysis included review of single nucleotide, indel, structural, and mitochondrial variants. Results We successfully solved 218/744 (29.3%) cases using GS, with most solves involving established disease genes (157/218, 72.0%). Of all solved cases, 148 (67.9%) had previously had non-diagnostic ES. We systematically evaluated the 218 causal variants for features requiring GS to identify and 61/218 (28.0%) met these criteria, representing 8.2% of the entire cohort. These included small structural variants (13), copy neutral inversions and complex rearrangements (8), tandem repeat expansions (6), deep intronic variants (15), and coding variants that may be more easily found using GS related to uniformity of coverage (19). Conclusion We describe the diagnostic yield of GS in a large and diverse cohort, illustrating several types of pathogenic variation eluding ES or other techniques. Our results reveal a higher diagnostic yield of GS, supporting the utility of a genome-first approach, with consideration of GS as a secondary or tertiary test when higher-resolution structural variant analysis is needed or there is a strong clinical suspicion for a condition and prior targeted genetic testing has been negative.
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9
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Morales-Rosado JA, Schwab TL, Macklin-Mantia SK, Foley AR, Pinto E Vairo F, Pehlivan D, Donkervoort S, Rosenfeld JA, Boyum GE, Hu Y, Cong ATQ, Lotze TE, Mohila CA, Saade D, Bharucha-Goebel D, Chao KR, Grunseich C, Bruels CC, Littel HR, Estrella EA, Pais L, Kang PB, Zimmermann MT, Lupski JR, Lee B, Schellenberg MJ, Clark KJ, Wierenga KJ, Bönnemann CG, Klee EW. Bi-allelic variants in HMGCR cause an autosomal-recessive progressive limb-girdle muscular dystrophy. Am J Hum Genet 2023; 110:989-997. [PMID: 37167966 PMCID: PMC10257193 DOI: 10.1016/j.ajhg.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
Statins are a mainstay intervention for cardiovascular disease prevention, yet their use can cause rare severe myopathy. HMG-CoA reductase, an essential enzyme in the mevalonate pathway, is the target of statins. We identified nine individuals from five unrelated families with unexplained limb-girdle like muscular dystrophy and bi-allelic variants in HMGCR via clinical and research exome sequencing. The clinical features resembled other genetic causes of muscular dystrophy with incidental high CPK levels (>1,000 U/L), proximal muscle weakness, variable age of onset, and progression leading to impaired ambulation. Muscle biopsies in most affected individuals showed non-specific dystrophic changes with non-diagnostic immunohistochemistry. Molecular modeling analyses revealed variants to be destabilizing and affecting protein oligomerization. Protein activity studies using three variants (p.Asp623Asn, p.Tyr792Cys, and p.Arg443Gln) identified in affected individuals confirmed decreased enzymatic activity and reduced protein stability. In summary, we showed that individuals with bi-allelic amorphic (i.e., null and/or hypomorphic) variants in HMGCR display phenotypes that resemble non-genetic causes of myopathy involving this reductase. This study expands our knowledge regarding the mechanisms leading to muscular dystrophy through dysregulation of the mevalonate pathway, autoimmune myopathy, and statin-induced myopathy.
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Affiliation(s)
- Joel A Morales-Rosado
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Tanya L Schwab
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MM, USA
| | - Sarah K Macklin-Mantia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics at Mayo Clinic, Jacksonville, FL, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA; Division of Neurology and Developmental Neuroscience and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA; Baylor Genetics Laboratories, Houston, TX, USA
| | - Grace E Boyum
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MM, USA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Anh T Q Cong
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MM, USA
| | - Timothy E Lotze
- Division of Neurology and Developmental Neuroscience and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Carrie A Mohila
- Department of Pathology & Immunology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Dimah Saade
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Diana Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA; Division of Neurology, Children's National Hospital, Washington, DC, USA
| | - Katherine R Chao
- Program in Medical and Population Genetics, Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher Grunseich
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Christine C Bruels
- Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Hannah R Littel
- Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Elicia A Estrella
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lynn Pais
- Program in Medical and Population Genetics, Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, USA; Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Peter B Kang
- Paul and Sheila Wellstone Muscular Dystrophy Center and Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, USA; Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | | | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MM, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics at Mayo Clinic, Jacksonville, FL, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA; Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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10
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Averdunk L, Donkervoort S, Horn D, Waldmüller S, Syeda S, Neuhaus SB, Chao KR, van Riesen A, Gauck D, Haack T, Japp AS, Lee U, Bönnemann CG, Mayatepek E, Distelmaier F. Recognizable Pattern of Arthrogryposis and Congenital Myopathy Caused by the Recurrent TTN Metatranscript-only c.39974-11T > G Splice Variant. Neuropediatrics 2022; 53:309-320. [PMID: 35605965 DOI: 10.1055/a-1859-0800] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Arthrogryposis is characterized by the presence of multiple contractures at birth and can be caused by pathogenic variants in TTN (Titin). Exons and variants that are not expressed in one of the three major isoforms of titin are referred to as "metatranscript-only" and have been considered to be only expressed during fetal development. Recently, the metatranscript-only variant (c.39974-11T > G) in TTN with a second truncating TTN variant has been linked to arthrogryposis multiplex congenita and myopathy. METHODS Via exome sequencing we identified the TTN c.39974-11T > G splice variant in trans with one of three truncating variants (p.Arg8922*, p.Lys32998Asnfs*63, p.Tyr10345*) in five individuals from three families. Clinical presentation and muscle ultrasound as well as MRI images were analyzed. RESULTS All five patients presented with generalized muscular hypotonia, reduced muscle bulk, and congenital contractures most prominently affecting the upper limbs and distal joints. Muscular hypotonia persisted and contractures improved over time. One individual, the recipient twin in the setting of twin-to-twin transfusion syndrome, died from severe cardiac hypertrophy 1 day after birth. Ultrasound and MRI imaging studies revealed a recognizable pattern of muscle involvement with striking fibrofatty involvement of the hamstrings and calves, and relative sparing of the femoral adductors and anterior segment of the thighs. CONCLUSION The recurrent TTN c.39974-11T > G variant consistently causes congenital arthrogryposis and persisting myopathy providing evidence that the metatranscript-only 213 to 217 exons impact muscle elasticity during early development and beyond. There is a recognizable pattern of muscle involvement, which is distinct from other myopathies and provides valuable clues for diagnostic work-up.
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Affiliation(s)
- Luisa Averdunk
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Stephan Waldmüller
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Safoora Syeda
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sarah B Neuhaus
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States
| | - Katherine R Chao
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
| | - Anne van Riesen
- Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department of Pediatric Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Darja Gauck
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Anna S Japp
- Institute of Pathology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Unaa Lee
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany
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11
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Karczewski KJ, Solomonson M, Chao KR, Goodrich JK, Tiao G, Lu W, Riley-Gillis BM, Tsai EA, Kim HI, Zheng X, Rahimov F, Esmaeeli S, Grundstad AJ, Reppell M, Waring J, Jacob H, Sexton D, Bronson PG, Chen X, Hu X, Goldstein JI, King D, Vittal C, Poterba T, Palmer DS, Churchhouse C, Howrigan DP, Zhou W, Watts NA, Nguyen K, Nguyen H, Mason C, Farnham C, Tolonen C, Gauthier LD, Gupta N, MacArthur DG, Rehm HL, Seed C, Philippakis AA, Daly MJ, Davis JW, Runz H, Miller MR, Neale BM. Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes. Cell Genom 2022; 2:100168. [PMID: 36778668 PMCID: PMC9903662 DOI: 10.1016/j.xgen.2022.100168] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 07/16/2022] [Indexed: 01/20/2023]
Abstract
Genome-wide association studies have successfully discovered thousands of common variants associated with human diseases and traits, but the landscape of rare variations in human disease has not been explored at scale. Exome-sequencing studies of population biobanks provide an opportunity to systematically evaluate the impact of rare coding variations across a wide range of phenotypes to discover genes and allelic series relevant to human health and disease. Here, we present results from systematic association analyses of 4,529 phenotypes using single-variant and gene tests of 394,841 individuals in the UK Biobank with exome-sequence data. We find that the discovery of genetic associations is tightly linked to frequency and is correlated with metrics of deleteriousness and natural selection. We highlight biological findings elucidated by these data and release the dataset as a public resource alongside the Genebass browser for rapidly exploring rare-variant association results.
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Affiliation(s)
- Konrad J. Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Katherine R. Chao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julia K. Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wenhan Lu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Hye In Kim
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Xiuwen Zheng
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Fedik Rahimov
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Sahar Esmaeeli
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | - Mark Reppell
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Jeff Waring
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Howard Jacob
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | | | - Xing Chen
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Xinli Hu
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Jacqueline I. Goldstein
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel King
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher Vittal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy Poterba
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Duncan S. Palmer
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claire Churchhouse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel P. Howrigan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas A. Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kevin Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Huy Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cara Mason
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christopher Farnham
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Charlotte Tolonen
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Laura D. Gauthier
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Namrata Gupta
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cotton Seed
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mark J. Daly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - J. Wade Davis
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | | | - Melissa R. Miller
- Worldwide Research Development and Medical, Pfizer, Inc., Cambridge, MA 02139, USA
| | - Benjamin M. Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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12
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Pais LS, Snow H, Weisburd B, Zhang S, Baxter SM, DiTroia S, O’Heir E, England E, Chao KR, Lemire G, Osei-Owusu I, VanNoy GE, Wilson M, Nguyen K, Arachchi H, Phu W, Solomonson M, Mano S, O’Leary M, Lovgren A, Babb L, Austin-Tse CA, Rehm HL, MacArthur DG, O’Donnell-Luria A. seqr: A web-based analysis and collaboration tool for rare disease genomics. Hum Mutat 2022; 43:698-707. [PMID: 35266241 PMCID: PMC9903206 DOI: 10.1002/humu.24366] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/23/2022] [Accepted: 03/04/2022] [Indexed: 02/04/2023]
Abstract
Exome and genome sequencing have become the tools of choice for rare disease diagnosis, leading to large amounts of data available for analyses. To identify causal variants in these datasets, powerful filtering and decision support tools that can be efficiently used by clinicians and researchers are required. To address this need, we developed seqr - an open-source, web-based tool for family-based monogenic disease analysis that allows researchers to work collaboratively to search and annotate genomic callsets. To date, seqr is being used in several research pipelines and one clinical diagnostic lab. In our own experience through the Broad Institute Center for Mendelian Genomics, seqr has enabled analyses of over 10,000 families, supporting the diagnosis of more than 3,800 individuals with rare disease and discovery of over 300 novel disease genes. Here, we describe a framework for genomic analysis in rare disease that leverages seqr's capabilities for variant filtration, annotation, and causal variant identification, as well as support for research collaboration and data sharing. The seqr platform is available as open source software, allowing low-cost participation in rare disease research, and a community effort to support diagnosis and gene discovery in rare disease.
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Affiliation(s)
- Lynn S. Pais
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hana Snow
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Shifa Zhang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samantha M. Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily O’Heir
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eleina England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Katherine R. Chao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ikeoluwa Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Grace E. VanNoy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kevin Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Harindra Arachchi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - William Phu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Stacy Mano
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Melanie O’Leary
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alysia Lovgren
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lawrence Babb
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christina A. Austin-Tse
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel G. MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, Australia,Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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13
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Donkervoort S, Krause N, Dergai M, Yun P, Koliwer J, Gorokhova S, Geist Hauserman J, Cummings BB, Hu Y, Smith R, Uapinyoying P, Ganesh VS, Ghosh PS, Monaghan KG, Edassery SL, Ferle PE, Silverstein S, Chao KR, Snyder M, Ellingwood S, Bharucha‐Goebel D, Iannaccone ST, Dal Peraro M, Foley AR, Savas JN, Bolduc V, Fasshauer D, Bönnemann CG, Schwake M. BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy. EMBO Mol Med 2021; 13:e13787. [PMID: 34779586 PMCID: PMC8649873 DOI: 10.15252/emmm.202013787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/26/2022] Open
Abstract
BET1 is required, together with its SNARE complex partners GOSR2, SEC22b, and Syntaxin-5 for fusion of endoplasmic reticulum-derived vesicles with the ER-Golgi intermediate compartment (ERGIC) and the cis-Golgi. Here, we report three individuals, from two families, with severe congenital muscular dystrophy (CMD) and biallelic variants in BET1 (P1 p.(Asp68His)/p.(Ala45Valfs*2); P2 and P3 homozygous p.(Ile51Ser)). Due to aberrant splicing and frameshifting, the variants in P1 result in low BET1 protein levels and impaired ER-to-Golgi transport. Since in silico modeling suggested that p.(Ile51Ser) interferes with binding to interaction partners other than SNARE complex subunits, we set off and identified novel BET1 interaction partners with low affinity for p.(Ile51Ser) BET1 protein compared to wild-type, among them ERGIC-53. The BET1/ERGIC-53 interaction was validated by endogenous co-immunoprecipitation with both proteins colocalizing to the ERGIC compartment. Mislocalization of ERGIC-53 was observed in P1 and P2's derived fibroblasts; while in the p.(Ile51Ser) P2 fibroblasts specifically, mutant BET1 was also mislocalized along with ERGIC-53. Thus, we establish BET1 as a novel CMD/epilepsy gene and confirm the emerging role of ER/Golgi SNAREs in CMD.
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Affiliation(s)
- Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Niklas Krause
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
| | - Mykola Dergai
- Department of Fundamental NeurosciencesUniversity of LausanneLausanneSwitzerland
| | - Pomi Yun
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Judith Koliwer
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
| | - Svetlana Gorokhova
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Service de Génétique MédicaleHôpital de la Timone, APHMMarseilleFrance
- INSERM, U1251‐MMGAix‐Marseille UniversitéMarseilleFrance
| | - Janelle Geist Hauserman
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Beryl B Cummings
- Center for Mendelian GenomicsProgram in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | | | - Prech Uapinyoying
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Research for Genetic MedicineChildren's National Medical CenterWashingtonDCUSA
| | - Vijay S Ganesh
- Center for Mendelian GenomicsProgram in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMAUSA
- Department of NeurologyBrigham & Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Partha S Ghosh
- Department of NeurologyBoston Children's HospitalBostonMAUSA
| | | | - Seby L Edassery
- Department of NeurologyFeinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Pia E Ferle
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
| | - Sarah Silverstein
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Rutgers New Jersey School of MedicineNewarkNJUSA
- Undiagnosed Diseases ProgramNational Human Genome Research InstituteNational Institute of HealthBethesdaMDUSA
| | - Katherine R Chao
- Center for Mendelian GenomicsProgram in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Molly Snyder
- Department of NeurologyChildren's HealthDallasTXUSA
| | | | - Diana Bharucha‐Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Division of NeurologyChildren’s National Medical CenterWashingtonDCUSA
| | - Susan T Iannaccone
- Division of Pediatric NeurologyDepartments of Pediatrics, Neurology and NeurotherapeuticsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Matteo Dal Peraro
- Institute of BioengineeringSchool of Life SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Jeffrey N Savas
- Department of NeurologyFeinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Véronique Bolduc
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Dirk Fasshauer
- Department of Fundamental NeurosciencesUniversity of LausanneLausanneSwitzerland
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Michael Schwake
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
- Department of NeurologyFeinberg School of MedicineNorthwestern UniversityChicagoILUSA
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14
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Zampaglione E, Maher M, Place EM, Wagner NE, DiTroia S, Chao KR, England E, Cmg B, Catomeris A, Nassiri S, Himes S, Pagliarulo J, Ferguson C, Galdikaité-Braziené E, Cole B, Pierce EA, Bujakowska KM. The importance of automation in genetic diagnosis: Lessons from analyzing an inherited retinal degeneration cohort with the Mendelian Analysis Toolkit (MATK). Genet Med 2021; 24:332-343. [PMID: 34906470 DOI: 10.1016/j.gim.2021.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/02/2021] [Accepted: 09/21/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE In Mendelian disease diagnosis, variant analysis is a repetitive, error-prone, and time consuming process. To address this, we have developed the Mendelian Analysis Toolkit (MATK), a configurable, automated variant ranking program. METHODS MATK aggregates variant information from multiple annotation sources and uses expert-designed rules with parameterized weights to produce a ranked list of potentially causal solutions. MATK performance was measured by a comparison between MATK-aided and human-domain expert analyses of 1060 families with inherited retinal degeneration (IRD), analyzed using an IRD-specific gene panel (589 individuals) and exome sequencing (471 families). RESULTS When comparing MATK-assisted analysis with expert curation in both the IRD-specific gene panel and exome sequencing (1060 subjects), 97.3% of potential solutions found by experts were also identified by the MATK-assisted analysis (541 solutions identified with MATK of 556 solutions found by conventional analysis). Furthermore, MATK-assisted analysis identified 114 additional potential solutions from the 504 cases unsolved by conventional analysis. CONCLUSION MATK expedites the process of identification of likely solving variants in Mendelian traits, and reduces variability stemming from human error and researcher bias. MATK facilitates data reanalysis to keep up with the constantly improving annotation sources and next-generation sequencing processing pipelines. The software is open source and available at https://gitlab.com/matthew_maher/mendelanalysis.
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Affiliation(s)
- Erin Zampaglione
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Matthew Maher
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Emily M Place
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Naomi E Wagner
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA; Invitae Corporation, San Francisco, CA
| | - Stephanie DiTroia
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Katherine R Chao
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Eleina England
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Broad Cmg
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | | | - Sherwin Nassiri
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL
| | - Seraphim Himes
- Touro University College of Osteopathic Medicine in California, Vallejo, CA
| | - Joey Pagliarulo
- Department of Genetic Counseling, School of Health and Rehab Sciences, MGH Institute of Health Professions, Boston, MA
| | - Charles Ferguson
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Eglé Galdikaité-Braziené
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Brian Cole
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA
| | - Kinga M Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA.
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15
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Scott HA, Larson A, Rong SS, Mehrotra S, Butcher R, Chao KR, Wiggs J, Place EM, Pierce EA, Bujakowska KM. A Hidden Structural Variation in a Known IRD Gene: A Cautionary Tale of Two New Disease Candidate Genes. Cold Spring Harb Mol Case Stud 2021; 8:mcs.a006131. [PMID: 34728537 PMCID: PMC8958919 DOI: 10.1101/mcs.a006131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/25/2021] [Indexed: 10/28/2022] Open
Abstract
Rod cone dystrophy (RCD), also known as retinitis pigmentosa, is an inherited condition leading to vision loss, affecting 1/3500 people. Over 270 genes are known to be implicated in the inherited retinal degenerations (IRDs), yet genetic diagnosis for ~30% IRD of patients remains elusive despite advances in sequencing technologies. The goal of this study was to determine the genetic causality in a family with Rod-cone dystrophy (RCD). Family members were given a full ophthalmic exam at the Retinal Service at MEE and consented to genetic testing. Whole exome sequencing (WES) was performed and variants of interest were Sanger validated. Functional assays were conducted in zebrafish along with splicing assays in relevant cell lines to determine the impact on retinal function. WES identified variants in two potential candidate genes that segregated with disease: GNL3 (G Protein Nucleolar 3) c.1187+3A>C and c.1568-8C>A; and PDE4DIP (Phosphodiester 4D Interacting Protein) c.3868G>A (p.Glu1290Lys) and c.4603G>A (p.Ala1535Thr). Both genes were promising candidates based on their retinal involvement (development and interactions with IRD-associated proteins), however the functional assays did not validate either gene. Subsequent WES reanalysis with an updated bioinformatics pipeline and widened search parameters led to the detection of a 94bp duplication in PRPF31 (pre-mRNA Processing Factor 31) c.73_266dup (p.Asp56GlyfsTer33) as the causal variant. Our study demonstrates the importance of thorough functional characterization of new disease candidate genes, and the value of reanalyzing NGS sequence data, which in our case led to identification of a hidden pathogenic variant in a known IRD gene.
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Affiliation(s)
- Hilary A Scott
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Anna Larson
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Shi Song Rong
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Sudeep Mehrotra
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Rossano Butcher
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Katherine R Chao
- Center for Mendelian Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Janey Wiggs
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Emily M Place
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Kinga M Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA;
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16
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Mohassel P, Donkervoort S, Lone MA, Nalls M, Gable K, Gupta SD, Foley AR, Hu Y, Saute JAM, Moreira AL, Kok F, Introna A, Logroscino G, Grunseich C, Nickolls AR, Pourshafie N, Neuhaus SB, Saade D, Gangfuß A, Kölbel H, Piccus Z, Le Pichon CE, Fiorillo C, Ly CV, Töpf A, Brady L, Specht S, Zidell A, Pedro H, Mittelmann E, Thomas FP, Chao KR, Konersman CG, Cho MT, Brandt T, Straub V, Connolly AM, Schara U, Roos A, Tarnopolsky M, Höke A, Brown RH, Lee CH, Hornemann T, Dunn TM, Bönnemann CG. Childhood amyotrophic lateral sclerosis caused by excess sphingolipid synthesis. Nat Med 2021; 27:1197-1204. [PMID: 34059824 PMCID: PMC9309980 DOI: 10.1038/s41591-021-01346-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, neurodegenerative disease of the lower and upper motor neurons with sporadic or hereditary occurrence. Age of onset, pattern of motor neuron degeneration and disease progression vary widely among individuals with ALS. Various cellular processes may drive ALS pathomechanisms, but a monogenic direct metabolic disturbance has not been causally linked to ALS. Here we show SPTLC1 variants that result in unrestrained sphingoid base synthesis cause a monogenic form of ALS. We identified four specific, dominantly acting SPTLC1 variants in seven families manifesting as childhood-onset ALS. These variants disrupt the normal homeostatic regulation of serine palmitoyltransferase (SPT) by ORMDL proteins, resulting in unregulated SPT activity and elevated levels of canonical SPT products. Notably, this is in contrast with SPTLC1 variants that shift SPT amino acid usage from serine to alanine, result in elevated levels of deoxysphingolipids and manifest with the alternate phenotype of hereditary sensory and autonomic neuropathy. We custom designed small interfering RNAs that selectively target the SPTLC1 ALS allele for degradation, leave the normal allele intact and normalize sphingolipid levels in vitro. The role of primary metabolic disturbances in ALS has been elusive; this study defines excess sphingolipid biosynthesis as a fundamental metabolic mechanism for motor neuron disease.
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Affiliation(s)
- Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Museer A Lone
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Matthew Nalls
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, USA
| | - Sita D Gupta
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jonas Alex Morales Saute
- Medical Genetics division and Neurology division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Graduate Program in Medicine: Medical Sciences, and Internal Medicine Department; Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Lucila Moreira
- Neurology Department, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Fernando Kok
- Neurogenetics Outpatient Service, Neurology Department, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil and Mendelics, São Paulo, Brazil
| | - Alessandro Introna
- Neurology Unit, Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari 'Aldo Moro', Bari, Italy
| | - Giancarlo Logroscino
- Neurology Unit, Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari 'Aldo Moro', Bari, Italy
- Department of Clinical Research in Neurology, Center for Neurodegenerative Diseases and the Aging Brain, University of Bari at 'Pia Fondazione Card G. Panico' Hospital Tricase (Le), Bari, Italy
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Alec R Nickolls
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Naemeh Pourshafie
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sarah B Neuhaus
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Dimah Saade
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Andrea Gangfuß
- Department of Paediatric Neurology, Center for Neuromuscular Disorders in Children and Adolescents, University Clinic Essen, University of Duisburg-Essen, Duisburg-Essen, Germany
| | - Heike Kölbel
- Department of Paediatric Neurology, Center for Neuromuscular Disorders in Children and Adolescents, University Clinic Essen, University of Duisburg-Essen, Duisburg-Essen, Germany
| | - Zoe Piccus
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Claire E Le Pichon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chiara Fiorillo
- Paediatric Neurology and Muscular Diseases Unit, G. Gaslini Institute and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health University of Genoa, Genoa, Italy
| | - Cindy V Ly
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Lauren Brady
- Division of Neuromuscular & Neurometabolic Disorders, Department of Paediatrics, McMaster University, Hamilton Health Sciences Centre, Hamilton, Ontario, Canada
| | - Sabine Specht
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Aliza Zidell
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Helio Pedro
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack Meridian School of Medicine, Hackensack, NJ, USA
| | - Eric Mittelmann
- Department of Neurology, Hereditary Neuropathy Foundation Center of Excellence, Neuroscience Institute, Hackensack University Medical Center, Hackensack Meridian School of Medicine, Hackensack, NJ, USA
| | - Florian P Thomas
- Department of Neurology, Hereditary Neuropathy Foundation Center of Excellence, Neuroscience Institute, Hackensack University Medical Center, Hackensack Meridian School of Medicine, Hackensack, NJ, USA
| | - Katherine R Chao
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chamindra G Konersman
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | | | | | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Anne M Connolly
- Department of Paediatrics, Neurology Division, Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Ulrike Schara
- Department of Paediatric Neurology, Center for Neuromuscular Disorders in Children and Adolescents, University Clinic Essen, University of Duisburg-Essen, Duisburg-Essen, Germany
| | - Andreas Roos
- Department of Paediatric Neurology, Center for Neuromuscular Disorders in Children and Adolescents, University Clinic Essen, University of Duisburg-Essen, Duisburg-Essen, Germany
| | - Mark Tarnopolsky
- Division of Neuromuscular & Neurometabolic Disorders, Department of Paediatrics, McMaster University, Hamilton Health Sciences Centre, Hamilton, Ontario, Canada
| | - Ahmet Höke
- Department of Neurology, Neuromuscular Division, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, USA.
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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17
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Wright CF, Quaife NM, Ramos-Hernández L, Danecek P, Ferla MP, Samocha KE, Kaplanis J, Gardner EJ, Eberhardt RY, Chao KR, Karczewski KJ, Morales J, Gallone G, Balasubramanian M, Banka S, Gompertz L, Kerr B, Kirby A, Lynch SA, Morton JEV, Pinz H, Sansbury FH, Stewart H, Zuccarelli BD, Cook SA, Taylor JC, Juusola J, Retterer K, Firth HV, Hurles ME, Lara-Pezzi E, Barton PJR, Whiffin N. Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms. Am J Hum Genet 2021; 108:1083-1094. [PMID: 34022131 PMCID: PMC8206381 DOI: 10.1016/j.ajhg.2021.04.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 02/08/2023] Open
Abstract
Clinical genetic testing of protein-coding regions identifies a likely causative variant in only around half of developmental disorder (DD) cases. The contribution of regulatory variation in non-coding regions to rare disease, including DD, remains very poorly understood. We screened 9,858 probands from the Deciphering Developmental Disorders (DDD) study for de novo mutations in the 5' untranslated regions (5' UTRs) of genes within which variants have previously been shown to cause DD through a dominant haploinsufficient mechanism. We identified four single-nucleotide variants and two copy-number variants upstream of MEF2C in a total of ten individual probands. We developed multiple bespoke and orthogonal experimental approaches to demonstrate that these variants cause DD through three distinct loss-of-function mechanisms, disrupting transcription, translation, and/or protein function. These non-coding region variants represent 23% of likely diagnoses identified in MEF2C in the DDD cohort, but these would all be missed in standard clinical genetics approaches. Nonetheless, these variants are readily detectable in exome sequence data, with 30.7% of 5' UTR bases across all genes well covered in the DDD dataset. Our analyses show that non-coding variants upstream of genes within which coding variants are known to cause DD are an important cause of severe disease and demonstrate that analyzing 5' UTRs can increase diagnostic yield. We also show how non-coding variants can help inform both the disease-causing mechanism underlying protein-coding variants and dosage tolerance of the gene.
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Affiliation(s)
- Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter EX2 5DW, UK
| | - Nicholas M Quaife
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK; Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals NHS Trust, London SW3 6NP, UK
| | - Laura Ramos-Hernández
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Petr Danecek
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Matteo P Ferla
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kaitlin E Samocha
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Joanna Kaplanis
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Eugene J Gardner
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Ruth Y Eberhardt
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Katherine R Chao
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK
| | - Giuseppe Gallone
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield S10 2TH, UK; Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield S10 2TH, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Lianne Gompertz
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Bronwyn Kerr
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Amelia Kirby
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Sally A Lynch
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, and Clinical Genetics, Temple Street Children's University Hospital, Dublin D01 XD99, Ireland
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Hailey Pinz
- Department of Pediatrics, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Francis H Sansbury
- All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4AY, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Britton D Zuccarelli
- Department of Neurology, University of Kansas School of Medicine-Salina Campus, Salina, KS 67401, USA
| | - Stuart A Cook
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | - Helen V Firth
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK; East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain; CIBER de enfermedades CardioVasculares (CIBERCV), 28029 Madrid, Spain
| | - Paul J R Barton
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK; Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals NHS Trust, London SW3 6NP, UK
| | - Nicola Whiffin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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18
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Coppens S, Barnard AM, Puusepp S, Pajusalu S, Õunap K, Vargas-Franco D, Bruels CC, Donkervoort S, Pais L, Chao KR, Goodrich JK, England EM, Weisburd B, Ganesh VS, Gudmundsson S, O’Donnell-Luria A, Nigul M, Ilves P, Mohassel P, Siddique T, Milone M, Nicolau S, Maroofian R, Houlden H, Hanna MG, Quinlivan R, Toosi MB, Karimiani EG, Costagliola S, Deconinck N, Kadhim H, Macke E, Lanpher BC, Klee EW, Łusakowska A, Kostera-Pruszczyk A, Hahn A, Schrank B, Nishino I, Ogasawara M, El Sherif R, Stojkovic T, Nelson I, Bonne G, Cohen E, Boland-Augé A, Deleuze JF, Meng Y, Töpf A, Vilain C, Pacak CA, Rivera-Zengotita ML, Bönnemann CG, Straub V, Handford PA, Draper I, Walter GA, Kang PB. A form of muscular dystrophy associated with pathogenic variants in JAG2. Am J Hum Genet 2021; 108:1164. [PMID: 34087166 PMCID: PMC8206378 DOI: 10.1016/j.ajhg.2021.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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19
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Coppens S, Barnard AM, Puusepp S, Pajusalu S, Õunap K, Vargas-Franco D, Bruels CC, Donkervoort S, Pais L, Chao KR, Goodrich JK, England EM, Weisburd B, Ganesh VS, Gudmundsson S, O'Donnell-Luria A, Nigul M, Ilves P, Mohassel P, Siddique T, Milone M, Nicolau S, Maroofian R, Houlden H, Hanna MG, Quinlivan R, Beiraghi Toosi M, Ghayoor Karimiani E, Costagliola S, Deconinck N, Kadhim H, Macke E, Lanpher BC, Klee EW, Łusakowska A, Kostera-Pruszczyk A, Hahn A, Schrank B, Nishino I, Ogasawara M, El Sherif R, Stojkovic T, Nelson I, Bonne G, Cohen E, Boland-Augé A, Deleuze JF, Meng Y, Töpf A, Vilain C, Pacak CA, Rivera-Zengotita ML, Bönnemann CG, Straub V, Handford PA, Draper I, Walter GA, Kang PB. A form of muscular dystrophy associated with pathogenic variants in JAG2. Am J Hum Genet 2021; 108:840-856. [PMID: 33861953 PMCID: PMC8206160 DOI: 10.1016/j.ajhg.2021.03.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/26/2021] [Indexed: 02/09/2023] Open
Abstract
JAG2 encodes the Notch ligand Jagged2. The conserved Notch signaling pathway contributes to the development and homeostasis of multiple tissues, including skeletal muscle. We studied an international cohort of 23 individuals with genetically unsolved muscular dystrophy from 13 unrelated families. Whole-exome sequencing identified rare homozygous or compound heterozygous JAG2 variants in all 13 families. The identified bi-allelic variants include 10 missense variants that disrupt highly conserved amino acids, a nonsense variant, two frameshift variants, an in-frame deletion, and a microdeletion encompassing JAG2. Onset of muscle weakness occurred from infancy to young adulthood. Serum creatine kinase (CK) levels were normal or mildly elevated. Muscle histology was primarily dystrophic. MRI of the lower extremities revealed a distinct, slightly asymmetric pattern of muscle involvement with cores of preserved and affected muscles in quadriceps and tibialis anterior, in some cases resembling patterns seen in POGLUT1-associated muscular dystrophy. Transcriptome analysis of muscle tissue from two participants suggested misregulation of genes involved in myogenesis, including PAX7. In complementary studies, Jag2 downregulation in murine myoblasts led to downregulation of multiple components of the Notch pathway, including Megf10. Investigations in Drosophila suggested an interaction between Serrate and Drpr, the fly orthologs of JAG1/JAG2 and MEGF10, respectively. In silico analysis predicted that many Jagged2 missense variants are associated with structural changes and protein misfolding. In summary, we describe a muscular dystrophy associated with pathogenic variants in JAG2 and evidence suggests a disease mechanism related to Notch pathway dysfunction.
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Affiliation(s)
- Sandra Coppens
- Center of Human Genetics, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Alison M Barnard
- Department of Physical Therapy, University of Florida College of Public Health and Health Professions, Gainesville, FL 32610, USA
| | - Sanna Puusepp
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Dorianmarie Vargas-Franco
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Christine C Bruels
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, NINDS, NIH, Bethesda, MD 20892, USA
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Katherine R Chao
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julia K Goodrich
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eleina M England
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ben Weisburd
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vijay S Ganesh
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sanna Gudmundsson
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anne O'Donnell-Luria
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mait Nigul
- Department of Radiology, Tartu University Hospital, Tartu 50406, Estonia
| | - Pilvi Ilves
- Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Department of Radiology, Tartu University Hospital, Tartu 50406, Estonia
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, NINDS, NIH, Bethesda, MD 20892, USA
| | - Teepu Siddique
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Stefan Nicolau
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London WC1E 6BT, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London WC1E 6BT, UK
| | - Michael G Hanna
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London WC1E 6BT, UK
| | - Ros Quinlivan
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London WC1E 6BT, UK
| | - Mehran Beiraghi Toosi
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad 9176999311, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London SW17 0RE, UK; Innovative Medical Research Center, Mashhad Branch, Islamic Azad University, Mashhad 9187147578, Iran
| | - Sabine Costagliola
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moleculaire, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Nicolas Deconinck
- Centre de Référence Neuromusculaire and Paediatric Neurology Department, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, 1020 Brussels, Belgium
| | - Hazim Kadhim
- Neuropathology Unit, Department of Anatomic Pathology and Reference Center for Neuromuscular Pathology, Brugmann University Hospital-Children's Hospital, Université Libre de Bruxelles, 1020 Brussels, Belgium
| | - Erica Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Anna Łusakowska
- Department of Neurology, Medical University of Warsaw, 02-091 Warsaw, Poland
| | | | - Andreas Hahn
- Department of Child Neurology, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Bertold Schrank
- Department of Neurology, DKD HELIOS Klinik Wiesbaden, 65191 Wiesbaden, Germany
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan
| | - Masashi Ogasawara
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan
| | - Rasha El Sherif
- Myo-Care Neuromuscular Center, Myo-Care National Foundation, Cairo 11865, Egypt
| | - Tanya Stojkovic
- APHP, Nord-Est/Ile-de-France Neuromuscular Reference Center, Myology Institute, Pitié-Salpêtrière Hospital, 75013 Paris, France; Sorbonne Université, INSERM, Center of Research in Myology, UMRS974, 75651 Paris Cedex 13, France
| | - Isabelle Nelson
- Sorbonne Université, INSERM, Center of Research in Myology, UMRS974, 75651 Paris Cedex 13, France
| | - Gisèle Bonne
- Sorbonne Université, INSERM, Center of Research in Myology, UMRS974, 75651 Paris Cedex 13, France
| | - Enzo Cohen
- Sorbonne Université, INSERM, Center of Research in Myology, UMRS974, 75651 Paris Cedex 13, France
| | - Anne Boland-Augé
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Yao Meng
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK
| | - Catheline Vilain
- Center of Human Genetics, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Christina A Pacak
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA; Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Department of Neurology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | | | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, NINDS, NIH, Bethesda, MD 20892, USA
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK
| | - Penny A Handford
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Isabelle Draper
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
| | - Glenn A Walter
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Peter B Kang
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA; Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Department of Neurology, University of Minnesota Medical School, Minneapolis, MN 55455, USA; Institute for Translational Neuroscience, University of Minnesota Medical School, Minneapolis, MN 55455, USA.
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20
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Wahlster L, Verboon JM, Ludwig LS, Black SC, Luo W, Garg K, Voit RA, Collins RL, Garimella K, Costello M, Chao KR, Goodrich JK, DiTroia SP, O'Donnell-Luria A, Talkowski ME, Michelson AD, Cantor AB, Sankaran VG. Familial thrombocytopenia due to a complex structural variant resulting in a WAC-ANKRD26 fusion transcript. J Exp Med 2021; 218:211998. [PMID: 33857290 PMCID: PMC8056752 DOI: 10.1084/jem.20210444] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
Advances in genome sequencing have resulted in the identification of the causes for numerous rare diseases. However, many cases remain unsolved with standard molecular analyses. We describe a family presenting with a phenotype resembling inherited thrombocytopenia 2 (THC2). THC2 is generally caused by single nucleotide variants that prevent silencing of ANKRD26 expression during hematopoietic differentiation. Short-read whole-exome and genome sequencing approaches were unable to identify a causal variant in this family. Using long-read whole-genome sequencing, a large complex structural variant involving a paired-duplication inversion was identified. Through functional studies, we show that this structural variant results in a pathogenic gain-of-function WAC-ANKRD26 fusion transcript. Our findings illustrate how complex structural variants that may be missed by conventional genome sequencing approaches can cause human disease.
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Affiliation(s)
- Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Jeffrey M Verboon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Leif S Ludwig
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Susan C Black
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Wendy Luo
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Kopal Garg
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Richard A Voit
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Ryan L Collins
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Kiran Garimella
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Maura Costello
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Katherine R Chao
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Julia K Goodrich
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Stephanie P DiTroia
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Anne O'Donnell-Luria
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Michael E Talkowski
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Alan D Michelson
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Alan B Cantor
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
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21
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Donkervoort S, Kutzner CE, Hu Y, Lornage X, Rendu J, Stojkovic T, Baets J, Neuhaus SB, Tanboon J, Maroofian R, Bolduc V, Mroczek M, Conijn S, Kuntz NL, Töpf A, Monges S, Lubieniecki F, McCarty RM, Chao KR, Governali S, Böhm J, Boonyapisit K, Malfatti E, Sangruchi T, Horkayne-Szakaly I, Hedberg-Oldfors C, Efthymiou S, Noguchi S, Djeddi S, Iida A, di Rosa G, Fiorillo C, Salpietro V, Darin N, Fauré J, Houlden H, Oldfors A, Nishino I, de Ridder W, Straub V, Pokrzywa W, Laporte J, Foley AR, Romero NB, Ottenheijm C, Hoppe T, Bönnemann CG. Pathogenic Variants in the Myosin Chaperone UNC-45B Cause Progressive Myopathy with Eccentric Cores. Am J Hum Genet 2020; 107:1078-1095. [PMID: 33217308 DOI: 10.1016/j.ajhg.2020.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/03/2020] [Indexed: 01/03/2023] Open
Abstract
The myosin-directed chaperone UNC-45B is essential for sarcomeric organization and muscle function from Caenorhabditis elegans to humans. The pathological impact of UNC-45B in muscle disease remained elusive. We report ten individuals with bi-allelic variants in UNC45B who exhibit childhood-onset progressive muscle weakness. We identified a common UNC45B variant that acts as a complex hypomorph splice variant. Purified UNC-45B mutants showed changes in folding and solubility. In situ localization studies further demonstrated reduced expression of mutant UNC-45B in muscle combined with abnormal localization away from the A-band towards the Z-disk of the sarcomere. The physiological relevance of these observations was investigated in C. elegans by transgenic expression of conserved UNC-45 missense variants, which showed impaired myosin binding for one and defective muscle function for three. Together, our results demonstrate that UNC-45B impairment manifests as a chaperonopathy with progressive muscle pathology, which discovers the previously unknown conserved role of UNC-45B in myofibrillar organization.
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Affiliation(s)
- Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carl E Kutzner
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xavière Lornage
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, Université de Strasbourg, BP 10142, 67404 Illkirch, France
| | - John Rendu
- Centre Hospitalier Universitaire de Grenoble Alpes, Biochimie Génétique et Moléculaire, Grenoble 38000, France; Grenoble Institut des Neurosciences-INSERM U1216 UGA, Grenoble 38000, France
| | - Tanya Stojkovic
- Centre de Référence des Maladies Neuromusculaires Nord/Est/Ile de France, Institut de Myologie, GHU La Pitié-Salpêtrière, Sorbonne Université, AP-HP, 75013 Paris, France
| | - Jonathan Baets
- Faculty of Medicine, University of Antwerp, 2610 Antwerp, Belgium; Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium; Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, 2650 Antwerp, Belgium
| | - Sarah B Neuhaus
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jantima Tanboon
- Department of Pathology, Faculty of Medicine, Siriraj Hospital, Mahidol University, 10700 Bangkok, Thailand; Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 187-8502 Tokyo, Japan
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Véronique Bolduc
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Magdalena Mroczek
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Stefan Conijn
- Department of Physiology, Amsterdam UMC (location VUmc), 1081 HZ Amsterdam, the Netherlands
| | - Nancy L Kuntz
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Soledad Monges
- Servicio de Neurología y Servicio de Patologia, Hospital de Pediatría Garrahan, C1245 AAM Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Servicio de Neurología y Servicio de Patologia, Hospital de Pediatría Garrahan, C1245 AAM Buenos Aires, Argentina
| | - Riley M McCarty
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine R Chao
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Serena Governali
- Department of Physiology, Amsterdam UMC (location VUmc), 1081 HZ Amsterdam, the Netherlands
| | - Johann Böhm
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, Université de Strasbourg, BP 10142, 67404 Illkirch, France
| | - Kanokwan Boonyapisit
- Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol, University, 10700 Bangkok, Thailand
| | - Edoardo Malfatti
- Neurology Department, Raymond-Poincaré teaching hospital, centre de référence des maladies neuromusculaires Nord/Est/Ile-de-France, AP-HP, 92380 Garches, France
| | - Tumtip Sangruchi
- Department of Pathology, Faculty of Medicine, Siriraj Hospital, Mahidol University, 10700 Bangkok, Thailand
| | | | - Carola Hedberg-Oldfors
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, University College London Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 187-8502 Tokyo, Japan; Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, 187-8551 Tokyo, Japan
| | - Sarah Djeddi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, Université de Strasbourg, BP 10142, 67404 Illkirch, France
| | - Aritoshi Iida
- Department of Clinical Genome Analysis, Medical Genome Center, National Center of Neurology and Psychiatry, 187-8551 Tokyo, Japan
| | - Gabriella di Rosa
- Division of Child Neurology and Psychiatry, Department of the Adult and Developmental Age Human Pathology, University of Messina, Messina 98125, Italy
| | - Chiara Fiorillo
- Pediatric Neurology and Muscular Diseases Unit, G. Gaslini Institute, 16147 Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132 Genoa, Italy
| | - Vincenzo Salpietro
- Pediatric Neurology and Muscular Diseases Unit, G. Gaslini Institute, 16147 Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132 Genoa, Italy
| | - Niklas Darin
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, 41650 Gothenburg, Sweden
| | - Julien Fauré
- Centre Hospitalier Universitaire de Grenoble Alpes, Biochimie Génétique et Moléculaire, Grenoble 38000, France; Grenoble Institut des Neurosciences-INSERM U1216 UGA, Grenoble 38000, France
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Anders Oldfors
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 187-8502 Tokyo, Japan; Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, 187-8551 Tokyo, Japan; Department of Clinical Genome Analysis, Medical Genome Center, National Center of Neurology and Psychiatry, 187-8551 Tokyo, Japan
| | - Willem de Ridder
- Faculty of Medicine, University of Antwerp, 2610 Antwerp, Belgium; Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium; Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, 2650 Antwerp, Belgium
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK; Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, Université de Strasbourg, BP 10142, 67404 Illkirch, France
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Norma B Romero
- Centre de Référence des Maladies Neuromusculaires Nord/Est/Ile de France, Institut de Myologie, GHU La Pitié-Salpêtrière, Sorbonne Université, AP-HP, 75013 Paris, France; Université Sorbonne, UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, GH Pitié-Salpêtrière, 75651 Paris, France; Neuromuscular Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, 75013 Paris, France
| | - Coen Ottenheijm
- Department of Physiology, Amsterdam UMC (location VUmc), 1081 HZ Amsterdam, the Netherlands; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85718, USA
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany.
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
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22
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D'Gama AM, England E, Madden JA, Shi J, Chao KR, Wojcik MH, Torres AR, Tan WH, Berry GT, Prabhu SP, Agrawal PB. Exome sequencing identifies novel missense and deletion variants in RTN4IP1 associated with optic atrophy, global developmental delay, epilepsy, ataxia, and choreoathetosis. Am J Med Genet A 2020; 185:203-207. [PMID: 33037779 DOI: 10.1002/ajmg.a.61910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 09/11/2020] [Accepted: 09/20/2020] [Indexed: 11/05/2022]
Abstract
Inherited optic neuropathies (IONs) are neurodegenerative disorders characterized by optic atrophy with or without extraocular manifestations. Optic atrophy-10 (OPA10) is an autosomal recessive ION recently reported to be caused by mutations in RTN4IP1, which encodes reticulon 4 interacting protein 1 (RTN4IP1), a mitochondrial ubiquinol oxydo-reductase. Here we report novel compound heterozygous mutations in RTN4IP1 in a male proband with developmental delay, epilepsy, optic atrophy, ataxia, and choreoathetosis. Workup was notable for transiently elevated lactate and lactate-to-pyruvate ratio, brain magnetic resonance imaging with optic atrophy and T2 signal abnormalities, and a nondiagnostic initial genetic workup, including chromosomal microarray and mitochondrial panel testing. Exome sequencing identified a paternally inherited missense variant (c.263T>G, p.Val88Gly) predicted to be deleterious and a maternally inherited deletion encompassing RTN4IP1. To our knowledge, this is the first report of a non-single nucleotide pathogenic variant associated with OPA10. This case highlights the expanding phenotypic spectrum of OPA10, the association between "syndromic" cases and severe RTN4IP1 mutations, and the importance of nonbiased genetic testing, such as ES, to analyze multiple genes and variants types, in patients suspected of having genetic disease.
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Affiliation(s)
- Alissa M D'Gama
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Eleina England
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jill A Madden
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jiahai Shi
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Katherine R Chao
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Monica H Wojcik
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alcy R Torres
- Division of Pediatric Neurology, Department of Pediatrics, Boston Medical Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Wen-Hann Tan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Gerard T Berry
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Sanjay P Prabhu
- Neuroradiology Division, Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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23
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Donkervoort S, Mohassel P, Laugwitz L, Zaki MS, Kamsteeg EJ, Maroofian R, Chao KR, Verschuuren-Bemelmans CC, Horber V, Fock AJM, McCarty RM, Jain MS, Biancavilla V, McMacken G, Nalls M, Voermans NC, Elbendary HM, Snyder M, Cai C, Lehky TJ, Stanley V, Iannaccone ST, Foley AR, Lochmüller H, Gleeson J, Houlden H, Haack TB, Horvath R, Bönnemann CG. Biallelic loss of function variants in SYT2 cause a treatable congenital onset presynaptic myasthenic syndrome. Am J Med Genet A 2020; 182:2272-2283. [PMID: 32776697 DOI: 10.1002/ajmg.a.61765] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/25/2020] [Accepted: 06/13/2020] [Indexed: 12/15/2022]
Abstract
Synaptotagmins are integral synaptic vesicle membrane proteins that function as calcium sensors and regulate neurotransmitter release at the presynaptic nerve terminal. Synaptotagmin-2 (SYT2), is the major isoform expressed at the neuromuscular junction. Recently, dominant missense variants in SYT2 have been reported as a rare cause of distal motor neuropathy and myasthenic syndrome, manifesting with stable or slowly progressive distal weakness of variable severity along with presynaptic NMJ impairment. These variants are thought to have a dominant-negative effect on synaptic vesicle exocytosis, although the precise pathomechanism remains to be elucidated. Here we report seven patients of five families, with biallelic loss of function variants in SYT2, clinically manifesting with a remarkably consistent phenotype of severe congenital onset hypotonia and weakness, with variable degrees of respiratory involvement. Electrodiagnostic findings were consistent with a presynaptic congenital myasthenic syndrome (CMS) in some. Treatment with an acetylcholinesterase inhibitor pursued in three patients showed clinical improvement with increased strength and function. This series further establishes SYT2 as a CMS-disease gene and expands its clinical and genetic spectrum to include recessive loss-of-function variants, manifesting as a severe congenital onset presynaptic CMS with potential treatment implications.
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Affiliation(s)
- Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Lucia Laugwitz
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Department of Paediatric Neurology, University Children's Hospital, Tübingen, Germany
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, UK
| | - Katherine R Chao
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Veronka Horber
- Department of Paediatric Neurology, University Children's Hospital, Tübingen, Germany
| | - Annemarie J M Fock
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Riley M McCarty
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Minal S Jain
- Rehabilitation Medicine Department, Clinical Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Victoria Biancavilla
- Rehabilitation Medicine Department, Clinical Research Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Grace McMacken
- Department of Neurosciences, Royal Victoria Hospital, Belfast, UK
| | - Matthew Nalls
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hasnaa M Elbendary
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Molly Snyder
- Department of Neurology, Children's Health, Dallas, Texas, USA
| | - Chunyu Cai
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Tanya J Lehky
- EMG Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Valentina Stanley
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Susan T Iannaccone
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Hanns Lochmüller
- Department of Neuropediatrics and Muscle Disorders, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Joseph Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, UK
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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24
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Scott HA, Place EM, Ferenchak K, Zampaglione E, Wagner NE, Chao KR, DiTroia SP, Navarro-Gomez D, Mukai S, Huckfeldt RM, Pierce EA, Bujakowska KM. Expanding the phenotypic spectrum in RDH12-associated retinal disease. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004754. [PMID: 32014858 PMCID: PMC6996522 DOI: 10.1101/mcs.a004754] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/05/2019] [Indexed: 11/25/2022] Open
Abstract
Retinol dehydrogenase 12, RDH12, plays a pivotal role in the visual cycle to ensure the maintenance of normal vision. Alterations in activity of this protein result in photoreceptor death and decreased vision beginning at an early age and progressing to substantial vision loss later in life. Here we describe 11 patients with retinal degeneration that underwent next-generation sequencing (NGS) with a targeted panel of all currently known inherited retinal degeneration (IRD) genes and whole-exome sequencing to identify the genetic causality of their retinal disease. These patients display a range of phenotypic severity prompting clinical diagnoses of macular dystrophy, cone-rod dystrophy, retinitis pigmentosa, and early-onset severe retinal dystrophy all attributed to biallelic recessive mutations in RDH12. We report 15 causal alleles and expand the repertoire of known RDH12 mutations with four novel variants: c.215A > G (p.Asp72Gly); c.362T > C (p.Ile121Thr); c.440A > C (p.Asn147Thr); and c.697G > A (p.Val233Ille). The broad phenotypic spectrum observed with biallelic RDH12 mutations has been observed in other genetic forms of IRDs, but the diversity is particularly notable here given the prior association of RDH12 primarily with severe early-onset disease. This breadth emphasizes the importance of broad genetic testing for inherited retinal disorders and extends the pool of individuals who may benefit from imminent gene-targeted therapies.
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Affiliation(s)
- Hilary A Scott
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Emily M Place
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Kevin Ferenchak
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Erin Zampaglione
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Naomi E Wagner
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Katherine R Chao
- Center for Mendelian Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Stephanie P DiTroia
- Center for Mendelian Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Daniel Navarro-Gomez
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Shizuo Mukai
- Retina Service, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Rachel M Huckfeldt
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Kinga M Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts 02114, USA
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25
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Bryen SJ, Ewans LJ, Pinner J, MacLennan SC, Donkervoort S, Castro D, Töpf A, O'Grady G, Cummings B, Chao KR, Weisburd B, Francioli L, Faiz F, Bournazos AM, Hu Y, Grosmann C, Malicki DM, Doyle H, Witting N, Vissing J, Claeys KG, Urankar K, Beleza-Meireles A, Baptista J, Ellard S, Savarese M, Johari M, Vihola A, Udd B, Majumdar A, Straub V, Bönnemann CG, MacArthur DG, Davis MR, Cooper ST. Recurrent TTN metatranscript-only c.39974-11T>G splice variant associated with autosomal recessive arthrogryposis multiplex congenita and myopathy. Hum Mutat 2019; 41:403-411. [PMID: 31660661 DOI: 10.1002/humu.23938] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/01/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022]
Abstract
We present eight families with arthrogryposis multiplex congenita and myopathy bearing a TTN intron 213 extended splice-site variant (NM_001267550.1:c.39974-11T>G), inherited in trans with a second pathogenic TTN variant. Muscle-derived RNA studies of three individuals confirmed mis-splicing induced by the c.39974-11T>G variant; in-frame exon 214 skipping or use of a cryptic 3' splice-site effecting a frameshift. Confounding interpretation of pathogenicity is the absence of exons 213-217 within the described skeletal muscle TTN N2A isoform. However, RNA-sequencing from 365 adult human gastrocnemius samples revealed that 56% specimens predominantly include exons 213-217 in TTN transcripts (inclusion rate ≥66%). Further, RNA-sequencing of five fetal muscle samples confirmed that 4/5 specimens predominantly include exons 213-217 (fifth sample inclusion rate 57%). Contractures improved significantly with age for four individuals, which may be linked to decreased expression of pathogenic fetal transcripts. Our study extends emerging evidence supporting a vital developmental role for TTN isoforms containing metatranscript-only exons.
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Affiliation(s)
- Samantha J Bryen
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Discipline of Child and Adolescent Health, The University of Sydney Children's Hospital Westmead Clinical School, Westmead, New South Wales, Australia
| | - Lisa J Ewans
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,Central Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jason Pinner
- Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, 2031, Australia
| | - Suzanna C MacLennan
- Neurology Department, Women's and Children's Hospital, North Adelaide, South Australia, Australia.,School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Sandra Donkervoort
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Diana Castro
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gina O'Grady
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Discipline of Child and Adolescent Health, The University of Sydney Children's Hospital Westmead Clinical School, Westmead, New South Wales, Australia
| | - Beryl Cummings
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Katherine R Chao
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Ben Weisburd
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Laurent Francioli
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Fathimath Faiz
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Adam M Bournazos
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Discipline of Child and Adolescent Health, The University of Sydney Children's Hospital Westmead Clinical School, Westmead, New South Wales, Australia
| | - Ying Hu
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Carla Grosmann
- Department of Neurology, Rady Children's Hospital University of California San Diego, San Diego, California
| | - Denise M Malicki
- Department of Pathology, Rady Children's Hospital University of California San Diego, San Diego, California
| | - Helen Doyle
- Department of Histopathology, The Children's Hospital at Westmead, Sydney Children's Hospital Network, Westmead, NSW, Australia
| | - Nanna Witting
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - John Vissing
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Kristl G Claeys
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium.,Laboratory for Muscle Diseases and Neuropathies, Department of Neurosciences, Experimental Neurology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Kathryn Urankar
- Department of Neuropathology, Southmead Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Ana Beleza-Meireles
- Clinical Genetics, Bristol Royal Hospital For Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Julia Baptista
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom.,Institute of Biomedical and Clinical Science, University of Exeter Medical School University of Exeter, Exeter, United Kingdom
| | - Sian Ellard
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom.,Institute of Biomedical and Clinical Science, University of Exeter Medical School University of Exeter, Exeter, United Kingdom
| | - Marco Savarese
- Folkhälsan Research Center, Medicum, University of Helsinki, Haartmaninkatu 8, Helsinki, 00290, Finland
| | - Mridul Johari
- Folkhälsan Research Center, Medicum, University of Helsinki, Haartmaninkatu 8, Helsinki, 00290, Finland
| | - Anna Vihola
- Folkhälsan Research Center, Medicum, University of Helsinki, Haartmaninkatu 8, Helsinki, 00290, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, Medicum, University of Helsinki, Haartmaninkatu 8, Helsinki, 00290, Finland.,Tampere Neuromuscular Center, Tampere University Hospital, Teiskontie 35, Tampere, 33520, Finland
| | - Anirban Majumdar
- Paediatric Neurology, Bristol Royal Hospital For Children, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Carsten G Bönnemann
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia.,Discipline of Child and Adolescent Health, The University of Sydney Children's Hospital Westmead Clinical School, Westmead, New South Wales, Australia.,Functional Neuromics, The Children's Medical Research Institute, Westmead, New South Wales, Australia
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26
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Lornage X, Romero NB, Grosgogeat CA, Malfatti E, Donkervoort S, Marchetti MM, Neuhaus SB, Foley AR, Labasse C, Schneider R, Carlier RY, Chao KR, Medne L, Deleuze JF, Orlikowski D, Bönnemann CG, Gupta VA, Fardeau M, Böhm J, Laporte J. ACTN2 mutations cause "Multiple structured Core Disease" (MsCD). Acta Neuropathol 2019; 137:501-519. [PMID: 30701273 DOI: 10.1007/s00401-019-01963-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/11/2022]
Abstract
The identification of genes implicated in myopathies is essential for diagnosis and for revealing novel therapeutic targets. Here we characterize a novel subclass of congenital myopathy at the morphological, molecular, and functional level. Through exome sequencing, we identified de novo ACTN2 mutations, a missense and a deletion, in two unrelated patients presenting with progressive early-onset muscle weakness and respiratory involvement. Morphological and ultrastructural analyses of muscle biopsies revealed a distinctive pattern with the presence of muscle fibers containing small structured cores and jagged Z-lines. Deeper analysis of the missense mutation revealed mutant alpha-actinin-2 properly localized to the Z-line in differentiating myotubes and its level was not altered in muscle biopsy. Modelling of the disease in zebrafish and mice by exogenous expression of mutated alpha-actinin-2 recapitulated the abnormal muscle function and structure seen in the patients. Motor deficits were noted in zebrafish, and muscle force was impaired in isolated muscles from AAV-transduced mice. In both models, sarcomeric disorganization was evident, while expression of wild-type alpha-actinin-2 did not result in muscle anomalies. The murine muscles injected with mutant ACTN2 displayed cores and Z-line defects. Dominant ACTN2 mutations were previously associated with cardiomyopathies, and our data demonstrate that specific mutations in the well-known Z-line regulator alpha-actinin-2 can cause a skeletal muscle disorder.
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Affiliation(s)
- Xavière Lornage
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1, rue Laurent Fries, BP 10142, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- CNRS, UMR7104, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Norma B Romero
- Université Sorbonne, UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, GH Pitié-Salpêtrière, 47 Boulevard de l'hôpital, 75013, Paris, France
- Centre de référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, 75013, Paris, France
- Neuromuscular Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, 75013, Paris, France
| | - Claire A Grosgogeat
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Edoardo Malfatti
- Centre de référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, 75013, Paris, France
- Neuromuscular Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, 75013, Paris, France
- Neurology Department, Raymond-Poincaré teaching hospital, Centre de référence des maladies neuromusculaires Nord/Est/Ile-de-France, AP-HP, 92380, Garches, France
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael M Marchetti
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah B Neuhaus
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Clémence Labasse
- Centre de référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, 75013, Paris, France
- Neuromuscular Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, 75013, Paris, France
| | - Raphaël Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1, rue Laurent Fries, BP 10142, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- CNRS, UMR7104, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Robert Y Carlier
- Neurolocomotor Division, Department of Radiology, Raymond Poincare Hospital, University Hospitals Paris-Ile-de-France West, Public Hospital Network of Paris, 92380, Garches, France
- Versailles Saint-Quentin-en-Yvelines University, 78000, Versailles, France
| | - Katherine R Chao
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02115, USA
| | - Livija Medne
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de biologie François Jacob, CEA, 91000, Evry, France
| | - David Orlikowski
- CIC 1429, INSERM, AP-HP, Hôpital Raymond Poincaré, 92380, Garches, France
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vandana A Gupta
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Michel Fardeau
- Université Sorbonne, UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, GH Pitié-Salpêtrière, 47 Boulevard de l'hôpital, 75013, Paris, France
- Centre de référence de Pathologie Neuromusculaire Paris-Est, Institut de Myologie, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, 75013, Paris, France
- Neuromuscular Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, 75013, Paris, France
| | - Johann Böhm
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1, rue Laurent Fries, BP 10142, 67404, Illkirch, France
- INSERM U1258, 67404, Illkirch, France
- CNRS, UMR7104, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1, rue Laurent Fries, BP 10142, 67404, Illkirch, France.
- INSERM U1258, 67404, Illkirch, France.
- CNRS, UMR7104, 67404, Illkirch, France.
- Université de Strasbourg, 67404, Illkirch, France.
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27
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Ulirsch JC, Verboon JM, Kazerounian S, Guo MH, Yuan D, Ludwig LS, Handsaker RE, Abdulhay NJ, Fiorini C, Genovese G, Lim ET, Cheng A, Cummings BB, Chao KR, Beggs AH, Genetti CA, Sieff CA, Newburger PE, Niewiadomska E, Matysiak M, Vlachos A, Lipton JM, Atsidaftos E, Glader B, Narla A, Gleizes PE, O'Donohue MF, Montel-Lehry N, Amor DJ, McCarroll SA, O'Donnell-Luria AH, Gupta N, Gabriel SB, MacArthur DG, Lander ES, Lek M, Da Costa L, Nathan DG, Korostelev AA, Do R, Sankaran VG, Gazda HT. The Genetic Landscape of Diamond-Blackfan Anemia. Am J Hum Genet 2019; 104:356. [PMID: 30735661 DOI: 10.1016/j.ajhg.2018.12.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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28
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Ulirsch JC, Verboon JM, Kazerounian S, Guo MH, Yuan D, Ludwig LS, Handsaker RE, Abdulhay NJ, Fiorini C, Genovese G, Lim ET, Cheng A, Cummings BB, Chao KR, Beggs AH, Genetti CA, Sieff CA, Newburger PE, Niewiadomska E, Matysiak M, Vlachos A, Lipton JM, Atsidaftos E, Glader B, Narla A, Gleizes PE, O'Donohue MF, Montel-Lehry N, Amor DJ, McCarroll SA, O'Donnell-Luria AH, Gupta N, Gabriel SB, MacArthur DG, Lander ES, Lek M, Da Costa L, Nathan DG, Korostelev AA, Do R, Sankaran VG, Gazda HT. The Genetic Landscape of Diamond-Blackfan Anemia. Am J Hum Genet 2018; 103:930-947. [PMID: 30503522 PMCID: PMC6288280 DOI: 10.1016/j.ajhg.2018.10.027] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/29/2018] [Indexed: 01/19/2023] Open
Abstract
Diamond-Blackfan anemia (DBA) is a rare bone marrow failure disorder that affects 7 out of 1,000,000 live births and has been associated with mutations in components of the ribosome. In order to characterize the genetic landscape of this heterogeneous disorder, we recruited a cohort of 472 individuals with a clinical diagnosis of DBA and performed whole-exome sequencing (WES). We identified relevant rare and predicted damaging mutations for 78% of individuals. The majority of mutations were singletons, absent from population databases, predicted to cause loss of function, and located in 1 of 19 previously reported ribosomal protein (RP)-encoding genes. Using exon coverage estimates, we identified and validated 31 deletions in RP genes. We also observed an enrichment for extended splice site mutations and validated their diverse effects using RNA sequencing in cell lines obtained from individuals with DBA. Leveraging the size of our cohort, we observed robust genotype-phenotype associations with congenital abnormalities and treatment outcomes. We further identified rare mutations in seven previously unreported RP genes that may cause DBA, as well as several distinct disorders that appear to phenocopy DBA, including nine individuals with biallelic CECR1 mutations that result in deficiency of ADA2. However, no new genes were identified at exome-wide significance, suggesting that there are no unidentified genes containing mutations readily identified by WES that explain >5% of DBA-affected case subjects. Overall, this report should inform not only clinical practice for DBA-affected individuals, but also the design and analysis of rare variant studies for heterogeneous Mendelian disorders.
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Affiliation(s)
- Jacob C Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey M Verboon
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shideh Kazerounian
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Guo
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Yuan
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Leif S Ludwig
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nour J Abdulhay
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elaine T Lim
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aaron Cheng
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beryl B Cummings
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine R Chao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Colin A Sieff
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Peter E Newburger
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Edyta Niewiadomska
- Department of Pediatric Hematology/Oncology, Medical University of Warsaw, Warsaw, Poland
| | - Michal Matysiak
- Department of Pediatric Hematology/Oncology, Medical University of Warsaw, Warsaw, Poland
| | - Adrianna Vlachos
- Feinstein Institute for Medical Research, Manhasset, NY; Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children's Medical Center, New Hyde Park, NY; Hofstra Northwell School of Medicine, Hempstead, NY 11030, USA
| | - Jeffrey M Lipton
- Feinstein Institute for Medical Research, Manhasset, NY; Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children's Medical Center, New Hyde Park, NY; Hofstra Northwell School of Medicine, Hempstead, NY 11030, USA
| | - Eva Atsidaftos
- Feinstein Institute for Medical Research, Manhasset, NY; Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children's Medical Center, New Hyde Park, NY; Hofstra Northwell School of Medicine, Hempstead, NY 11030, USA
| | - Bertil Glader
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 02114, USA
| | - Anupama Narla
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 02114, USA
| | - Pierre-Emmanuel Gleizes
- Laboratory of Eukaryotic Molecular Biology, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Marie-Françoise O'Donohue
- Laboratory of Eukaryotic Molecular Biology, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Nathalie Montel-Lehry
- Laboratory of Eukaryotic Molecular Biology, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anne H O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacey B Gabriel
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eric S Lander
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lydie Da Costa
- University Paris VII Denis DIDEROT, Faculté de Médecine Xavier Bichat, 75019 Paris, France; Laboratory of Excellence for Red Cell, LABEX GR-Ex, 75015 Paris, France
| | - David G Nathan
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ron Do
- Department of Genetics and Genomic Sciences and The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - Hanna T Gazda
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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29
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Dobyns WB, Aldinger KA, Ishak GE, Mirzaa GM, Timms AE, Grout ME, Dremmen MH, Schot R, Vandervore L, van Slegtenhorst MA, Wilke M, Kasteleijn E, Lee AS, Barry BJ, Chao KR, Szczałuba K, Kobori J, Hanson-Kahn A, Bernstein JA, Carr L, D’Arco F, Miyana K, Okazaki T, Saito Y, Sasaki M, Das S, Wheeler MM, Bamshad MJ, Nickerson DA, Engle EC, Verheijen FW, Doherty D, Mancini GM, Doherty D, Mancini GMS. MACF1 Mutations Encoding Highly Conserved Zinc-Binding Residues of the GAR Domain Cause Defects in Neuronal Migration and Axon Guidance. Am J Hum Genet 2018; 103:1009-1021. [PMID: 30471716 DOI: 10.1016/j.ajhg.2018.10.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/22/2018] [Indexed: 01/08/2023] Open
Abstract
To date, mutations in 15 actin- or microtubule-associated genes have been associated with the cortical malformation lissencephaly and variable brainstem hypoplasia. During a multicenter review, we recognized a rare lissencephaly variant with a complex brainstem malformation in three unrelated children. We searched our large brain-malformation databases and found another five children with this malformation (as well as one with a less severe variant), analyzed available whole-exome or -genome sequencing data, and tested ciliogenesis in two affected individuals. The brain malformation comprised posterior predominant lissencephaly and midline crossing defects consisting of absent anterior commissure and a striking W-shaped brainstem malformation caused by small or absent pontine crossing fibers. We discovered heterozygous de novo missense variants or an in-frame deletion involving highly conserved zinc-binding residues within the GAR domain of MACF1 in the first eight subjects. We studied cilium formation and found a higher proportion of mutant cells with short cilia than of control cells with short cilia. A ninth child had similar lissencephaly but only subtle brainstem dysplasia associated with a heterozygous de novo missense variant in the spectrin repeat domain of MACF1. Thus, we report variants of the microtubule-binding GAR domain of MACF1 as the cause of a distinctive and most likely pathognomonic brain malformation. A gain-of-function or dominant-negative mechanism appears likely given that many heterozygous mutations leading to protein truncation are included in the ExAC Browser. However, three de novo variants in MACF1 have been observed in large schizophrenia cohorts.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam 3015 CN, the Netherlands.
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30
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Qualls AE, Donkervoort S, Herkert JC, D'gama AM, Bharucha-Goebel D, Collins J, Chao KR, Foley AR, Schoots MH, Jongbloed JDH, Bönnemann CG, Agrawal PB. Novel SPEG mutations in congenital myopathies: Genotype-phenotype correlations. Muscle Nerve 2018; 59:357-362. [PMID: 30412272 DOI: 10.1002/mus.26378] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2018] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Centronuclear myopathies (CNMs) are a subtype of congenital myopathies (CMs) characterized by muscle weakness, predominant type 1 fibers, and increased central nuclei. SPEG (striated preferentially expressed protein kinase) mutations have recently been identified in 7 CM patients (6 with CNMs). We report 2 additional patients with SPEG mutations expanding the phenotype and evaluate genotype-phenotype correlations associated with SPEG mutations. METHODS Using whole exome/genome sequencing in CM families, we identified novel recessive SPEG mutations in 2 patients. RESULTS Patient 1, with severe muscle weakness requiring respiratory support, dilated cardiomyopathy, ophthalmoplegia, and findings of nonspecific CM on muscle biopsy carried a homozygous SPEG mutation (p.Val3062del). Patient 2, with milder muscle weakness, ophthalmoplegia, and CNM carried compound heterozygous mutations (p.Leu728Argfs*82) and (p.Val2997Glyfs*52). CONCLUSIONS The 2 patients add insight into genotype-phenotype correlations of SPEG-associated CMs. Clinicians should consider evaluating a CM patient for SPEG mutations even in the absence of CNM features. Muscle Nerve 59:357-362, 2019.
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Affiliation(s)
- Anita E Qualls
- Division of Newborn Medicine, Division of Genetics and Genomics, and The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood, National Institutes of Health, Bethesda, Maryland, USA
| | - Johanna C Herkert
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Alissa M D'gama
- Division of Newborn Medicine, Division of Genetics and Genomics, and The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA
| | - Diana Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood, National Institutes of Health, Bethesda, Maryland, USA.,Division of Neurology, Children's National Health System, Washington, DC, USA
| | - James Collins
- Mercy Clinic Pediatric Neurology, Springfield, Missouri, USA
| | - Katherine R Chao
- Center for Mendelian Genomics at the Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood, National Institutes of Health, Bethesda, Maryland, USA
| | - Mirthe H Schoots
- Department of Pathology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Jan D H Jongbloed
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood, National Institutes of Health, Bethesda, Maryland, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine, Division of Genetics and Genomics, and The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA
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Chao HT, Davids M, Burke E, Pappas JG, Rosenfeld JA, McCarty AJ, Davis T, Wolfe L, Toro C, Tifft C, Xia F, Stong N, Johnson TK, Warr CG, Yamamoto S, Adams DR, Markello TC, Gahl WA, Bellen HJ, Wangler MF, Malicdan MCV, Adams DR, Adams CJ, Alejandro ME, Allard P, Ashley EA, Bacino CA, Balasubramanyam A, Barseghyan H, Beggs AH, Bellen HJ, Bernstein JA, Bick DP, Birch CL, Boone BE, Briere LC, Brown DM, Brush M, Burrage LC, Chao KR, Clark GD, Cogan JD, Cooper CM, Craigen WJ, Davids M, Dayal JG, Dell'Angelica EC, Dhar SU, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Draper DD, Dries AM, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fisher PG, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Goldstein DB, Gordon M“GG, Gould SE, Gourdine JPF, Graham BH, Groden CA, Gropman AL, Hackbarth ME, Haendel M, Hamid R, Hanchard NA, Handley LH, Hardee I, Herzog MR, Holm IA, Howerton EM, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Koehler AE, Koeller DM, Kohane IS, Kohler JN, Krasnewich DM, Krieg EL, Krier JB, Kyle JE, Lalani SR, Latham L, Latour YL, Lau CC, Lazar J, Lee BH, Lee H, Lee PR, Levy SE, Levy DJ, Lewis RA, Liebendorder AP, Lincoln SA, Loomis CR, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Mashid AS, Mazur P, McCarty AJ, McConkie-Rosell A, McCray AT, Metz TO, Might M, Moretti PM, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Ramoni RB, Rodan LH, Sadozai S, Schaffer KE, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Silverman EK, Sinsheimer JS, Soldatos AG, Spillmann RC, Splinter K, Stoler JM, Stong N, Strong KA, Sullivan JA, Sweetser DA, Thomas SP, Tift CJ, Tolman NJ, Toro C, Tran AA, Valivullah ZM, Vilain E, Waggott DM, Wahl CE, Walley NM, Walsh CA, Wangler MF, Warburton M, Ward PA, Waters KM, Webb-Robertson BJM, Weech AA, Westerfield M, Wheeler MT, Wise AL, Worthe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zornio PA. A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. Am J Hum Genet 2017; 100:128-137. [PMID: 28017372 PMCID: PMC5223093 DOI: 10.1016/j.ajhg.2016.11.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
Early B cell factor 3 (EBF3) is a member of the highly evolutionarily conserved Collier/Olf/EBF (COE) family of transcription factors. Prior studies on invertebrate and vertebrate animals have shown that EBF3 homologs are essential for survival and that loss-of-function mutations are associated with a range of nervous system developmental defects, including perturbation of neuronal development and migration. Interestingly, aristaless-related homeobox (ARX), a homeobox-containing transcription factor critical for the regulation of nervous system development, transcriptionally represses EBF3 expression. However, human neurodevelopmental disorders related to EBF3 have not been reported. Here, we describe three individuals who are affected by global developmental delay, intellectual disability, and expressive speech disorder and carry de novo variants in EBF3. Associated features seen in these individuals include congenital hypotonia, structural CNS malformations, ataxia, and genitourinary abnormalities. The de novo variants affect a single conserved residue in a zinc finger motif crucial for DNA binding and are deleterious in a fly model. Our findings indicate that mutations in EBF3 cause a genetic neurodevelopmental syndrome and suggest that loss of EBF3 function might mediate a subset of neurologic phenotypes shared by ARX-related disorders, including intellectual disability, abnormal genitalia, and structural CNS malformations.
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Shashi V, Pena LD, Kim K, Burton B, Hempel M, Schoch K, Walkiewicz M, McLaughlin HM, Cho M, Stong N, Hickey SE, Shuss CM, Freemark MS, Bellet JS, Keels MA, Bonner MJ, El-Dairi M, Butler M, Kranz PG, Stumpel CT, Klinkenberg S, Oberndorff K, Alawi M, Santer R, Petrovski S, Kuismin O, Korpi-Heikkilä S, Pietilainen O, Aarno P, Kurki MI, Hoischen A, Need AC, Goldstein DB, Kortüm F, Bacino A, Lee BH, Balasubramanyam A, Burrage LC, Clark GD, Craigen WJ, Dhar SU, Emrick LT, Graham BH, Jain M, Lalani SR, Lewis RA, Moretti PM, Nicholas SK, Orange JS, Posey JE, Potocki L, Rosenfeld JA, Scott DA, Hanchard NA, Alyssa TA, Mercedes AE, Mashid AS, Bellen HJ, Yamamoto S, Wangler MF, Westerfield M, Postlethwait JH, Eng CM, Yang Y, Muzny DM, Ward PA, Ramoni RB, McCray AT, Kohane IS, Holm IA, Might M, Mazur P, Splinter K, Esteves C, Shashi V, Jiang YH, Pena LD, McConkie-Rosell A, Schoch K, Spillmann RC, Sullivan JA, Walley NM, Goldstein DB, Stong N, Beggs AH, Loscalzo J, MacRae CA, Silverman EK, Stoler JM, Sweetser DA, Maas RL, Krier JB, Rodan LH, Walsh CA, Cooper CM, Pallais JC, Donnell-Fink LA, Krieg EL, Lincoln SA, Briere LC, Jacob HJ, Worthey EA, Lazar J, Strong KA, Handley LH, Newberry JS, Bick DP, Schroeder MC, Brown DM, Birch CL, Levy SE, Boone BE, Dorset DC, Jones AL, Manolio TA, Mulvihill JJ, Wise AL, Dayal JG, Eckstein DJ, Krasnewich DM, Loomis CR, Mamounas LA, Iglesias B, Martin C, Koeller DM, Metz TO, Ashley EA, Fisher PG, Bernstein JA, Wheeler MT, Zornio PA, Waggott DM, Dries AM, Kohler JN, Dipple KM, Nelson SF, Palmer CG, Vilain E, Allard P, Dell Angelica EC, Lee H, Sinsheimer JS, Papp JC, Dorrani N, Herzog MR, Barseghyan H, Adams DR, Adams CJ, Burke EA, Chao KR, Davids M, Draper DD, Estwick T, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Gordon MG, Groden CA, Gropman AL, Hackbarth ME, Hardee I, Johnston JM, Koehler AE, Latham L, Latour YL, Lau CYC, Lee PR, Levy DJ, Liebendorder AP, Macnamara EF, Maduro VV, Malicdan MV, Markello TC, McCarty AJ, Murphy JL, Nehrebecky ME, Novacic D, Pusey BN, Sadozai S, Schaffer KE, Sharma P, Soldatos AG, Thomas SP, Tifft CJ, Tolman NJ, Toro C, Valivullah ZM, Wahl CE, Warburton M, Weech AA, Wolfe LA, Yu G, Hamid R, Newman JH, Phillips JA, Cogan JD. De Novo Truncating Variants in ASXL2 Are Associated with a Unique and Recognizable Clinical Phenotype. Am J Hum Genet 2016; 99:991-999. [PMID: 27693232 PMCID: PMC5065681 DOI: 10.1016/j.ajhg.2016.08.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/24/2016] [Indexed: 12/14/2022] Open
Abstract
The ASXL genes (ASXL1, ASXL2, and ASXL3) participate in body patterning during embryogenesis and encode proteins involved in epigenetic regulation and assembly of transcription factors to specific genomic loci. Germline de novo truncating variants in ASXL1 and ASXL3 have been respectively implicated in causing Bohring-Opitz and Bainbridge-Ropers syndromes, which result in overlapping features of severe intellectual disability and dysmorphic features. ASXL2 has not yet been associated with a human Mendelian disorder. In this study, we performed whole-exome sequencing in six unrelated probands with developmental delay, macrocephaly, and dysmorphic features. All six had de novo truncating variants in ASXL2. A careful review enabled the recognition of a specific phenotype consisting of macrocephaly, prominent eyes, arched eyebrows, hypertelorism, a glabellar nevus flammeus, neonatal feeding difficulties, hypotonia, and developmental disabilities. Although overlapping features with Bohring-Opitz and Bainbridge-Ropers syndromes exist, features that distinguish the ASXL2-associated condition from ASXL1- and ASXL3-related disorders are macrocephaly, absence of growth retardation, and more variability in the degree of intellectual disabilities. We were also able to demonstrate with mRNA studies that these variants are likely to exert a dominant-negative effect, given that both alleles are expressed in blood and the mutated ASXL2 transcripts escape nonsense-mediated decay. In conclusion, de novo truncating variants in ASXL2 underlie a neurodevelopmental syndrome with a clinically recognizable phenotype. This report expands the germline disorders that are linked to the ASXL genes.
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Davids M, Kane MS, He M, Wolfe LA, Li X, Raihan MA, Chao KR, Bone WP, Boerkoel CF, Gahl WA, Toro C. Disruption of Golgi morphology and altered protein glycosylation in PLA2G6-associated neurodegeneration. J Med Genet 2015; 53:180-9. [PMID: 26668131 DOI: 10.1136/jmedgenet-2015-103338] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/09/2015] [Indexed: 01/07/2023]
Abstract
BACKGROUND Mutations in PLA2G6, which encodes the calcium-independent phospholipase A2 group VI, cause neurodegeneration and diffuse cortical Lewy body formation by a yet undefined mechanism. We assessed whether altered protein glycosylation due to abnormal Golgi morphology might be a factor in the pathology of this disease. METHODS Three patients presented with PLA2G6-associated neurodegeneration (PLAN); two had infantile neuroaxonal dystrophy (INAD) and one had adult-onset dystonia-parkinsonism. We analysed protein N-linked and O-linked glycosylation in cerebrospinal fluid, plasma, urine, and cultured skin fibroblasts using high performance liquid chromatography (HPLC) and matrix-assisted laser desorption ionization--time of flight/mass spectrometry (MALDI-TOF/MS). We also assessed sialylation and Golgi morphology in cultured fibroblasts by immunofluorescence and performed rescue experiments using a lentiviral vector. RESULTS The patients with INAD had PLA2G6 mutations NM_003560.2: c.[950G>T];[426-1077dup] and c.[1799G>A];[2221C>T] and the patient with dystonia-parkinsonism had PLA2G6 mutations NM_003560.2: c.[609G>A];[2222G>A]. All three patients had altered Golgi morphology and abnormalities of protein O-linked glycosylation and sialylation in cultured fibroblasts that were rescued by lentiviral overexpression of wild type PLA2G6. CONCLUSIONS Our findings add altered Golgi morphology, O-linked glycosylation and sialylation defects to the phenotypical spectrum of PLAN; these pathways are essential for correct processing and distribution of proteins. Lewy body and Tau pathology, two neuropathological features of PLAN, could emerge from these defects. Therefore, Golgi morphology, O-linked glycosylation and sialylation may play a role in the pathogenesis of PLAN and perhaps other neurodegenerative disorders.
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Affiliation(s)
- Mariska Davids
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland, USA Office of the Clinical Director, NHGRI, National Institutes of Health, Bethesda, Maryland, USA
| | - Megan S Kane
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland, USA Office of the Clinical Director, NHGRI, National Institutes of Health, Bethesda, Maryland, USA
| | - Miao He
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA The Michael J Palmieri Metabolic Laboratory, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lynne A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland, USA Office of the Clinical Director, NHGRI, National Institutes of Health, Bethesda, Maryland, USA
| | - Xueli Li
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA The Michael J Palmieri Metabolic Laboratory, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Mohd A Raihan
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA The Michael J Palmieri Metabolic Laboratory, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Katherine R Chao
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland, USA Office of the Clinical Director, NHGRI, National Institutes of Health, Bethesda, Maryland, USA
| | - William P Bone
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland, USA Office of the Clinical Director, NHGRI, National Institutes of Health, Bethesda, Maryland, USA
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland, USA Office of the Clinical Director, NHGRI, National Institutes of Health, Bethesda, Maryland, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland, USA Office of the Clinical Director, NHGRI, National Institutes of Health, Bethesda, Maryland, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland, USA Office of the Clinical Director, NHGRI, National Institutes of Health, Bethesda, Maryland, USA
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