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Sun Y, Zhao X, Fan X, Wang M, Li C, Liu Y, Wu P, Yan Q, Sun L. Assessing the impact of sequencing platforms and analytical pipelines on whole-exome sequencing. Front Genet 2024; 15:1334075. [PMID: 38818042 PMCID: PMC11137314 DOI: 10.3389/fgene.2024.1334075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/30/2024] [Indexed: 06/01/2024] Open
Affiliation(s)
- Yanping Sun
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xiaochao Zhao
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xue Fan
- Clinical Research Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Miao Wang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Chaoyang Li
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Ping Wu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Sun
- GeneMind Biosciences Company Limited, Shenzhen, China
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2
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Yin R, Gutierrez A, Kobren SN, Avillach P. VarPPUD: Variant post prioritization developed for undiagnosed genetic disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.15.24305876. [PMID: 38699371 PMCID: PMC11065012 DOI: 10.1101/2024.04.15.24305876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Rare and ultra-rare genetic conditions are estimated to impact nearly 1 in 17 people worldwide, yet accurately pinpointing the diagnostic variants underlying each of these conditions remains a formidable challenge. Because comprehensive, in vivo functional assessment of all possible genetic variants is infeasible, clinicians instead consider in silico variant pathogenicity predictions to distinguish plausibly disease-causing from benign variants across the genome. However, in the most difficult undiagnosed cases, such as those accepted to the Undiagnosed Diseases Network (UDN), existing pathogenicity predictions cannot reliably discern true etiological variant(s) from other deleterious candidate variants that were prioritized through N-of-1 efforts. Pinpointing the disease-causing variant from a pool of plausible candidates remains a largely manual effort requiring extensive clinical workups, functional and experimental assays, and eventual identification of genotype- and phenotype-matched individuals. Here, we introduce VarPPUD, a tool trained on prioritized variants from UDN cases, that leverages gene-, amino acid-, and nucleotide-level features to discern pathogenic variants from other deleterious variants that are unlikely to be confirmed as disease relevant. VarPPUD achieves a cross-validated accuracy of 79.3% and precision of 77.5% on a held-out subset of uniquely challenging UDN cases, respectively representing an average 18.6% and 23.4% improvement over nine traditional pathogenicity prediction approaches on this task. We validate VarPPUD's ability to discriminate likely from unlikely pathogenic variants on synthetic, GAN-generated candidate variants as well. Finally, we show how VarPPUD can be probed to evaluate each input feature's importance and contribution toward prediction-an essential step toward understanding the distinct characteristics of newly-uncovered disease-causing variants. Significance Statement Patients with chronic, undiagnosed and underdiagnosed genetic conditions often endure expensive and excruciating years-long diagnostic odysseys without clear results. In many instances, clinical genome sequencing of patients and their family members fails to reveal known disease-causing variants, although compelling variants of uncertain significance are frequently encountered. Existing computational tools struggle to reliably differentiate truly disease-causing variants from other plausible candidate variants within these prioritized sets. Consequently, the confirmation of disease-causing variants often necessitates extensive experimental follow-up, including studies in model organisms and identification of other similarly presenting genotype-matched individuals, a process that can extend for several years. Here, we present VarPPUD, a tool trained specifically to distinguish likely from unlikely to be confirmed pathogenic variants that were prioritized across cases in the Undiagnosed Diseases Network. By evaluating the importance and impact of different input feature values on prediction, we gain deeper insights into the distinctive attributes of difficult-to-identify diagnostic variants. For patients who remain undiagnosed following comprehensive whole genome sequencing, our new method VarPPUD may reveal pathogenic variants amid a pool of candidate variants, thereby advancing diagnostic efforts where progress has otherwise stalled.
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3
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Taruscio D, Gahl WA. Rare diseases: challenges and opportunities for research and public health. Nat Rev Dis Primers 2024; 10:13. [PMID: 38424095 DOI: 10.1038/s41572-024-00505-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Affiliation(s)
| | - William A Gahl
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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4
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Mattijssen S, Kerkhofs K, Stephen J, Yang A, Han CG, Tadafumi Y, Iben JR, Mishra S, Sakhawala RM, Ranjan A, Gowda M, Gahl WA, Gu S, Malicdan MC, Maraia RJ. A POLR3B-variant reveals a Pol III transcriptome response dependent on La protein/SSB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.577363. [PMID: 38410490 PMCID: PMC10896340 DOI: 10.1101/2024.02.05.577363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. Human POLR3 pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a human POLR3B:c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing of POLR3B. Genome-edited POLR3B1625A>G HEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunit POLR3E. La protein was increased relative to its abundant pre-tRNA ligands which bind via their U(n)U-3'-termini. Assays for cellular transcription revealed greater deficiencies for tRNA genes bearing terminators comprised of 4Ts than of ≥5Ts. La-knockdown decreased Pol III ncRNA expression unlinked to RNA stability. Consistent with these effects, small-RNAseq showed that POLR3B1625A>G and patient fibroblasts express more tRNA fragments (tRFs) derived from pre-tRNA 3'-trailers (tRF-1) than from mature-tRFs, and higher levels of multiple miRNAs, relative to control cells. The data indicate that decreased levels of Pol III transcripts can lead to functional excess of La protein which reshapes small ncRNA profiles revealing new depth in the Pol III system. Finally, patient cell RNA analysis uncovered a strategy for tRF-1/tRF-3 as POLR3-deficiency biomarkers.
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Affiliation(s)
- Sandy Mattijssen
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Kyra Kerkhofs
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Joshi Stephen
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Acong Yang
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - Chen G. Han
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Yokoyama Tadafumi
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - James R. Iben
- Molecular Genetics Core, NICHD, NIH, Bethesda, MD 20892, USA
| | - Saurabh Mishra
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Rima M. Sakhawala
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Amitabh Ranjan
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mamatha Gowda
- Department of Obstetrics & Gynaecology, Jawaharlal Institute of Post-Graduate Medical Education and Research, Puducherry, India
| | - William A. Gahl
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Shuo Gu
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - May C. Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Richard J. Maraia
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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5
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Siebold D, Denton J, Hurst ACE, Moss I, Korf B. A qualitative evaluation of patient and parent experiences with an undiagnosed diseases program. Am J Med Genet A 2024; 194:131-140. [PMID: 37750194 DOI: 10.1002/ajmg.a.63417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/03/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
Previous studies have explored patient experiences before being seen or at the beginning of their evaluation by undiagnosed diseases programs. This study provides additional insight into experiences after participation through in-depth, qualitative evaluation, allowing for reflection of current practice and patient/parent needs. Semi-structured interviews were conducted with patients and parents of patients seen at the University of Alabama at Birmingham (UAB)'s unique, clinically focused Undiagnosed Diseases Program (UDP). Analysis of the interviews was guided by a thematic approach. Participants had undergone a diagnostic odyssey before being evaluated by the UDP and remained hopeful for a diagnosis. They appreciated the opportunity to be seen by the UDP. However, perception of experiences differed based on whether evaluation by the UDP led to a diagnosis. Additionally, while participants were pleased with initial communication, they indicated that there were unmet needs regarding follow-up. Patients and parents of patients believe that participation in an undiagnosed diseases program is the best option for diagnosis. The findings of this study provide a general overview of patient experiences and highlight strengths of the UAB UDP while also emphasizing areas to focus the improvement to optimize the benefit to patients and families with undiagnosed and rare diseases, which could be used helpful in the development of similar clinics.
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Affiliation(s)
- Dorothea Siebold
- University of Alabama (UAB), School of Health Professions, Birmingham, Alabama, USA
| | - Jessica Denton
- University of Alabama (UAB), School of Health Professions, Birmingham, Alabama, USA
| | | | - Irene Moss
- UAB Department of Genetics, Birmingham, Alabama, USA
| | - Bruce Korf
- UAB Department of Genetics, Birmingham, Alabama, USA
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6
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Novacic D, Uldrick T, Dulau-Florea A, Howe CE, Lee CCR, Kong HH, Gahl WA. Calciphylaxis in POEMS syndrome: Case report. RARE : OPEN RESEARCH IN RARE DISEASES 2024; 2:100019. [PMID: 38435320 PMCID: PMC10907981 DOI: 10.1016/j.rare.2024.100019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
POEMS Syndrome is a constellation of findings including Polyneuropathy, Organomegaly, Endocrinopathy, Monoclonal plasma cell disorder, and Skin changes. Calciphylaxis, a microangiopathy involving vascular calcification and thrombotic occlusions, occurs rarely in POEMS. We present a case of prominent calciphylaxis that antedated the diagnosis of POEMS. The patient presented with extensive ecchymoses progressing to necrotic lesions in the setting of acute renal injury. Previously, she had chronic slowly progressive polyneuropathy, splenomegaly, hypothyroidism, amenorrhea, and ascites. Calciphylaxis was diagnosed on skin biopsy, and POEMS was diagnosed based upon clinical findings plus a bone marrow biopsy showing 15% lambda chain restricted plasma cells. Treatment for the calciphylaxis was supportive with fluids, tissue debridement, wound vacuum devices and antibiotics for secondary infection. Myeloma was treated with bortezomib and steroids. All aspects of the patient's manifestations improved. We conclude that calciphylaxis can be a prominent feature of POEMS and can appear prior to recognition of the full-blown syndrome.
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Affiliation(s)
- Danica Novacic
- Undiagnosed Diseases Program, National Institutes of Health (NIH) Common Fund, Office of the Director, NIH, Bethesda, MD, USA
| | - Thomas Uldrick
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Colleen Evans Howe
- Undiagnosed Diseases Program, National Institutes of Health (NIH) Common Fund, Office of the Director, NIH, Bethesda, MD, USA
| | - Chyi-Chia R. Lee
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, NIH, USA
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, USA
| | - William A. Gahl
- Undiagnosed Diseases Program, National Institutes of Health (NIH) Common Fund, Office of the Director, NIH, Bethesda, MD, USA
- Medical Genetics Branch, National Human Genome Research Institute, NIH, USA
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7
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Benavides D, Ebrahim A, Ravell JC, Lenardo M, Gahl WA, Toro C. Adult-onset neurodegeneration in XMEN disease. J Neuroimmunol 2024; 386:578251. [PMID: 38041964 PMCID: PMC10842803 DOI: 10.1016/j.jneuroim.2023.578251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/10/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023]
Abstract
BACKGROUND XMEN (X-linked immunodeficiency with magnesium defect, Epstein-Barr virus (EBV), and N-linked glycosylation defect) disease results from loss-of-function mutations in MAGT1, a protein that serves as a magnesium transporter and a subunit of the oligosaccharyltransferase (OST) complex. MAGT1 deficiency disrupts N-linked glycosylation, a critical regulator of immune function. XMEN results in recurrent EBV infections and a propensity for EBV-driven malignancies. Although XMEN is recognized as a systemic congenital disorder of glycosylation (CDG), its neurological involvement is rare and poorly characterized. CASES Two young men, ages 32 and 33, are described here with truncating mutations in MAGT1, progressive behavioral changes, and neurodegenerative symptoms. These features manifested well into adulthood. Both patients still presented with many of the molecular and clinical hallmarks of the typical XMEN patient, including chronic EBV viremia and decreased expression of NKG2D. CONCLUSION While previously unrecognized, XMEN may include prominent and disabling CNS manifestations. How MAGT1 deficiency directly or indirectly contributes to neurodegeneration remains unclear. Elucidating this mechanism may contribute to the understanding of neurodegeneration more broadly.
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Affiliation(s)
- Daniel Benavides
- Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA.
| | - Anusha Ebrahim
- Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA.
| | - Juan C Ravell
- Center for Allergy, Asthma, & Immune Disorders, Hackensack University Medical Center, Hackensack, NJ, USA; Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD, USA.
| | - Michael Lenardo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD, USA.
| | - William A Gahl
- Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Camilo Toro
- Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA.
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8
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Curic E, Ewans L, Pysar R, Taylan F, Botto LD, Nordgren A, Gahl W, Palmer EE. International Undiagnosed Diseases Programs (UDPs): components and outcomes. Orphanet J Rare Dis 2023; 18:348. [PMID: 37946247 PMCID: PMC10633944 DOI: 10.1186/s13023-023-02966-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Over the last 15 years, Undiagnosed Diseases Programs have emerged to address the significant number of individuals with suspected but undiagnosed rare genetic diseases, integrating research and clinical care to optimize diagnostic outcomes. This narrative review summarizes the published literature surrounding Undiagnosed Diseases Programs worldwide, including thirteen studies that evaluate outcomes and two commentary papers. Commonalities in the diagnostic and research process of Undiagnosed Diseases Programs are explored through an appraisal of available literature. This exploration allowed for an assessment of the strengths and limitations of each of the six common steps, namely enrollment, comprehensive clinical phenotyping, research diagnostics, data sharing and matchmaking, results, and follow-up. Current literature highlights the potential utility of Undiagnosed Diseases Programs in research diagnostics. Since participants have often had extensive previous genetic studies, research pipelines allow for diagnostic approaches beyond exome or whole genome sequencing, through reanalysis using research-grade bioinformatics tools and multi-omics technologies. The overall diagnostic yield is presented by study, since different selection criteria at enrollment and reporting processes make comparisons challenging and not particularly informative. Nonetheless, diagnostic yield in an undiagnosed cohort reflects the potential of an Undiagnosed Diseases Program. Further comparisons and exploration of the outcomes of Undiagnosed Diseases Programs worldwide will allow for the development and improvement of the diagnostic and research process and in turn improve the value and utility of an Undiagnosed Diseases Program.
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Affiliation(s)
- Ela Curic
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
| | - Lisa Ewans
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ryan Pysar
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - William Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Elizabeth Emma Palmer
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia.
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia.
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9
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Macnamara EF, Loydpierson A, Latour YL, D'Souza P, Murphy J, Wolfe L, Estwick T, Johnston JM, Yang J, Acosta MT, Lee PR, Pierson TM, Soldatos A, Toro C, Markello T, Adams DR, Gahl WA, Yousef M, Tifft CJ. Risks and benefits of anesthesia for combined pediatric procedures in the NIH undiagnosed diseases program. Mol Genet Metab 2023; 140:107707. [PMID: 37883914 DOI: 10.1016/j.ymgme.2023.107707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/28/2023]
Abstract
PURPOSE The NIH Undiagnosed Diseases Program (UDP) aims to provide diagnoses to patients who have previously received exhaustive evaluations yet remain undiagnosed. Patients undergo procedural anesthesia for deep phenotyping for analysis with genomic testing. METHODS A retrospective chart review was performed to determine the safety and benefit of procedural anesthesia in pediatric patients in the UDP. Adverse perioperative events were classified as anesthesia-related complications or peri-procedural complications. The contribution of procedures performed under anesthesia to arriving at a diagnosis was also determined. RESULTS From 2008 to 2020, 249 pediatric patients in the UDP underwent anesthesia for diagnostic procedures. The majority had a severe systemic disease (American Society for Anesthesiology status III, 79%) and/or a neurologic condition (91%). Perioperative events occurred in 45 patients; six of these were attributed to anesthesia. All patients recovered fully without sequelae. Nearly half of the 249 patients (49%) received a diagnosis, and almost all these diagnoses (88%) took advantage of information gleaned from procedures performed under anesthesia. CONCLUSIONS The benefits of anesthesia involving multiple diagnostic procedures in a well-coordinated, multidisciplinary, research setting, such as in the pediatric UDP, outweigh the risks.
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Affiliation(s)
- Ellen F Macnamara
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Amelia Loydpierson
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; University of North Carolina School of Medicine, Chapel Hill, NC, United States of America
| | - Yvonne L Latour
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, United States of America; Department of Pathology, Immunology, and Microbiology, Vanderbilt University, Nashville, TN, United States of America
| | - Precilla D'Souza
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; Hummingbird House Children's Hospice, 60 Curwen Terrace, Chermside, Queensland 4032, Australia
| | - Jennifer Murphy
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; Hummingbird House Children's Hospice, 60 Curwen Terrace, Chermside, Queensland 4032, Australia
| | - Lynne Wolfe
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Tyra Estwick
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States of America
| | - Jean M Johnston
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - John Yang
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Maria T Acosta
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Paul R Lee
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; Division of Neurology 2, Office of Neuroscience, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Tyler Mark Pierson
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; Departments of Pediatrics and Neurology & The Board of Governors, Regenerative Medicine Institute and the Cedars Sinai Center for the Undiagnosed Patient, Cedars Sinai Medical Center, Los Angeles, CA, United States of America
| | - Ariane Soldatos
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, United States of America
| | - Camilo Toro
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Tom Markello
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - David R Adams
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; National Human Genome Research Institute, NIH, Bethesda, MD, United States of America
| | - William A Gahl
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Muhammad Yousef
- National Institutes of Health Clinical Center, Department of Perioperative Medicine, Pediatric Anesthesiology, Bethesda, MD, United States of America
| | - Cynthia J Tifft
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; National Human Genome Research Institute, NIH, Bethesda, MD, United States of America.
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10
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Alsentzer E, Finlayson SG, Li MM, Kobren SN, Kohane IS. Simulation of undiagnosed patients with novel genetic conditions. Nat Commun 2023; 14:6403. [PMID: 37828001 PMCID: PMC10570269 DOI: 10.1038/s41467-023-41980-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Rare Mendelian disorders pose a major diagnostic challenge and collectively affect 300-400 million patients worldwide. Many automated tools aim to uncover causal genes in patients with suspected genetic disorders, but evaluation of these tools is limited due to the lack of comprehensive benchmark datasets that include previously unpublished conditions. Here, we present a computational pipeline that simulates realistic clinical datasets to address this deficit. Our framework jointly simulates complex phenotypes and challenging candidate genes and produces patients with novel genetic conditions. We demonstrate the similarity of our simulated patients to real patients from the Undiagnosed Diseases Network and evaluate common gene prioritization methods on the simulated cohort. These prioritization methods recover known gene-disease associations but perform poorly on diagnosing patients with novel genetic disorders. Our publicly-available dataset and codebase can be utilized by medical genetics researchers to evaluate, compare, and improve tools that aid in the diagnostic process.
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Grants
- U01 HG007690 NHGRI NIH HHS
- U54 NS108251 NINDS NIH HHS
- U01 HG010219 NHGRI NIH HHS
- U01 HG007672 NHGRI NIH HHS
- U01 HG010233 NHGRI NIH HHS
- U01 HG010230 NHGRI NIH HHS
- U01 HG007943 NHGRI NIH HHS
- U01 HG010217 NHGRI NIH HHS
- U01 HG007942 NHGRI NIH HHS
- U01 HG010215 NHGRI NIH HHS
- U01 HG007708 NHGRI NIH HHS
- T32 HG002295 NHGRI NIH HHS
- T32 GM007753 NIGMS NIH HHS
- U01 HG007674 NHGRI NIH HHS
- U01 TR001395 NCATS NIH HHS
- U01 HG007709 NHGRI NIH HHS
- U54 NS093793 NINDS NIH HHS
- U01 HG007530 NHGRI NIH HHS
- U01 TR002471 NCATS NIH HHS
- U01 HG007703 NHGRI NIH HHS
- UDN research reported in this manuscript was supported by the NIH Common Fund, through the Office of Strategic Coordination/Office of the NIH Director under Award Number(s) U01HG007709, U01HG010219, U01HG010230, U01HG010217, U01HG010233, U01HG010215, U01HG007672, U01HG007690, U01HG007708, U01HG007703, U01HG007674, U01HG007530, U01HG007942, U01HG007943, U01TR001395, U01TR002471, U54NS108251, and U54NS093793.
- E.A. is supported by a Microsoft Research PhD Fellowship.
- S.F. is supported by award Number T32GM007753 from the National Institute of General Medical Sciences.
- M.L. is supported by T32HG002295 from the National Human Genome Research Institute and a National Science Foundation Graduate Research Fellowship.
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Affiliation(s)
- Emily Alsentzer
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Program in Health Sciences and Technology, MIT, Cambridge, MA, 02139, USA
| | - Samuel G Finlayson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Program in Health Sciences and Technology, MIT, Cambridge, MA, 02139, USA
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, 98105, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98105, USA
| | - Michelle M Li
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, 02115, USA
| | - Shilpa N Kobren
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
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11
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Jo HS, Yang M, Ahn SY, Sung SI, Park WS, Jang JH, Chang YS. Optimal Protocols and Management of Clinical and Genomic Data Collection to Assist in the Early Diagnosis and Treatment of Multiple Congenital Anomalies. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1673. [PMID: 37892336 PMCID: PMC10605914 DOI: 10.3390/children10101673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/01/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023]
Abstract
Standardized protocols have been designed and developed specifically for clinical information collection and obtaining trio genomic information from infants affected with congenital anomalies (CA) and their parents, as well as securing human biological resources. The protocols include clinical and genomic information collection on multiple CA that were difficult to diagnose using pre-existing screening methods. We obtained human-derived resources and genomic information from 138 cases, including 45 families of infants with CA and their parent trios. For the clinical information collection protocol, criteria for target patient selection and a consent system for collecting and utilizing research resources are crucial. Whole genome sequencing data were generated for all participants, and standardized protocols were developed for resource collection and manufacturing. We recorded the phenotype information according to the Human Phenotype Ontology term, and epidemiological information was collected through an environmental factor questionnaire. Updating and recording of clinical symptoms and genetic information that have been newly added or changed over time are significant. The protocols enabled long-term tracking by including the growth and development status that reflect the important characteristics of newborns. Using these clinical and genetic information collection protocols for CA, an essential platform for early genetic diagnosis and diagnostic research can be established, and new genetic diagnostic guidelines can be presented in the near future.
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Affiliation(s)
- Heui Seung Jo
- Department of Pediatrics, Kangwon National University Hospital, Kangwon National University School of Medicine, Kangwon 24289, Republic of Korea
| | - Misun Yang
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - So Yoon Ahn
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Se In Sung
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Won Soon Park
- Department of Pediatrics, CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Yun Sil Chang
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Cell and Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Republic of Korea
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12
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Xiao C, Cassini T, Benavides D, Ebrahim A, Adams D, Toro C. Genomic Diagnoses for Ectopic Intracerebral Calcifications. Neurol Genet 2023; 9:e200083. [PMID: 37547187 PMCID: PMC10399077 DOI: 10.1212/nxg.0000000000200083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/24/2023] [Indexed: 08/08/2023]
Abstract
Background and Objectives Ectopic intracerebral calcifications (EICs) in the basal ganglia, thalamus, cerebellum, or white matter are seen in a variety of disease states or may be found incidentally on brain imaging. The clinical significance and proportion of cases attributable to an underlying genetic cause is unknown. Methods This retrospective cohort study details the clinical, imaging, and genomic findings of 44 patients with EICs who had no established diagnosis despite extensive medical workup. Results In total, 15 of 44 patients received a diagnosis through genomic testing explaining their calcifications, and 2 more received a diagnosis that has not been previously associated with EICs. Six of the 15 were found to have one of the 4 genes (PDGFB, PDGFRB, SLC20A2, and XPR1) conventionally associated with the phenotypic term "idiopathic basal ganglia calcifications." Discussion These findings support the use of genomic testing for symptomatic patients with EICs.
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Affiliation(s)
- Changrui Xiao
- From the National Human Genome Research Institute (C.X., T.C., D.B., A.E., D.A., C.T.), Bethesda, MD; and Department of Neurology (C.X.), University of California - Irvine
| | - Thomas Cassini
- From the National Human Genome Research Institute (C.X., T.C., D.B., A.E., D.A., C.T.), Bethesda, MD; and Department of Neurology (C.X.), University of California - Irvine
| | - Daniel Benavides
- From the National Human Genome Research Institute (C.X., T.C., D.B., A.E., D.A., C.T.), Bethesda, MD; and Department of Neurology (C.X.), University of California - Irvine
| | - Anusha Ebrahim
- From the National Human Genome Research Institute (C.X., T.C., D.B., A.E., D.A., C.T.), Bethesda, MD; and Department of Neurology (C.X.), University of California - Irvine
| | - David Adams
- From the National Human Genome Research Institute (C.X., T.C., D.B., A.E., D.A., C.T.), Bethesda, MD; and Department of Neurology (C.X.), University of California - Irvine
| | - Camilo Toro
- From the National Human Genome Research Institute (C.X., T.C., D.B., A.E., D.A., C.T.), Bethesda, MD; and Department of Neurology (C.X.), University of California - Irvine
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13
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Riboldi GM, Di Fonzo AB, Stephen CD. Editorial: Genetic advances and translational applications in movement disorders. Front Neurol 2023; 14:1280958. [PMID: 37799287 PMCID: PMC10548374 DOI: 10.3389/fneur.2023.1280958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023] Open
Affiliation(s)
- Giulietta M. Riboldi
- Department of Neurology, The Marlene and Paolo Fresco Institute for Parkinson's and Movement Disorders, NYU Langone Health, New York, NY, United States
| | - Alessio B. Di Fonzo
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Christopher D. Stephen
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
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14
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Guthrie J, Ko¨stel Bal S, Lombardo SD, Mu¨ller F, Sin C, Hu¨tter CV, Menche J, Boztug K. AutoCore: A network-based definition of the core module of human autoimmunity and autoinflammation. SCIENCE ADVANCES 2023; 9:eadg6375. [PMID: 37656781 PMCID: PMC10848965 DOI: 10.1126/sciadv.adg6375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Although research on rare autoimmune and autoinflammatory diseases has enabled definition of nonredundant regulators of homeostasis in human immunity, because of the single gene-single disease nature of many of these diseases, contributing factors were mostly unveiled in sequential and noncoordinated individual studies. We used a network-based approach for integrating a set of 186 inborn errors of immunity with predominant autoimmunity/autoinflammation into a comprehensive map of human immune dysregulation, which we termed "AutoCore." The AutoCore is located centrally within the interactome of all protein-protein interactions, connecting and pinpointing multidisease markers for a range of common, polygenic autoimmune/autoinflammatory diseases. The AutoCore can be subdivided into 19 endotypes that correspond to molecularly and phenotypically cohesive disease subgroups, providing a molecular mechanism-based disease classification and rationale toward systematic targeting for therapeutic purposes. Our study provides a proof of concept for using network-based methods to systematically investigate the molecular relationships between individual rare diseases and address a range of conceptual, diagnostic, and therapeutic challenges.
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Affiliation(s)
- Julia Guthrie
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Zimmermannplatz 10, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Sevgi Ko¨stel Bal
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Zimmermannplatz 10, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Zimmermannplatz 10, A-1090 Vienna, Austria
| | - Salvo Danilo Lombardo
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Felix Mu¨ller
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Celine Sin
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Christiane V. R. Hu¨tter
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter, A-1030 Vienna, Austria
| | - Jo¨rg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
- Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, A-1090 Vienna, Austria
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Zimmermannplatz 10, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Zimmermannplatz 10, A-1090 Vienna, Austria
- St. Anna Children’s Hospital, Kinderspitalgasse 6, A-1090, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Währinger Gürtel 18-20, A-1090 Vienna, Austria
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15
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McFadden JR, Tolete CDP, Huang Y, Macnamara E, Sept D, Nesterova G, Gahl WA, Sackett DL, Malicdan MCV. Clinical, genetic, and structural characterization of a novel TUBB4B tubulinopathy. Mol Genet Metab Rep 2023; 36:100990. [PMID: 37448631 PMCID: PMC10336574 DOI: 10.1016/j.ymgmr.2023.100990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Microtubules are cytoskeletal polymers of ⍺/β-tubulin heterodimers essential for a wide range of cellular processes. Pathogenic variations in microtubule-encoding genes (e.g., TUBB4B, which encodes the β-4B tubulin isotype) are responsible for a wide spectrum of cerebral malformations, collectively referred to as "tubulinopathies." The phenotypic manifestation of TUBB4B-associated tubulinopathy is Leber congenital amaurosis with early-onset deafness (LCAEOD), an autosomal dominant syndrome characterized by photoreceptor and cochlear cell loss; all known patients have pathogenic variations in amino acid R391. We present the clinical and molecular genetics findings of a 16-year-old female with a de novo missense variant in exon 1 of TUBB4B, c.32 A > G (p.Gln11Arg; Q11R). In addition to hearing loss and hyperopia without retinal abnormalities, our proband presented with two phenotypes of unknown genetic etiology, i.e., renal tubular Fanconi Syndrome (FS) and hypophosphatemic rickets (HR). The Q11R variant expands the genetic basis of early sensory hearing loss; its consequences with respect to microtubule structure are described. A mechanistic explanation for the FS and rickets, involving microtubule-mediated translocation of transporter proteins to and from the apical membrane of renal proximal tubular cells, is proposed.
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Affiliation(s)
- Jason R. McFadden
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Christina Deanne P. Tolete
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Yan Huang
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ellen Macnamara
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - David Sept
- Departments of Biomedical Engineering and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Galina Nesterova
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - William A. Gahl
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892-1851, USA
| | - Dan L. Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - May Christine V. Malicdan
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892-1851, USA
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16
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Trivellin G, Daly AF, Hernández-Ramírez LC, Araldi E, Tatsi C, Dale RK, Fridell G, Mittal A, Faucz FR, Iben JR, Li T, Vitali E, Stojilkovic SS, Kamenicky P, Villa C, Baussart B, Chittiboina P, Toro C, Gahl WA, Eugster EA, Naves LA, Jaffrain-Rea ML, de Herder WW, Neggers SJCMM, Petrossians P, Beckers A, Lania AG, Mains RE, Eipper BA, Stratakis CA. Germline loss-of-function PAM variants are enriched in subjects with pituitary hypersecretion. Front Endocrinol (Lausanne) 2023; 14:1166076. [PMID: 37388215 PMCID: PMC10303134 DOI: 10.3389/fendo.2023.1166076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/10/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction Pituitary adenomas (PAs) are common, usually benign tumors of the anterior pituitary gland which, for the most part, have no known genetic cause. PAs are associated with major clinical effects due to hormonal dysregulation and tumoral impingement on vital brain structures. PAM encodes a multifunctional protein responsible for the essential C-terminal amidation of secreted peptides. Methods Following the identification of a loss-of-function variant (p.Arg703Gln) in the peptidylglycine a-amidating monooxygenase (PAM) gene in a family with pituitary gigantism, we investigated 299 individuals with sporadic PAs and 17 familial isolated PA kindreds for PAM variants. Genetic screening was performed by germline and tumor sequencing and germline copy number variation (CNV) analysis. Results In germline DNA, we detected seven heterozygous, likely pathogenic missense, truncating, and regulatory SNVs. These SNVs were found in sporadic subjects with growth hormone excess (p.Gly552Arg and p.Phe759Ser), pediatric Cushing disease (c.-133T>C and p.His778fs), or different types of PAs (c.-361G>A, p.Ser539Trp, and p.Asp563Gly). The SNVs were functionally tested in vitro for protein expression and trafficking by Western blotting, splicing by minigene assays, and amidation activity in cell lysates and serum samples. These analyses confirmed a deleterious effect on protein expression and/or function. By interrogating 200,000 exomes from the UK Biobank, we confirmed a significant association of the PAM gene and rare PAM SNVs with diagnoses linked to pituitary gland hyperfunction. Conclusion The identification of PAM as a candidate gene associated with pituitary hypersecretion opens the possibility of developing novel therapeutics based on altering PAM function.
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Affiliation(s)
- Giampaolo Trivellin
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Adrian F. Daly
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, University of Liège, Domaine Universitaire du Sart-Tilman, Liège, Belgium
| | - Laura C. Hernández-Ramírez
- Red de Apoyo a la Investigación, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Elisa Araldi
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Christina Tatsi
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Ryan K. Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Gus Fridell
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Arjun Mittal
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Fabio R. Faucz
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - James R. Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Tianwei Li
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | | | - Stanko S. Stojilkovic
- Section on Cellular Signaling, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Peter Kamenicky
- Université Paris-Saclay, Institut national de la santé et de la recherche médicale (INSERM), Physiologie et Physiopathologie Endocriniennes, Le Kremlin-Bicêtre, France
| | - Chiara Villa
- Département de Neuropathologie de la Pitié Salpêtrière, Hôpital de la Pitié-Salpêtrière - Assistance Publique–Hôpitaux de Paris (APHP) Sorbonne Université, Paris, France
- Institut national de la santé et de la recherche médicale (INSERM) U1016, Centre national de la recherche scientifique Unité Mixte de Recherche (CNRS UMR) 8104, Institut Cochin, Paris, France
| | - Bertrand Baussart
- Institut national de la santé et de la recherche médicale (INSERM) U1016, Centre national de la recherche scientifique Unité Mixte de Recherche (CNRS UMR) 8104, Institut Cochin, Paris, France
- Service de Neurochirurgie, Hôpital Pitié-Salpêtrière, AP-HP Sorbonne, Paris, France
| | - Prashant Chittiboina
- Neurosurgery Unit for Pituitary and Inheritable Diseases and Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Camilo Toro
- National Institutes of Health (NIH) Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - William A. Gahl
- National Institutes of Health (NIH) Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Erica A. Eugster
- Division of Endocrinology and Diabetes, Department of Pediatrics, Riley Hospital for Children at Indiana University (IU) Health, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Luciana A. Naves
- Service of Endocrinology, University Hospital, Faculty of Medicine, University of Brasilia, Brasilia, Brazil
| | - Marie-Lise Jaffrain-Rea
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
- Neuromed Institute, Istituto di Ricovero e Cura a Carattere Scientifico, Pozzilli, Italy
| | - Wouter W. de Herder
- Department of Medicine, Section Endocrinology, Pituitary Center Rotterdam, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Sebastian JCMM Neggers
- Department of Medicine, Section Endocrinology, Pituitary Center Rotterdam, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Patrick Petrossians
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, University of Liège, Domaine Universitaire du Sart-Tilman, Liège, Belgium
| | - Albert Beckers
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, University of Liège, Domaine Universitaire du Sart-Tilman, Liège, Belgium
| | - Andrea G. Lania
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Richard E. Mains
- Department of Neuroscience, University of Connecticut (UConn) Health, Farmington, CT, United States
| | - Betty A. Eipper
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Constantine A. Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
- Human Genetics and Precision Medicine, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology Hellas, Heraklion, Greece
- Research Institute, ELPEN, Athens, Greece
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17
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Cai M, Guo C, Wang X, Lin M, Xu S, Huang H, Lin N, Xu L. Classifying and evaluating fetuses with multicystic dysplastic kidney in etiologic studies. Exp Biol Med (Maywood) 2023; 248:858-865. [PMID: 37208928 PMCID: PMC10484196 DOI: 10.1177/15353702231164933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/18/2023] [Indexed: 05/21/2023] Open
Abstract
Multicystic dysplastic kidney (MCDK) is one of the most common fetal malformations, but its etiology remains unclear. Identification of the molecular etiology could provide a basis for prenatal diagnosis, consultation, and prognosis evaluation for MCDK fetuses. We used chromosome microarray analysis (CMA) and whole-exome sequencing (WES) to conduct genetic tests on MCDK fetuses and explore their genetic etiology. A total of 108 MCDK fetuses with or without other extrarenal abnormalities were selected. Karyotype analysis of 108 MCDK fetuses showed an abnormal karyotype in 4 (3.7%, 4/108) of the fetuses. However, CMA detected 15 abnormal copy number variations (CNVs) (14 pathogenic CNVs, and one variant of unknown significance [VUS] CNVs), in addition to four cases that were consistent with the results of karyotype analysis. Out of the 14 pathogenic CNVs cases, three were of 17q12 microdeletion, two of 22q11.21 microdeletion, 22q11.21 microduplication uniparental disomy (UPD), and one case of 4q31.3q32.2 microdeletion, 7q11.23 microduplication, 15q11.2 microdeletion, 16p11.2 microdeletion, and 17p12 microdeletion. Of the 89 MCDK fetuses with normal karyotype analysis and CMA, 15 were tested by WES. Two (13.3%, 2/15) fetuses were identified by WES as Bardet-Biedl syndrome (BBS) 1 and BBS2. Combined application of CMA-WES to detect MCDK fetuses can significantly improve the detection rate of genetic etiology, providing a basis for consultation, and prognosis evaluation.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Chong Guo
- Child Healthcare Department, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, China
| | - Xinrui Wang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Shiyi Xu
- Guangxi Medical University, Guangxi 541000, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
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18
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Frost FG, Morimoto M, Sharma P, Ruaud L, Belnap N, Calame DG, Uchiyama Y, Matsumoto N, Oud MM, Ferreira EA, Narayanan V, Rangasamy S, Huentelman M, Emrick LT, Sato-Shirai I, Kumada S, Wolf NI, Steinbach PJ, Huang Y, Pusey BN, Passemard S, Levy J, Drunat S, Vincent M, Guet A, Agolini E, Novelli A, Digilio MC, Rosenfeld JA, Murphy JL, Lupski JR, Vezina G, Macnamara EF, Adams DR, Acosta MT, Tifft CJ, Gahl WA, Malicdan MCV. Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis. Am J Hum Genet 2023; 110:663-680. [PMID: 36965478 PMCID: PMC10119142 DOI: 10.1016/j.ajhg.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/28/2023] [Indexed: 03/27/2023] Open
Abstract
The vast majority of human genes encode multiple isoforms through alternative splicing, and the temporal and spatial regulation of those isoforms is critical for organismal development and function. The spliceosome, which regulates and executes splicing reactions, is primarily composed of small nuclear ribonucleoproteins (snRNPs) that consist of small nuclear RNAs (snRNAs) and protein subunits. snRNA gene transcription is initiated by the snRNA-activating protein complex (SNAPc). Here, we report ten individuals, from eight families, with bi-allelic, deleterious SNAPC4 variants. SNAPC4 encoded one of the five SNAPc subunits that is critical for DNA binding. Most affected individuals presented with delayed motor development and developmental regression after the first year of life, followed by progressive spasticity that led to gait alterations, paraparesis, and oromotor dysfunction. Most individuals had cerebral, cerebellar, or basal ganglia volume loss by brain MRI. In the available cells from affected individuals, SNAPC4 abundance was decreased compared to unaffected controls, suggesting that the bi-allelic variants affect SNAPC4 accumulation. The depletion of SNAPC4 levels in HeLa cell lines via genomic editing led to decreased snRNA expression and global dysregulation of alternative splicing. Analysis of available fibroblasts from affected individuals showed decreased snRNA expression and global dysregulation of alternative splicing compared to unaffected cells. Altogether, these data suggest that these bi-allelic SNAPC4 variants result in loss of function and underlie the neuroregression and progressive spasticity in these affected individuals.
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Affiliation(s)
- F Graeme Frost
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Marie Morimoto
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Prashant Sharma
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Lyse Ruaud
- APHP.Nord, Robert Debré University Hospital, Department of Genetics, Paris, France; Université Paris Cité, Inserm UMR 1141, NeuroDiderot, 75019 Paris, France
| | - Newell Belnap
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Yuri Uchiyama
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan; Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Machteld M Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elise A Ferreira
- Department of Pediatrics, Emma Children's Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, the Netherlands; United for Metabolic Diseases, Amsterdam, the Netherlands
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sampath Rangasamy
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Matt Huentelman
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Lisa T Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Ikuko Sato-Shirai
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan; Department of Pediatrics, Shimada Ryoiku Medical Center Hachioji for Challenged Children, Tokyo, Japan
| | - Satoko Kumada
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Nicole I Wolf
- Amsterdam Leukodystrophy Center, Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Vrije Universiteit, Amsterdam, the Netherlands
| | - Peter J Steinbach
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yan Huang
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Barbara N Pusey
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Sandrine Passemard
- Université Paris Cité, Inserm UMR 1141, NeuroDiderot, 75019 Paris, France; Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, Paris, France
| | - Jonathan Levy
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France; Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France
| | - Séverine Drunat
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France; Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France; INSERM UMR1141, Neurodiderot, University of Paris, Paris, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, Nantes, France; Inserm, CNRS, University Nantes, l'institut du thorax, Nantes, France
| | - Agnès Guet
- APHP.Nord, Louis Mourier Hospital, Pediatrics Department, Paris, France
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer L Murphy
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - James R Lupski
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Gilbert Vezina
- Department of Diagnostic Radiology and Imaging, Children's National Hospital, Washington, DC, USA
| | - Ellen F Macnamara
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - David R Adams
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria T Acosta
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - William A Gahl
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - May Christine V Malicdan
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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Reid KM, Steel D, Nair S, Bhate S, Biassoni L, Sudhakar S, Heys M, Burke E, Kamsteeg EJ, Hameed B, Zech M, Mencacci NE, Barwick K, Topf M, Kurian MA. Loss-of-Function Variants in DRD1 in Infantile Parkinsonism-Dystonia. Cells 2023; 12:cells12071046. [PMID: 37048120 PMCID: PMC10093404 DOI: 10.3390/cells12071046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
The human dopaminergic system is vital for a broad range of neurological processes, including the control of voluntary movement. Here we report a proband presenting with clinical features of dopamine deficiency: severe infantile parkinsonism-dystonia, characterised by frequent oculogyric crises, dysautonomia and global neurodevelopmental impairment. CSF neurotransmitter analysis was unexpectedly normal. Triome whole-genome sequencing revealed a homozygous variant (c.110C>A, (p.T37K)) in DRD1, encoding the most abundant dopamine receptor (D1) in the central nervous system, most highly expressed in the striatum. This variant was absent from gnomAD, with a CADD score of 27.5. Using an in vitro heterologous expression system, we determined that DRD1-T37K results in loss of protein function. Structure-function modelling studies predicted reduced substrate binding, which was confirmed in vitro. Exposure of mutant protein to the selective D1 agonist Chloro APB resulted in significantly reduced cyclic AMP levels. Numerous D1 agonists failed to rescue the cellular defect, reflected clinically in the patient, who had no benefit from dopaminergic therapy. Our study identifies DRD1 as a new disease-associated gene, suggesting a crucial role for the D1 receptor in motor control.
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20
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Morimoto M, Bhambhani V, Gazzaz N, Davids M, Sathiyaseelan P, Macnamara EF, Lange J, Lehman A, Zerfas PM, Murphy JL, Acosta MT, Wang C, Alderman E, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Cassini T, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fieg EL, Fisher PG, Fogel BL, Forghani I, Glass I, Gochuico B, Goddard PC, Godfrey RA, Golden-Grant K, Grajewski A, Gutierrez I, Hadley D, Hahn S, Halley MC, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne WJ, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, LeBlanc K, Lee BH, Levitt R, Lewis RA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacRae CA, Maduro VV, Mahoney R, Mak BC, Mamounas LA, Manolio TA, Mao R, Maravilla K, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti P, Nakano-Okuno M, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Pusey Swerdzewski BN, Quinlan A, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Toro C, Tran AA, Ungar RA, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Weisz Hubshman M, Wener M, Wenger T, Wesseling Perry K, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV. Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ Genom Med 2023; 8:4. [PMID: 36765070 PMCID: PMC9918471 DOI: 10.1038/s41525-022-00343-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/06/2022] [Indexed: 02/12/2023] Open
Abstract
Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or "primed" by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.
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Affiliation(s)
- Marie Morimoto
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vikas Bhambhani
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Nour Gazzaz
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada ,grid.412125.10000 0001 0619 1117Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mariska Davids
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paalini Sathiyaseelan
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Ellen F. Macnamara
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Anna Lehman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Patricia M. Zerfas
- grid.94365.3d0000 0001 2297 5165Diagnostic and Research Services Branch, Office of Research Services, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jennifer L. Murphy
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Maria T. Acosta
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Camille Wang
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Emily Alderman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | | | - Sara Reichert
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Audrey Thurm
- grid.94365.3d0000 0001 2297 5165Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892 USA
| | - David R. Adams
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wendy J. Introne
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sharon M. Gorski
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cornelius F. Boerkoel
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - William A. Gahl
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Cynthia J. Tifft
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - May Christine V. Malicdan
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
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Peretz RH, Zein WM, Hufnagel RB, Ku C, Godfrey R, Wolfe L, Adams D, Gahl W, Toro C. A de novo hexokinase 1 (HK1) variant presenting as Boucher-Neuhäuser syndrome. Am J Med Genet A 2023; 191:624-629. [PMID: 36541585 DOI: 10.1002/ajmg.a.63045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022]
Abstract
Boucher-Neuhäuser syndrome (BNHS) is characterized by chorioretinal dystrophy, hypogonadotropic hypogonadism, and cerebellar dysfunction and atrophy. The disorder has been associated with biallelic pathogenic variants in the patatin-like phospholipase domain-containing protein 6 (PNPLA6) gene. We present an individual with a clinical diagnosis consistent with BNHS who lacked any PNPLA6 variants but on quartet family exome sequencing had a de novo variant in the hexokinase 1 (HK1) gene (NM_000188.2 [GRCh37/hg19]: g.71139826G>A, c.1240G>A, p.Gly414Arg), suggesting genetic heterogeneity for BNHS. Longitudinal follow-up indicated neurological deterioration, neuropsychiatric symptoms, and progressive cerebellar atrophy. The BNHS phenotype overlaps and expands the known HK1 genotypic and phenotypic spectrum. Individuals with variants in HK1 should undergo evaluation for hypogonadotropic hypogonadism, potentially amenable to treatment.
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Affiliation(s)
- Ryan H Peretz
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Wadih M Zein
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert B Hufnagel
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Christine Ku
- Department of Ophthalmology, Kaiser Permanente Medical Center, Santa Rosa, California, USA
| | - Rena Godfrey
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lynne Wolfe
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - David Adams
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - William Gahl
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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22
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Abstract
Exome sequencing (ES) and genome sequencing (GS) have radically transformed the diagnostic approach to undiagnosed rare/ultrarare Mendelian diseases. Next-generation sequencing (NGS), the technology integral for ES, GS, and most large (100+) gene panels, has enabled previously unimaginable diagnoses, changes in medical management, new treatments, and accurate reproductive risk assessments for patients, as well as new disease gene discoveries. Yet, challenges remain, as most individuals remain undiagnosed with current NGS. Improved NGS technology has resulted in long-read sequencing, which may resolve diagnoses in some patients who do not obtain a diagnosis with current short-read ES and GS, but its effectiveness is unclear, and it is expensive. Other challenges that persist include the resolution of variants of uncertain significance, the urgent need for patients with ultrarare disorders to have access to therapeutics, the need for equity in patient access to NGS-based testing, and the study of ethical concerns. However, the outlook for undiagnosed disease resolution is bright, due to continual advancements in the field.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
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23
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Trivellin G, Daly AF, Hernández-Ramírez LC, Araldi E, Tatsi C, Dale RK, Fridell G, Mittal A, Faucz FR, Iben JR, Li T, Vitali E, Stojilkovic SS, Kamenicky P, Villa C, Baussart B, Chittiboina P, Toro C, Gahl WA, Eugster EA, Naves LA, Jaffrain-Rea ML, de Herder WW, Neggers SJCMM, Petrossians P, Beckers A, Lania AG, Mains RE, Eipper BA, Stratakis CA. Germline loss-of-function PAM variants are enriched in subjects with pituitary hypersecretion. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.20.23284646. [PMID: 36711613 PMCID: PMC9882627 DOI: 10.1101/2023.01.20.23284646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Pituitary adenomas (PAs) are common, usually benign tumors of the anterior pituitary gland which, for the most part, have no known genetic cause. PAs are associated with major clinical effects due to hormonal dysregulation and tumoral impingement on vital brain structures. Following the identification of a loss-of-function variant (p.Arg703Gln) in the PAM gene in a family with pituitary gigantism, we investigated 299 individuals with sporadic PAs and 17 familial isolated pituitary adenomas kindreds for PAM variants. PAM encodes a multifunctional protein responsible for the essential C-terminal amidation of secreted peptides. Genetic screening was performed by germline and tumor sequencing and germline copy number variation (CNV) analysis. No germline CNVs or somatic single nucleotide variants (SNVs) were identified. We detected seven likely pathogenic heterozygous missense, truncating, and regulatory SNVs. These SNVs were found in sporadic subjects with GH excess (p.Gly552Arg and p.Phe759Ser), pediatric Cushing disease (c.-133T>C and p.His778fs), or with different types of PAs (c.-361G>A, p.Ser539Trp, and p.Asp563Gly). The SNVs were functionally tested in vitro for protein expression and trafficking by Western blotting, for splicing by minigene assays, and for amidation activity in cell lysates and serum samples. These analyses confirmed a deleterious effect on protein expression and/or function. By interrogating 200,000 exomes from the UK Biobank, we confirmed a significant association of the PAM gene and rare PAM SNVs to diagnoses linked to pituitary gland hyperfunction. Identification of PAM as a candidate gene associated with pituitary hypersecretion opens the possibility of developing novel therapeutics based on altering PAM function.
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Affiliation(s)
- Giampaolo Trivellin
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele – Milan, Italy
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano – Milan, Italy
| | - Adrian F. Daly
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, University of Liège, Domaine Universitaire du Sart-Tilman, 4000 Liège, Belgium
| | - Laura C. Hernández-Ramírez
- Red de Apoyo a la Investigación, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán. Tlalpan, CDMX 14080, Mexico
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Elisa Araldi
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Christina Tatsi
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Ryan K. Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Gus Fridell
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Arjun Mittal
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Fabio R. Faucz
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - James R. Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Tianwei Li
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Eleonora Vitali
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano – Milan, Italy
| | - Stanko S. Stojilkovic
- Section on Cellular Signaling, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Peter Kamenicky
- Université Paris-Saclay, INSERM, Physiologie et Physiopathologie Endocriniennes, 94270 Le Kremlin-Bicêtre, France
| | - Chiara Villa
- Département de Neuropathologie de la Pitié Salpêtrière, Hôpital de la Pitié-Salpêtrière - APHP Sorbonne Université, 47-83 Bd de l’Hôpital 75651, Paris, France
- INSERM U1016, CNRS UMR 8104, Institut Cochin, 75014 Paris, France
| | - Bertrand Baussart
- INSERM U1016, CNRS UMR 8104, Institut Cochin, 75014 Paris, France
- Service de Neurochirurgie, Hôpital Pitié-Salpêtrière, AP-HP Sorbonne, 47-83 Boulevard de l’Hôpital, 75651 Paris, France
| | - Prashant Chittiboina
- Neurosurgery Unit for Pituitary and Inheritable Diseases and Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - William A. Gahl
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Erica A. Eugster
- Division of Endocrinology & Diabetes, Department of Pediatrics, Riley Hospital for Children at IU Health, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Luciana A. Naves
- Service of Endocrinology, University Hospital, Faculty of Medicine, University of Brasilia, 70910900 Brasilia, Brazil
| | - Marie-Lise Jaffrain-Rea
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
- Neuromed Institute, Istituto di Ricovero e Cura a Carattere Scientifico, 86077 Pozzilli, Italy
| | - Wouter W. de Herder
- Department of Medicine, Section Endocrinology, Pituitary Center Rotterdam, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Sebastian JCMM Neggers
- Department of Medicine, Section Endocrinology, Pituitary Center Rotterdam, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Patrick Petrossians
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, University of Liège, Domaine Universitaire du Sart-Tilman, 4000 Liège, Belgium
| | - Albert Beckers
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, University of Liège, Domaine Universitaire du Sart-Tilman, 4000 Liège, Belgium
| | - Andrea G. Lania
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele – Milan, Italy
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano – Milan, Italy
| | - Richard E. Mains
- Department of Neuroscience, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Betty A. Eipper
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Constantine A. Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
- Human Genetics & Precision Medicine, IMBB, Foundation for Research & Technology Hellas, 70013 Heraklion, Crete, Greece
- Research Institute, ELPEN, Pikermi, 19009 Athens, Greece
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24
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Turkyilmaz A, Donmez AS, Cayir A. A Genetic Approach in the Evaluation of Short Stature. Eurasian J Med 2022; 54:179-186. [PMID: 36655465 PMCID: PMC11163345 DOI: 10.5152/eurasianjmed.2022.22171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/28/2022] [Indexed: 01/19/2023] Open
Abstract
Short stature is considered a condition in which the height is 2 standard deviations below the mean height of a given age, sex, and population group. Human height is a polygenic and heterogeneous characteristic, and its heritability is reported to be approximately 80%. More than 600 variants associated with human growth were detected in the genome-wide association studies. Rare and common variants concurrently affect human height. The rare variations that play a role in human height determination and have a strong impact on protein functions lead to monogenic short stature phenotypes, which are a highly heterogeneous group. With rapidly developing technologies in the last decade, molecular genetic tests have begun to be used widely in clinical genetics, and thus, the genetic etiology of several rare diseases has been elucidated. Identifying the genetic etiology underlying idiopathic short stature which represents phenotypically heterogeneous group of diseases ranging from isolated short stature to severe and syndromic short stature has promoted the understanding of the genetic regulation of growth plate and longitudinal bone growth. In cases of short stature, definite molecular diagnosis based on genetic evaluation enables the patient and family to receive genetic counseling on the natural course of the disease, prognosis, genetic basis, and recurrence risk. The determination of the genetic etiology in growth disorders is essential for the development of novel targeted therapies and crucial in the development of mutation-specific treatments in the future.
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Affiliation(s)
- Ayberk Turkyilmaz
- Department of Medical Genetics, Karadeniz Technical University Faculty of Medicine, Trabzon, Turkey
| | - Ayse Sena Donmez
- Department of Pediatrics, Regional Training and Research Hospital, Erzurum, Turkey
| | - Atilla Cayir
- Department of Pediatric Endocrinology, Regional Training and Research Hospital, Erzurum, Turkey
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25
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Al-Ali S, Jeffries L, Faustino EVS, Ji W, Mis E, Konstantino M, Zerillo C, Jiang YH, Spencer-Manzon M, Bale A, Zhang H, McGlynn J, McGrath JM, Tremblay T, Brodsky NN, Lucas CL, Pierce R, Deniz E, Khokha MK, Lakhani SA. A retrospective cohort analysis of the Yale pediatric genomics discovery program. Am J Med Genet A 2022; 188:2869-2878. [PMID: 35899841 PMCID: PMC9474639 DOI: 10.1002/ajmg.a.62918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/29/2022] [Accepted: 07/10/2022] [Indexed: 01/31/2023]
Abstract
The Pediatric Genomics Discovery Program (PGDP) at Yale uses next-generation sequencing (NGS) and translational research to evaluate complex patients with a wide range of phenotypes suspected to have rare genetic diseases. We conducted a retrospective cohort analysis of 356 PGDP probands evaluated between June 2015 and July 2020, querying our database for participant demographics, clinical characteristics, NGS results, and diagnostic and research findings. The three most common phenotypes among the entire studied cohort (n = 356) were immune system abnormalities (n = 105, 29%), syndromic or multisystem disease (n = 103, 29%), and cardiovascular system abnormalities (n = 62, 17%). Of 216 patients with final classifications, 77 (36%) received new diagnoses and 139 (64%) were undiagnosed; the remaining 140 patients were still actively being investigated. Monogenetic diagnoses were found in 67 (89%); the largest group had variants in known disease genes but with new contributions such as novel variants (n = 31, 40%) or expanded phenotypes (n = 14, 18%). Finally, five PGDP diagnoses (8%) were suggestive of novel gene-to-phenotype relationships. A broad range of patients can benefit from single subject studies combining NGS and functional molecular analyses. All pediatric providers should consider further genetics evaluations for patients lacking precise molecular diagnoses.
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Affiliation(s)
- Samir Al-Ali
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - E. Vincent S. Faustino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emily Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Cynthia Zerillo
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yong-hui Jiang
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Michele Spencer-Manzon
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Julie McGlynn
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - James M. McGrath
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | | | - Nina N. Brodsky
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Carrie L. Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard Pierce
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Engin Deniz
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, US
| | - Saquib A. Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
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26
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Mintoff D, Pace NP, Borg I. Interpreting the spectrum of gamma-secretase complex missense variation in the context of hidradenitis suppurativa—An in-silico study. Front Genet 2022; 13:962449. [PMID: 36118898 PMCID: PMC9478468 DOI: 10.3389/fgene.2022.962449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/08/2022] [Indexed: 11/23/2022] Open
Abstract
Hidradenitis suppurativa (HS) is a disease of the pilosebaceous unit characterized by recurrent nodules, abscesses and draining tunnels with a predilection to intertriginous skin. The pathophysiology of HS is complex. However, it is known that inflammation and hyperkeratinization at the hair follicle play crucial roles in disease manifestation. Genetic and environmental factors are considered the main drivers of these two pathophysiological processes. Despite a considerable proportion of patients having a positive family history of disease, only a minority of patients suffering from HS have been found to harbor monogenic variants which segregate to affected kindreds. Most of these variants are in the ɣ secretase complex (GSC) protein-coding genes. In this manuscript, we set out to characterize the burden of missense pathogenic variants in healthy reference population using large scale genomic dataset thereby providing a standard for comparing genomic variation in GSC protein-coding genes in the HS patient cohort.
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Affiliation(s)
- Dillon Mintoff
- Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Nikolai P. Pace
- Centre for Molecular Biology and Biobanking, University of Malta, Msida, Malta
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
- *Correspondence: Nikolai P. Pace,
| | - Isabella Borg
- Department of Pathology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
- Centre for Molecular Biology and Biobanking, University of Malta, Msida, Malta
- Department of Pathology, Mater Dei Hospital, Msida, Malta
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27
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Montano C, Cassini T, Ziegler SG, Boehm M, Nicoli ER, Mindell JA, Soldatos AG, Manoli I, Wolfe L, Macnamara EF, Malicdan MCV, Adams DR, Tifft CJ, Toro C, Gahl WA. Diagnosis and discovery: Insights from the NIH Undiagnosed Diseases Program. J Inherit Metab Dis 2022; 45:907-918. [PMID: 35490291 DOI: 10.1002/jimd.12506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/14/2022] [Accepted: 04/27/2022] [Indexed: 11/11/2022]
Abstract
Living with an undiagnosed medical condition places a tremendous burden on patients, their families, and their healthcare providers. The Undiagnosed Diseases Program (UDP) was established at the National Institutes of Health (NIH) in 2008 with the primary goals of providing a diagnosis for patients with mysterious conditions and advancing medical knowledge about rare and common diseases. The program reviews applications from referring clinicians for cases that are considered undiagnosed despite a thorough evaluation. Those that are accepted receive clinical evaluations involving deep phenotyping and genetic testing that includes exome and genomic sequencing. Selected candidate gene variants are evaluated by collaborators using functional assays. Since its inception, the UDP has received more than 4500 applications and has completed evaluations on nearly 1300 individuals. Here we present six cases that exemplify the discovery of novel disease mechanisms, the importance of deep phenotyping for rare diseases, and how genetic diagnoses have led to appropriate treatment. The creation of the Undiagnosed Diseases Network (UDN) in 2014 has substantially increased the number of patients evaluated and allowed for greater opportunities for data sharing. Expansion to the Undiagnosed Diseases Network International (UDNI) has the possibility to extend this reach even farther. Together, networks of undiagnosed diseases programs are powerful tools to advance our knowledge of pathophysiology, accelerate accurate diagnoses, and improve patient care for patients with rare conditions.
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Affiliation(s)
- Carolina Montano
- Medical Genetics & Genomic Medicine Training Program, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Thomas Cassini
- Medical Genetics & Genomic Medicine Training Program, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Shira G Ziegler
- Departments of Pediatrics and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Manfred Boehm
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Elena-Raluca Nicoli
- Glycosphingolipid and Glycoprotein Disorders Unit, Medical Genetics Branch, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Joseph A Mindell
- Membrane Transport Biophysics Section, National Institute of Neurological Disorders and Stroke (NINDS), NIH, Bethesda, Maryland, USA
| | - Ariane G Soldatos
- Office of the Clinical Director, National Institute of Neurological Disorders and Stroke (NINDS), NIH, Bethesda, Maryland, USA
| | - Irini Manoli
- Organic Acid Research Section, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Lynne Wolfe
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Ellen F Macnamara
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | | | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - Cynthia J Tifft
- Glycosphingolipid and Glycoprotein Disorders Unit, Medical Genetics Branch, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - William A Gahl
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
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28
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Narita K, Muramatsu H, Narumi S, Nakamura Y, Okuno Y, Suzuki K, Hamada M, Yamaguchi N, Suzuki A, Nishio Y, Shiraki A, Yamamori A, Tsumura Y, Sawamura F, Kawaguchi M, Wakamatsu M, Kataoka S, Kato K, Asada H, Kubota T, Muramatsu Y, Kidokoro H, Natsume J, Mizuno S, Nakata T, Inagaki H, Ishihara N, Yonekawa T, Okumura A, Ogi T, Kojima S, Kaname T, Hasegawa T, Saitoh S, Takahashi Y. Whole-exome analysis of 177 pediatric patients with undiagnosed diseases. Sci Rep 2022; 12:14589. [PMID: 36028527 PMCID: PMC9418234 DOI: 10.1038/s41598-022-14161-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/02/2022] [Indexed: 11/09/2022] Open
Abstract
Recently, whole-exome sequencing (WES) has been used for genetic diagnoses of patients who remain otherwise undiagnosed. WES was performed in 177 Japanese patients with undiagnosed conditions who were referred to the Tokai regional branch of the Initiative on Rare and Undiagnosed Diseases (IRUD) (TOKAI-IRUD). This study included only patients who had not previously received genome-wide testing. Review meetings with specialists in various medical fields were held to evaluate the genetic diagnosis in each case, which was based on the guidelines of the American College of Medical Genetics and Genomics. WES identified diagnostic single-nucleotide variants in 66 patients and copy number variants (CNVs) in 11 patients. Additionally, a patient was diagnosed with Angelman syndrome with a complex clinical phenotype upon detection of a paternally derived uniparental disomy (UPD) [upd(15)pat] wherein the patient carried a homozygous DUOX2 p.E520D variant in the UPD region. Functional analysis confirmed that this DUOX2 variant was a loss-of-function missense substitution and the primary cause of congenital hypothyroidism. A significantly higher proportion of genetic diagnoses was achieved compared to previous reports (44%, 78/177 vs. 24-35%, respectively), probably due to detailed discussions and the higher rate of CNV detection.
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Affiliation(s)
- Kotaro Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health, Tokyo, Japan.,Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Yuji Nakamura
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan.,Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kyogo Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Motoharu Hamada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Naoya Yamaguchi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Atsushi Suzuki
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Yosuke Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Anna Shiraki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Ayako Yamamori
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yusuke Tsumura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Fumi Sawamura
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Masahiro Kawaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Shinsuke Kataoka
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kohji Kato
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Hideyuki Asada
- Department of Pediatrics, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Japan
| | - Tetsuo Kubota
- Department of Pediatrics, Anjo Kosei Hospital, Anjo, Japan
| | - Yukako Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hiroyuki Kidokoro
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Jun Natsume
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Seiji Mizuno
- Department of Clinical Genetics, Aichi Developmental Disability Center Central Hospital, Kasugai, Japan
| | - Tomohiko Nakata
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Naoko Ishihara
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Takahiro Yonekawa
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Akihisa Okumura
- Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan.
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
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29
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Martinussen J, Chalk M, Elliott J, Gallacher L. Receiving Genomic Sequencing Results through the Victorian Undiagnosed Disease Program: Exploring Parental Experiences. J Pers Med 2022; 12:jpm12081250. [PMID: 36013198 PMCID: PMC9410238 DOI: 10.3390/jpm12081250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/24/2022] [Indexed: 11/16/2022] Open
Abstract
Rare diseases cumulatively affect a significant number of people, and for many, a diagnosis remains elusive. The Victorian Undiagnosed Disease Program (UDP-Vic) utilizes deep phenotyping, advanced genomic sequencing and functional studies to diagnose children with rare diseases for which previous clinical testing has been non-diagnostic. Whereas the diagnostic outcomes of undiagnosed disease programs have been well-described, here, we explore how parents experience participation in the UDP-Vic and the impact of receiving both diagnostic and non-diagnostic genomic sequencing results for their children. Semi-structured interviews ranging in length from 25 to 105 min were conducted with 21 parents of children in the program. Ten participants were parents of children who received a diagnosis through the program, and eleven were parents of children who remain undiagnosed. Although the experiences of families varied, five shared themes emerged from the data: (1) searching for a diagnosis, (2) varied impact of receiving a result, (3) feelings of relief and disappointment, (4) seeking connection and (5) moving towards acceptance. The findings demonstrate the shared experience of parents of children with rare disease both before and after a genomic sequencing result. The results have implications for genetic counselors and clinicians offering genomic sequencing and supporting families of children with rare diseases.
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Affiliation(s)
- Jo Martinussen
- Department of Paediatrics, The University of Melbourne, Melbourne 3010, Australia; (J.M.); (M.C.)
| | - Michal Chalk
- Department of Paediatrics, The University of Melbourne, Melbourne 3010, Australia; (J.M.); (M.C.)
| | - Justine Elliott
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne 3052, Australia;
| | - Lyndon Gallacher
- Department of Paediatrics, The University of Melbourne, Melbourne 3010, Australia; (J.M.); (M.C.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne 3052, Australia;
- Correspondence:
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30
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Havrilla JM, Singaravelu A, Driscoll DM, Minkovsky L, Helbig I, Medne L, Wang K, Krantz I, Desai BR. PheNominal: an EHR-integrated web application for structured deep phenotyping at the point of care. BMC Med Inform Decis Mak 2022; 22:198. [PMID: 35902925 PMCID: PMC9335954 DOI: 10.1186/s12911-022-01927-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/06/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Clinical phenotype information greatly facilitates genetic diagnostic interpretations pipelines in disease. While post-hoc extraction using natural language processing on unstructured clinical notes continues to improve, there is a need to improve point-of-care collection of patient phenotypes. Therefore, we developed "PheNominal", a point-of-care web application, embedded within Epic electronic health record (EHR) workflows, to permit capture of standardized phenotype data. METHODS Using bi-directional web services available within commercial EHRs, we developed a lightweight web application that allows users to rapidly browse and identify relevant terms from the Human Phenotype Ontology (HPO). Selected terms are saved discretely within the patient's EHR, permitting reuse both in clinical notes as well as in downstream diagnostic and research pipelines. RESULTS In the 16 months since implementation, PheNominal was used to capture discrete phenotype data for over 1500 individuals and 11,000 HPO terms during clinic and inpatient encounters for a genetic diagnostic consultation service within a quaternary-care pediatric academic medical center. An average of 7 HPO terms were captured per patient. Compared to a manual workflow, the average time to enter terms for a patient was reduced from 15 to 5 min per patient, and there were fewer annotation errors. CONCLUSIONS Modern EHRs support integration of external applications using application programming interfaces. We describe a practical application of these interfaces to facilitate deep phenotype capture in a discrete, structured format within a busy clinical workflow. Future versions will include a vendor-agnostic implementation using FHIR. We describe pilot efforts to integrate structured phenotyping through controlled dictionaries into diagnostic and research pipelines, reducing manual effort for phenotype documentation and reducing errors in data entry.
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Affiliation(s)
- James M. Havrilla
- grid.239552.a0000 0001 0680 8770Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Anbumalar Singaravelu
- grid.239552.a0000 0001 0680 8770Emerging Technology and Transformation Team, Information Services, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Dennis M. Driscoll
- grid.239552.a0000 0001 0680 8770Emerging Technology and Transformation Team, Information Services, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Leonard Minkovsky
- grid.239552.a0000 0001 0680 8770Emerging Technology and Transformation Team, Information Services, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Ingo Helbig
- grid.239552.a0000 0001 0680 8770Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, USA ,grid.239552.a0000 0001 0680 8770Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104 USA
| | - Livija Medne
- grid.239552.a0000 0001 0680 8770Roberts Individualized Medical Genetics Center, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Kai Wang
- grid.239552.a0000 0001 0680 8770Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
| | - Ian Krantz
- grid.239552.a0000 0001 0680 8770Roberts Individualized Medical Genetics Center, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Bimal R. Desai
- grid.25879.310000 0004 1936 8972Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
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31
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Xiao C, Koziura M, Cope H, Spillman R, Tan K, Hisama FM, Tifft CJ, Toro C. Adults with lysosomal storage diseases in the undiagnosed diseases network. Mol Genet Genomic Med 2022; 10:e2013. [PMID: 35848209 PMCID: PMC9482386 DOI: 10.1002/mgg3.2013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/17/2022] [Accepted: 06/15/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES To review the referral and clinical characteristics of adult patients diagnosed with lysosomal storage diseases (LSD) through the Undiagnosed Diseases Network (UDN). METHODS Retrospective review of both application and evaluation records for adults admitted to the UDN with a final diagnosis of a lysosomal storage disease. RESULTS Ten patients were identified. Final diagnoses included late onset Tay Sachs, attenuated MPS I, MPS IIIA, MPS IIIB, and MPS IIIC. Most patients presented with neurocognitive changes. Prior to referral, all patients had been evaluated by neurology, four patients underwent phenotype specific panel testing that did not include the causative gene, and four patients had non-diagnostic clinical exome sequencing. CONCLUSIONS LSDs figure highly in the differential diagnosis of neurometabolic disorders in pediatric onset progressive diseases. In adults, their subtle initial presentations overlap with symptoms of more common disorders and less practitioner awareness may lead to prolonged diagnostic challenges.
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Affiliation(s)
- Changrui Xiao
- National Human Genome Research InstituteBethesdaMarylandUSA
| | - Mary Koziura
- Department of PediatricsDivision of Medical Genetics and Genomic MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Heidi Cope
- Department of Pediatrics, Medical GeneticsDuke University Medical CenterDurhamNorth CarolinaUSA
| | - Rebecca Spillman
- Department of Pediatrics, Medical GeneticsDuke University Medical CenterDurhamNorth CarolinaUSA
| | - Khoon Tan
- Department of Pediatrics, Medical GeneticsDuke University Medical CenterDurhamNorth CarolinaUSA
| | - Fuki M. Hisama
- Department of MedicineDivision of Medical GeneticsUniversity of Washington School of MedicineSeattleWashingtonUSA
| | | | - Camilo Toro
- National Human Genome Research InstituteBethesdaMarylandUSA
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32
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Markello C, Huang C, Rodriguez A, Carroll A, Chang PC, Eizenga J, Markello T, Haussler D, Paten B. A complete pedigree-based graph workflow for rare candidate variant analysis. Genome Res 2022; 32:893-903. [PMID: 35483961 PMCID: PMC9104704 DOI: 10.1101/gr.276387.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/24/2022] [Indexed: 11/24/2022]
Abstract
Methods that use a linear genome reference for genome sequencing data analysis are reference-biased. In the field of clinical genetics for rare diseases, a resulting reduction in genotyping accuracy in some regions has likely prevented the resolution of some cases. Pangenome graphs embed population variation into a reference structure. Although pangenome graphs have helped to reduce reference mapping bias, further performance improvements are possible. We introduce VG-Pedigree, a pedigree-aware workflow based on the pangenome-mapping tool of Giraffe and the variant calling tool DeepTrio using a specially trained model for Giraffe-based alignments. We demonstrate mapping and variant calling improvements in both single-nucleotide variants (SNVs) and insertion and deletion (indel) variants over those produced by alignments created using BWA-MEM to a linear-reference and Giraffe mapping to a pangenome graph containing data from the 1000 Genomes Project. We have also adapted and upgraded deleterious-variant (DV) detecting methods and programs into a streamlined workflow. We used these workflows in combination to detect small lists of candidate DVs among 15 family quartets and quintets of the Undiagnosed Diseases Program (UDP). All candidate DVs that were previously diagnosed using the Mendelian models covered by the previously published methods were recapitulated by these workflows. The results of these experiments indicate that a slightly greater absolute count of DVs are detected in the proband population than in their matched unaffected siblings.
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Affiliation(s)
- Charles Markello
- UC Santa Cruz Genomics Institute, Santa Cruz, California 95060, USA
| | - Charles Huang
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Alex Rodriguez
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Andrew Carroll
- Google Incorporated, Mountain View, California 94043, USA
| | - Pi-Chuan Chang
- Google Incorporated, Mountain View, California 94043, USA
| | - Jordan Eizenga
- UC Santa Cruz Genomics Institute, Santa Cruz, California 95060, USA
| | - Thomas Markello
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, California 95060, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, Santa Cruz, California 95060, USA
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33
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Wang Q, Tang X, Yang K, Huo X, Zhang H, Ding K, Liao S. Deep phenotyping and whole-exome sequencing improved the diagnostic yield for nuclear pedigrees with neurodevelopmental disorders. Mol Genet Genomic Med 2022; 10:e1918. [PMID: 35266334 PMCID: PMC9034680 DOI: 10.1002/mgg3.1918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 02/18/2022] [Accepted: 02/25/2022] [Indexed: 12/21/2022] Open
Abstract
Background Neurodevelopmental disorders, a group of early‐onset neurological disorders with significant clinical and genetic heterogeneity, remain a diagnostic challenge for clinical genetic evaluation. Therefore, we assessed the diagnostic yield by combining standard phenotypes and whole‐exome sequencing in families with these disorders that were “not yet diagnosed” by the traditional testing methods. Methods Using a standardized vocabulary of phenotypic abnormalities from human phenotype ontology (HPO), we performed deep phenotyping for 45 “not yet diagnosed” pedigrees to characterize multiple clinical features extracted from Chinese electronic medical records (EMRs). By matching HPO terms with known human diseases and phenotypes from model organisms, together with whole‐exome sequencing data, we prioritized candidate mutations/genes. We made probable genetic diagnoses for the families. Results We obtained a diagnostic yield of 29% (13 out of 45) with probably genetic diagnosis, of which compound heterozygosity and de novo mutations accounted for 77% (10/13) of the diagnosis. Of note, these pedigrees are accompanied by a more significant number of non‐neurological features. Conclusions Deep phenotyping and whole‐exome sequencing improve the etiological evaluation for neurodevelopmental disorders in the clinical setting.
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Affiliation(s)
- Qingqing Wang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Xia Tang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Ke Yang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Xiaodong Huo
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Hui Zhang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Keyue Ding
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
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34
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Fernández-Eulate G, Carreau C, Benoist JF, Lamari F, Rucheton B, Shor N, Nadjar Y. Diagnostic approach in adult-onset neurometabolic diseases. J Neurol Neurosurg Psychiatry 2022; 93:413-421. [PMID: 35140137 PMCID: PMC8921565 DOI: 10.1136/jnnp-2021-328045] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/02/2022] [Indexed: 12/31/2022]
Abstract
Neurometabolic diseases are a group of individually rare but numerous and heterogeneous genetic diseases best known to paediatricians. The more recently reported adult forms may present with phenotypes strikingly different from paediatric ones and may mimic other more common neurological disorders in adults. Furthermore, unlike most neurogenetic diseases, many neurometabolic diseases are treatable, with both conservative and more recent innovative therapeutics. However, the phenotypical complexity of this group of diseases and the growing number of specialised biochemical tools account for a significant diagnostic delay and underdiagnosis. We reviewed all series and case reports of patients with a confirmed neurometabolic disease and a neurological onset after the age of 10 years, with a focus on the 36 treatable ones, and classified these diseases according to their most relevant clinical manifestations. The biochemical diagnostic approach of neurometabolic diseases lays on the use of numerous tests studying a set of metabolites, an enzymatic activity or the function of a given pathway; and therapeutic options aim to restore the enzyme activity or metabolic function, limit the accumulation of toxic substrates or substitute the deficient products. A quick diagnosis of a treatable neurometabolic disease can have a major impact on patients, leading to the stabilisation of the disease and cease of repeated diagnostic investigations, and allowing for familial screening. For the aforementioned, in addition to an exhaustive and clinically meaningful review of these diseases, we propose a simplified diagnostic approach for the neurologist with the aim to help determine when to suspect a neurometabolic disease and how to proceed in a rational manner. We also discuss the place of next-generation sequencing technologies in the diagnostic process, for which deep phenotyping of patients (both clinical and biochemical) is necessary for improving their diagnostic yield.
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Affiliation(s)
- Gorka Fernández-Eulate
- Neuro-Metabolism Unit, Reference Center for Lysosomal Diseases, Neurology Department, Pitié-Salpêtrière University Hospital, APHP, Paris, France.,Reference Center for Neuromuscular Diseases, Neuro-myology Department, Pitié-Salpêtrière University Hospital, APHP, Paris, France
| | - Christophe Carreau
- Neurology Department, Saint-Louis University Hospital, APHP, Paris, France
| | - Jean-François Benoist
- Metabolic Biochemistry Laboratory, Necker Enfants Malades University Hospital, APHP, Paris-Saclay University, Paris, France
| | - Foudil Lamari
- Department of Biochemistry of Neurometabolic Diseases, Pitié-Salpêrière University Hospital, APHP, Paris, Fance
| | - Benoit Rucheton
- Department of Biochemistry of Neurometabolic Diseases, Pitié-Salpêrière University Hospital, APHP, Paris, Fance
| | - Natalia Shor
- Neuroradiology Department, Pitié-Salpêtrière University Hospital, APHP, Sorbonne University, Paris, France
| | - Yann Nadjar
- Neuro-Metabolism Unit, Reference Center for Lysosomal Diseases, Neurology Department, Pitié-Salpêtrière University Hospital, APHP, Paris, France
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35
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Chatrathi HE, Collins JC, Wolfe LA, Markello TC, Adams DR, Gahl WA, Werner A, Sharma P. Novel CUL3 Variant Causing Familial Hyperkalemic Hypertension Impairs Regulation and Function of Ubiquitin Ligase Activity. Hypertension 2022; 79:60-75. [PMID: 34878901 PMCID: PMC8667186 DOI: 10.1161/hypertensionaha.121.17624] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Familial hyperkalemic hypertension is caused by pathogenic variants in genes of the CUL3 (cullin-3)-KLHL3 (kelch-like-family-member-3)-WNK (with no-lysine [K] kinase) pathway, manifesting clinically as hyperkalemia, metabolic acidosis, and high systolic blood pressure. The ubiquitin E3 ligase CUL3-KLHL3 targets WNK kinases for degradation to limit activation of the thiazide-sensitive NCC (Na-Cl cotransporter). All known variants in CUL3 lead to exon 9 skipping (CUL3Δ9) and typically result in severe familial hyperkalemic hypertension and growth disturbances in patients. Whether other variants in CUL3 cause familial hyperkalemic hypertension is unknown. Here, we identify a novel de novo heterozygous CUL3 variant (CUL3Δ474-477) in a pediatric familial hyperkalemic hypertension patient with multiple congenital anomalies and reveal molecular mechanisms by which CUL3Δ474-477 leads to dysregulation of the CUL3-KLHL3-WNK signaling axis. Using patient-derived urinary extracellular vesicles and dermal fibroblasts, in vitro assays, and cultured kidney cells, we demonstrate that CUL3Δ474-477 causes reduced total CUL3 levels due to increased autoubiquitination. The CUL3Δ474-477 that escapes autodegradation shows enhanced modification with NEDD8 (neural precursor cell expressed developmentally down-regulated protein 8) and increased formation of CUL3-KLHL3 complexes that are impaired in ubiquitinating WNK4. Proteomic analysis of CUL3 complexes revealed that, in addition to increased KLHL3 binding, the CUL3Δ474-477 variant also exhibits increased interactions with other BTB (Bric-a-brac, Tramtrack, and Broad complex) substrate adaptors, providing a rationale for the patient's diverse phenotypes. We conclude that the pathophysiological effects of CUL3Δ474-477 are caused by reduced CUL3 levels and formation of catalytically impaired CUL3 ligase complexes.
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Affiliation(s)
- Harish E. Chatrathi
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland 20892, USA,Share the first authorship position
| | - Jason C. Collins
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA,Share the first authorship position
| | - Lynne A. Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Thomas C. Markello
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland 20892, USA,Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland Bethesda, Maryland 20892, USA
| | - David R. Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland 20892, USA,Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland Bethesda, Maryland 20892, USA
| | - William A. Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland 20892, USA,Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland Bethesda, Maryland 20892, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Prashant Sharma
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland 20892, USA,Correspondence: Prashant Sharma, NIH Undiagnosed Diseases Program, National Human Genome Research Institute, 5625 Fishers Lane, Rockville, MD.
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36
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Haimel M, Pazmandi J, Heredia RJ, Dmytrus J, Bal SK, Zoghi S, van Daele P, Briggs TA, Wouters C, Bader-Meunier B, Aeschlimann FA, Caorsi R, Eleftheriou D, Hoppenreijs E, Salzer E, Bakhtiar S, Derfalvi B, Saettini F, Kusters MAA, Elfeky R, Trück J, Rivière JG, van der Burg M, Gattorno M, Seidel MG, Burns S, Warnatz K, Hauck F, Brogan P, Gilmour KC, Schuetz C, Simon A, Bock C, Hambleton S, de Vries E, Robinson PN, van Gijn M, Boztug K. Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity. J Allergy Clin Immunol 2022; 149:369-378. [PMID: 33991581 PMCID: PMC9346194 DOI: 10.1016/j.jaci.2021.04.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Accurate, detailed, and standardized phenotypic descriptions are essential to support diagnostic interpretation of genetic variants and to discover new diseases. The Human Phenotype Ontology (HPO), extensively used in rare disease research, provides a rich collection of vocabulary with standardized phenotypic descriptions in a hierarchical structure. However, to date, the use of HPO has not yet been widely implemented in the field of inborn errors of immunity (IEIs), mainly due to a lack of comprehensive IEI-related terms. OBJECTIVES We sought to systematically review available terms in HPO for the depiction of IEIs, to expand HPO, yielding more comprehensive sets of terms, and to reannotate IEIs with HPO terms to provide accurate, standardized phenotypic descriptions. METHODS We initiated a collaboration involving expert clinicians, geneticists, researchers working on IEIs, and bioinformaticians. Multiple branches of the HPO tree were restructured and extended on the basis of expert review. Our ontology-guided machine learning coupled with a 2-tier expert review was applied to reannotate defined subgroups of IEIs. RESULTS We revised and expanded 4 main branches of the HPO tree. Here, we reannotated 73 diseases from 4 International Union of Immunological Societies-defined IEI disease subgroups with HPO terms. We achieved a 4.7-fold increase in the number of phenotypic terms per disease. Given the new HPO annotations, we demonstrated improved ability to computationally match selected IEI cases to their known diagnosis, and improved phenotype-driven disease classification. CONCLUSIONS Our targeted expansion and reannotation presents enhanced precision of disease annotation, will enable superior HPO-based IEI characterization, and hence benefit both IEI diagnostic and research activities.
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Affiliation(s)
- Matthias Haimel
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Julia Pazmandi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Raúl Jiménez Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jasmin Dmytrus
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sevgi Köstel Bal
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Samaneh Zoghi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Paul van Daele
- Department of Clinical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tracy A Briggs
- NW Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Carine Wouters
- Department of Microbiology and Immunology, Immunobiology, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Pediatric Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Brigitte Bader-Meunier
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker Hospital for Sick Children - AP-HP, Paris, France; Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Paris, France
| | - Florence A Aeschlimann
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker Hospital for Sick Children - AP-HP, Paris, France; Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Paris, France
| | - Roberta Caorsi
- Center for Autoinflammatory Diseases and Immunodeficiency, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Despina Eleftheriou
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Esther Hoppenreijs
- Department of Paediatric Rheumatology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Elisabeth Salzer
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; St Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Shahrzad Bakhtiar
- Department for Children and Adolescents, Division for Stem Cell Transplantation, Immunology and Intensive Care Unit, Goethe University, Frankfurt, Germany
| | - Beata Derfalvi
- Department of Pediatrics, Division of Immunology, Dalhousie University/IWK Health Centre Halifax, Halifax, Nova Scotia, Canada
| | - Francesco Saettini
- Pediatric Hematology Department, Fondazione MBBM, University of Milano Bicocca, via Pergolesi 33, Monza, Italy
| | - Maaike A A Kusters
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Reem Elfeky
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Johannes Trück
- Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jacques G Rivière
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Mirjam van der Burg
- Department of Immunology, University Medical Center Rotterdam, Rotterdam, The Netherlands; Laboratory for Pediatric Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiency, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Markus G Seidel
- Research Unit for Pediatric Hematology and Immunology, Division of Pediatric Hemato-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University Graz, Graz, Austria
| | - Siobhan Burns
- Department of Immunology, UCL Institute of Immunity & Transplantation, Department of Immunology, Royal Free Hospital NHS Foundation Trust, London, United Kingdom
| | - Klaus Warnatz
- Division of Immunodeficiency, Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; Munich Centre for Rare Diseases (M-ZSE(LMU)), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paul Brogan
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Kimberly C Gilmour
- Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Catharina Schuetz
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Anna Simon
- Radboudumc Expertise Centre for Immunodeficiency and Autoinflammation (REIA), Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Christoph Bock
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Sophie Hambleton
- Immunity and Inflammation Theme, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Esther de Vries
- Tranzo, Tilburg University, Tilburg, The Netherlands; Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | | | - Marielle van Gijn
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands.
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria; St Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.
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Swanson LC, Ahmed R. Epilepsy Syndromes: Current Classifications and Future Directions. Neurosurg Clin N Am 2021; 33:113-134. [PMID: 34801136 DOI: 10.1016/j.nec.2021.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This review describes the clinical presentations and treatment options for commonly recognized epilepsy syndromes in the pediatric age group, based on the 2017 International League Against Epilepsy classification. Structural epilepsies that are amenable to surgical intervention are discussed. Lastly, emerging technologies are reviewed that are expanding our knowledge of underlying epilepsy pathologies and will guide future syndromic classification systems including genetic testing and tissue repositories.
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Affiliation(s)
- Laura C Swanson
- Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E. Chicago Ave. #18, Chicago, IL 60611, USA
| | - Raheel Ahmed
- Department of Neurosurgery, University of Wisconsin-Madison School of Medicine and Public Health, 1675 Highland Avenue #0002, Madison, WI 53705, USA.
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38
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Diagnostic yield and recognized barriers of an adult neurogenetics clinic. J Community Genet 2021; 12:569-576. [PMID: 34478057 DOI: 10.1007/s12687-021-00547-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 08/02/2021] [Indexed: 11/27/2022] Open
Abstract
The advent of molecular genetic technologies paved a path for the diagnosis of many neurological disorders. Joint evaluation by a neurologist and a medical genetics specialist can potentially increase diagnostic effectiveness by ensuring the exclusion of non-genetic conditions with similar phenotypes and by rationally selecting appropriate genetic diagnostic tools. Therefore, a monthly adult neurogenetics clinic was established. A retrospective review of medical records of all patients who attended the clinic from April 2015 to March 2019 was conducted. Eighty-two patients were evaluated (age: 47.1 ± 15.7, male: 37(45%), 42 (51%) had a positive family history). Disease duration was typically long (11.4 ± 0.9 years). Futile use of diagnostic modalities was very common (45 (55%) had repeated MRI, 28 (34%) hospitalized for observation in neurologic departments, 12 (14%) had a normal metabolic workup, 4 (5%) with a non-conclusive muscle biopsy, 1 with a normal cerebral angiography). Following clinical evaluation, molecular genetic testing was offered to 67 (82%) patients. In the other 15 (18%), routine workup for the exclusion of non-genetic conditions was not complete; obtainable information regarding family members was missing or that a neurogenetic disorder seemed improbable. Twenty-seven (33%) patients received a definitive diagnosis, either a genetic (23, 28%) or non-genetic (4, 5%). Excluding 4 cases of pre-symptomatic diagnosis, the diagnostic yield was 30%. The adherence to genetic testing recommendations was 62%. The reasons for non-adherence were lack of public funding for the required test (52%) and patient decision not to proceed (48%). Given the frequent futile use of diagnostic modalities, referral of non-genetic conditions with similar phenotypes among neurogenetic disorders, and the complexity of clinical genomic data analysis, a multi-disciplinary neurogenetics clinic seems justified.
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39
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Zhang F, Long W, Zhou Q, Wang J, Shi Y, Liu J, Wang Q. Is Prenatal Diagnosis Necessary for Fetal Isolated Nasal Bone Absence or Hypoplasia? Int J Gen Med 2021; 14:4435-4441. [PMID: 34408481 PMCID: PMC8364966 DOI: 10.2147/ijgm.s322359] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022] Open
Abstract
Purpose This study aimed to explore the value of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in the prenatal diagnosis of fetal isolated nasal bone absence (INBA) or isolated nasal bone hypoplasia (INBH). We hope to provide additional relevant information for clinical counseling. Patients and Methods From November 1, 2018, to March 1, 2020, 55 pregnant women with isolated nasal bone dysplasia were admitted to the Changzhou Maternity and Child Health Care Hospital. Based on the degree of abnormality, the patients were divided into two groups: INBA and INBH. CMA was performed on all patients. The clinical data and prenatal genetic diagnoses of the two groups were retrospectively analyzed. According to the requirements of WES for samples, 12 cases with negative CMA results were selected for the WES test. Results A total of 55 cases with INBA or INBH met the inclusion criteria. In 35INBA fetuses, there was one case of trisomy 21 and one case of 10q11.22 deletion (5.7Mb), and the abnormality rate was 5.71% (2/35). Compared with INBA fetuses, the abnormality rate was increased in the fetuses with INBH [15.00% (3/20)] (15.00% vs 5.71%); there was one case of 1q21.1 duplication (1.3Mb), one case of Xp22.31 duplication (1.67Mb), and one case of 4p deletion (7.6Mb). In a later retrospective study, two pathogenic variants were identified in two cases after the WES test; the abnormality rate was 16.67% (2/12), which involved RUNX2 and CDH4 genes, respectively. Conclusion A preliminary study confirmed that molecular prenatal diagnosis should be performed in fetuses with INBA or INBH. CMA followed by WES is an effective method.
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Affiliation(s)
- Feng Zhang
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Wei Long
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Qin Zhou
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Jing Wang
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Ye Shi
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Jianbing Liu
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Qiuwei Wang
- Clinical Laboratory, Changzhou Children's Hospital Affiliated to Nantong Medical University, Changzhou, Jiangsu Province, People's Republic of China
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40
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Berisha SZ, Shetty S, Prior TW, Mitchell AL. Cytogenetic and molecular diagnostic testing associated with prenatal and postnatal birth defects. Birth Defects Res 2021; 112:293-306. [PMID: 32115903 PMCID: PMC9290954 DOI: 10.1002/bdr2.1648] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 11/23/2022]
Abstract
Genetic testing is beneficial for patients and providers when in search of answers to medical problems related to the prenatal or early postnatal period. It can help to identify the cause or confirm a diagnosis associated with developmental delay, intellectual disability, dysmorphic features, heart defects, multiple malformations, short stature, stillbirth, neonatal death, or fertility problems. Genetic testing can be used to rule out single‐gene or chromosome abnormalities. Different diagnostic cytogenetic and molecular genetic techniques are applied in clinical genetics laboratories, from conventional ones to the state of the art chromosomal microarrays and next‐generation sequencing. Each of the genetic techniques or methods has its strengths and limitations, however different methods complement each‐other in trying to identify the genetic variation(s) responsible for a medical condition, especially the ones related to birth defects.
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Affiliation(s)
- Stela Z Berisha
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Shashi Shetty
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Pathology, Case Western Reserve University, University Hospitals, Cleveland, Ohio
| | - Thomas W Prior
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Pathology, Case Western Reserve University, University Hospitals, Cleveland, Ohio
| | - Anna L Mitchell
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Genetics and Genome Sciences, Case Western Reserve University, University Hospitals, Cleveland, Ohio
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Yates J, Gutiérrez-Sacristán A, Jouhet V, LeBlanc K, Esteves C, DeSain TN, Benik N, Stedman J, Palmer N, Mellon G, Kohane I, Avillach P. Finding commonalities in rare diseases through the undiagnosed diseases network. J Am Med Inform Assoc 2021; 28:1694-1702. [PMID: 34009343 PMCID: PMC8324228 DOI: 10.1093/jamia/ocab050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 11/14/2022] Open
Abstract
Objective When studying any specific rare disease, heterogeneity and scarcity of affected individuals has historically hindered investigators from discerning on what to focus to understand and diagnose a disease. New nongenomic methodologies must be developed that identify similarities in seemingly dissimilar conditions. Materials and Methods This observational study analyzes 1042 patients from the Undiagnosed Diseases Network (2015-2019), a multicenter, nationwide research study using phenotypic data annotated by specialized staff using Human Phenotype Ontology terms. We used Louvain community detection to cluster patients linked by Jaccard pairwise similarity and 2 support vector classifier to assign new cases. We further validated the clusters’ most representative comorbidities using a national claims database (67 million patients). Results Patients were divided into 2 groups: those with symptom onset before 18 years of age (n = 810) and at 18 years of age or older (n = 232) (average symptom onset age: 10 [interquartile range, 0-14] years). For 810 pediatric patients, we identified 4 statistically significant clusters. Two clusters were characterized by growth disorders, and developmental delay enriched for hypotonia presented a higher likelihood of diagnosis. Support vector classifier showed 0.89 balanced accuracy (0.83 for Human Phenotype Ontology terms only) on test data. Discussions To set the framework for future discovery, we chose as our endpoint the successful grouping of patients by phenotypic similarity and provide a classification tool to assign new patients to those clusters. Conclusion This study shows that despite the scarcity and heterogeneity of patients, we can still find commonalities that can potentially be harnessed to uncover new insights and targets for therapy.
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Affiliation(s)
- Josephine Yates
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Vianney Jouhet
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Cecilia Esteves
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Thomas N DeSain
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Nick Benik
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason Stedman
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Nathan Palmer
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Guillaume Mellon
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Isaac Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Corresponding Author: Paul Avillach, MD, PhD, 10 Shattuck Street, 02115 Boston, MA, USA;
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Debs S, Ferreira CR, Groden C, Kim HJ, King KA, King MC, Lehky T, Cowen EW, Brown LH, Merideth M, Owen CM, Macnamara E, Toro C, Gahl WA, Soldatos A. Adult diagnosis of congenital serine biosynthesis defect: A treatable cause of progressive neuropathy. Am J Med Genet A 2021; 185:2102-2107. [PMID: 34089226 DOI: 10.1002/ajmg.a.62245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/14/2020] [Indexed: 11/07/2022]
Abstract
A woman with ichthyosis, contractures, and progressive neuropathy represents the first case of phosphoserine aminotransferase deficiency diagnosed and treated in an adult. She has novel compound heterozygous mutations in the gene PSAT1. Treatment with high dose oral L-serine completely resolved the ichthyosis. Consideration of this diagnosis is important because early treatment with L-serine repletion can halt progression of neurodegeneration and potentially improve neurological disabilities. As exome sequencing becomes more widely implemented in the diagnostic evaluation of progressive neurodegenerative phenotypes, adult neurologists and geneticists will increasingly encounter later onset manifestations of inborn errors of metabolism classically considered in infancy and early childhood.
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Affiliation(s)
- Sarah Debs
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA.,Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Catherine Groden
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - H Jeffrey Kim
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Kelly A King
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Monique C King
- Rehabilitation Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Tanya Lehky
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Edward W Cowen
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura H Brown
- Johns Hopkins Community Physicians_North Bethesda, Rockville, MD, USA
| | - Melissa Merideth
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Carter M Owen
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ellen Macnamara
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Camilo Toro
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - William A Gahl
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ariane Soldatos
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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Kyle JE, Stratton KG, Zink EM, Kim YM, Bloodsworth KJ, Monroe ME, Waters KM, Webb-Robertson BJM, Koeller DM, Metz TO. A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases. Sci Data 2021; 8:114. [PMID: 33883556 PMCID: PMC8060404 DOI: 10.1038/s41597-021-00894-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/09/2021] [Indexed: 12/27/2022] Open
Abstract
Every year individuals experience symptoms that remain undiagnosed by healthcare providers. In the United States, these rare diseases are defined as a condition that affects fewer than 200,000 individuals. However, there are an estimated 7000 rare diseases, and there are an estimated 25-30 million Americans in total (7.6-9.2% of the population as of 2018) affected by such disorders. The NIH Common Fund Undiagnosed Diseases Network (UDN) seeks to provide diagnoses for individuals with undiagnosed disease. Mass spectrometry-based metabolomics and lipidomics analyses could advance the collective understanding of individual symptoms and advance diagnoses for individuals with heretofore undiagnosed disease. Here, we report the mass spectrometry-based metabolomics and lipidomics analyses of blood plasma, urine, and cerebrospinal fluid from 148 patients within the UDN and their families, as well as from a reference population of over 100 individuals with no known metabolic diseases. The raw and processed data are available to the research community so that they might be useful in the diagnoses of current or future patients suffering from undiagnosed disorders.
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Affiliation(s)
- Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kelly G Stratton
- Computing and Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Erika M Zink
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kent J Bloodsworth
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Katrina M Waters
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - David M Koeller
- Molecular and Medical Genetics, School of Medicine, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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Yubero D, Natera-de Benito D, Pijuan J, Armstrong J, Martorell L, Fernàndez G, Maynou J, Jou C, Roldan M, Ortez C, Nascimento A, Hoenicka J, Palau F. The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases. Int J Mol Sci 2021; 22:4274. [PMID: 33924139 PMCID: PMC8074304 DOI: 10.3390/ijms22084274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing either the clinical exome/genome or the whole exome or genome. However, as of today, there are still many patients in whom the causative genetic variant cannot be definitely established and variants of uncertain significance are often found. In this review, we address these drawbacks by incorporating two additional biological omics approaches into the molecular diagnostic process of NMDs. First, functional genomics by introducing experimental cell and molecular biology to analyze and validate the variant for its biological effect in an in-house translational diagnostic program, and second, incorporating a multi-omics approach including RNA-seq, metabolomics, and proteomics in the molecular diagnosis of neuromuscular disease. Both translational diagnostics programs and omics are being implemented as part of the diagnostic process in academic centers and referral hospitals and, therefore, an increase in the proportion of neuromuscular patients with a molecular diagnosis is expected. This improvement in the process and diagnostic performance of patients will allow solving aspects of their health problems in a precise way and will allow them and their families to take a step forward in their lives.
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Affiliation(s)
- Dèlia Yubero
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
| | - Jordi Pijuan
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Judith Armstrong
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Loreto Martorell
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Guerau Fernàndez
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Joan Maynou
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Cristina Jou
- Department of Pathology, Hospital Sant Joan de Déu, Pediatric Biobank for Research, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Mònica Roldan
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Confocal Microscopy and Cellular Imaging Unit, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
- Division of Pediatrics, Clinic Institute of Medicine & Dermatology, Hospital Clínic, University of Barcelona School of Medicine and Health Sciences, 08950 Barcelona, Spain
| | - Andrés Nascimento
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
| | - Janet Hoenicka
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Francesc Palau
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
- Department of Pathology, Hospital Sant Joan de Déu, Pediatric Biobank for Research, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
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Klee EW, Cousin MA, Pinto E Vairo F, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN. Impact of integrated translational research on clinical exome sequencing. Genet Med 2021; 23:498-507. [PMID: 33144682 DOI: 10.1038/s41436-020-01005-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Exome sequencing often identifies pathogenic genetic variants in patients with undiagnosed diseases. Nevertheless, frequent findings of variants of uncertain significance necessitate additional efforts to establish causality before reaching a conclusive diagnosis. To provide comprehensive genomic testing to patients with undiagnosed disease, we established an Individualized Medicine Clinic, which offered clinical exome testing and included a Translational Omics Program (TOP) that provided variant curation, research activities, or research exome sequencing. METHODS From 2012 to 2018, 1101 unselected patients with undiagnosed diseases received exome testing. Outcomes were reviewed to assess impact of the TOP and patient characteristics on diagnostic rates through descriptive and multivariate analyses. RESULTS The overall diagnostic yield was 24.9% (274 of 1101 patients), with 174 (15.8% of 1101) diagnosed on the basis of clinical exome sequencing alone. Four hundred twenty-three patients with nondiagnostic or without access to clinical exome sequencing were evaluated by the TOP, with 100 (9% of 1101) patients receiving a diagnosis, accounting for 36.5% of the diagnostic yield. The identification of a genetic diagnosis was influenced by the age at time of testing and the disease phenotype of the patient. CONCLUSION Integration of translational research activities into clinical practice of a tertiary medical center can significantly increase the diagnostic yield of patients with undiagnosed disease.
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Affiliation(s)
- Eric W Klee
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
| | - Margot A Cousin
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Joel A Morales-Rosado
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - W Garrett Jenkinson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alejandro Ferrer
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ashley N Sigafoos
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Tanya L Schwab
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul A Urrutia
- Division of Research, Department of Surgery and the Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Aditi Gupta
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick R Blackburn
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole J Boczek
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carri A Prochnow
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rebecca J Lowy
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay A Mulvihill
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tammy M McAllister
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Stacy L Aoudia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Teresa M Kruisselbrink
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jennifer L Kemppainen
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Laura J Fisher
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Megan M Hager
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Sarah A Kroc
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Bertsch
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Katherine E Agre
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Laura M Rust
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Scott A Beck
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Marissa S Ellingson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sarah S Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kristen J Rasmussen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carrie A Lahner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Zhiyv Niu
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Ferber
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Karl J Clark
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - David R Deyle
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eva Morava-Kozicz
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H Gavrilova
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Radhika Dhamija
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA.,Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Gianrico Farrugia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lisa A Schimmenti
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Konstantinos N Lazaridis
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA.
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Scantlebury MH, Barrett KT, Jacinto S, Corbin DOC, Kerr M, Khan A. Cou Cou, flying fish and a whole exome please... lessons learned from genetic testing in Barbados. Pan Afr Med J 2021; 38:111. [PMID: 33912281 PMCID: PMC8051213 DOI: 10.11604/pamj.2021.38.111.27969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 11/11/2022] Open
Abstract
Millions of patients, with suspected complex neurogenetic disorders, living in resource limited regions around the world have no access to genetic testing despite the rapidly expanding availability and decreasing costs of genetic testing in first world nations. The barriers to increasing availability of genetic testing in resource limited nations are multifactorial but can be attributed, in large part, to a lack of awareness of the power of genetic testing to lead to a rapid, cost-effective, diagnosis that potentially will have profound clinical implications on treatment and patient outcomes. We report our experience with whole exome sequencing (WES) done for the first time in 5 patients of African descent with a suspected neurogenetic disorder living in a resource limited setting on the Eastern Caribbean island of Barbados. A diagnostic pathogenic mutation was found in 3 patients in the SCN1A, STXBP1 and SCN4A, who clinically were diagnosed with Dravet syndrome, Lennox-Gastaut syndrome, paramytonia and seizures respectively. A variant of undetermined significance was found in a patient with global developmental delays, hypotonia, with abnormal eye movements. In one patient WES was non-diagnostic. This result highlights the high yield of WES in carefully selected patients with a neurologic disease and the need for increase access to genetic testing in resource limited settings globally.
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Affiliation(s)
- Morris Hilary Scantlebury
- Departments of Pediatrics and Clinical Neuroscience, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Karlene Tanechia Barrett
- Departments of Pediatrics and Clinical Neuroscience, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | | | - Marina Kerr
- Discovery DNA Incorporated, Calgary, Alberta, Canada
| | - Aneal Khan
- Departments of Pediatrics and Clinical Neuroscience, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Discovery DNA Incorporated, Calgary, Alberta, Canada.,Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Abstract
Xia-Gibbs syndrome (XGS) is a rare genetic disorder that has been discovered as a distinct clinical entity in the recent past. The occurrence has been attributed to the mutation of AT Hook DNA binding motif Containing 1 (AHDC1) gene that is carried on chromosome 1p36. The concerned gene participates in deoxyribonucleic acid (DNA) repair apart from other crucial functions. The mutation results in dysfunction that leads to neurodevelopmental delay. The spectrum of manifestations constitutes intellectual disabilities, hypotonia, expressive language delay, sleep difficulties, and short stature. Dysmorphic facial features include depressed nasal bridge, hypertelorism, down-slanting or up-slanting palpebral fissures, horizontal eyebrows, dysplastic dentition, thin upper lip vermilion, and micrognathia. The phenotype is still expanding. The condition may range from mild to severe dysfunction depending on the area and site of genetic aberration but variation is evident. Thus, the correlation between genotype and phenotype is largely unclear. XGS should be considered as a differential diagnosis for patients presenting with intellectual as well as developmental disabilities. Whole-exome sequencing (WES) is the genetic test that is largely used for the confirmation of diagnosis. Less is known about the natural history as only a few adults with XGS have been documented in the literature. Age-appropriate cancer screening is recommended for patients with XGS as the gene mutation alters DNA repair mechanisms that may trigger tumour formation. The management of patients diagnosed with XGS is an area that needs investigation. Though use of growth hormone replacement therapy and physiotherapy intervention have been reported as effective in previous studies, research on effective means of care of these patients is warranted on a larger number of patients. We present a review of current literature on what is known about XGS that would facilitate to identify knowledge gaps for paving a way for further studies. This, in turn, will help in provision of early and effective rehabilitation services for patients with XGS.
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Affiliation(s)
- Chanan Goyal
- Physiotherapy, Datta Meghe Institute of Medical Sciences, Wardha, IND
| | - Waqar M Naqvi
- Physiotherapy, Datta Meghe Institute of Medical Sciences, Wardha, IND
| | - Arti Sahu
- Physiotherapy, Datta Meghe Institute of Medical Sciences, Wardha, IND
| | - Ashish S Aujla
- Paediatric Neurology, Kids Care Paediatric Neurology Center, Raipur, IND
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48
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Rubinstein YR, Robinson PN, Gahl WA, Avillach P, Baynam G, Cederroth H, Goodwin RM, Groft SC, Hansson MG, Harris NL, Huser V, Mascalzoni D, McMurry JA, Might M, Nellaker C, Mons B, Paltoo DN, Pevsner J, Posada M, Rockett-Frase AP, Roos M, Rubinstein TB, Taruscio D, van Enckevort E, Haendel MA. The case for open science: rare diseases. JAMIA Open 2020; 3:472-486. [PMID: 33426479 PMCID: PMC7660964 DOI: 10.1093/jamiaopen/ooaa030] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/30/2020] [Accepted: 06/23/2020] [Indexed: 01/04/2023] Open
Abstract
The premise of Open Science is that research and medical management will progress faster if data and knowledge are openly shared. The value of Open Science is nowhere more important and appreciated than in the rare disease (RD) community. Research into RDs has been limited by insufficient patient data and resources, a paucity of trained disease experts, and lack of therapeutics, leading to long delays in diagnosis and treatment. These issues can be ameliorated by following the principles and practices of sharing that are intrinsic to Open Science. Here, we describe how the RD community has adopted the core pillars of Open Science, adding new initiatives to promote care and research for RD patients and, ultimately, for all of medicine. We also present recommendations that can advance Open Science more globally.
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Affiliation(s)
- Yaffa R Rubinstein
- Special Volunteer in the Office of Strategic Initiatives, National Library of Medicine, Bethesda, Maryland, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - William A Gahl
- Undiagnosed Diseases Program and Office of the Clinical Director, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, Maryland, USA
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Telethon Kids Institute, Perth, Australia
| | | | - Rebecca M Goodwin
- Department of Health and Human Services, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen C Groft
- NCATS, National Institutes of Health, Bethesda, Maryland, USA
| | - Mats G Hansson
- Center for Research Ethics and Bioethics, Uppsala Universitet, Uppsala, Sweden
| | - Nomi L Harris
- Department of Environmental Genomics & System Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vojtech Huser
- Department of Health and Human Services, NCBI, National Institutes of Health, Bethesda, Maryland, USA
| | - Deborah Mascalzoni
- Center for Research Ethics and Bioethics, Uppsala University, Sweden and EURAC Research, Bolzano, Italy
| | - Julie A McMurry
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, USA
| | - Matthew Might
- Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christoffer Nellaker
- Nuffield Department of Women's and Reproductive Health, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Barend Mons
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Dina N Paltoo
- Department of Health and Human Services, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute and Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Manuel Posada
- Rare Diseases Research Institute & CIBERER, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Marco Roos
- Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Tamar B Rubinstein
- Children Hospital at Montefiore/Albert Einstein College of Medicine—Pediatrics, Bronx, New York, USA
| | - Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Esther van Enckevort
- Department of Genetics, University Medical Center Groningen, University of Groningen, Leiden, Netherlands
| | - Melissa A Haendel
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, USA
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49
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Johnstone T, Wang J, Ross D, Balanda N, Huang Y, Godfrey R, Groden C, Barton BR, Gahl W, Toro C, Malicdan MCV. Biallelic variants in two complex I genes cause abnormal splicing defects in probands with mild Leigh syndrome. Mol Genet Metab 2020; 131:98-106. [PMID: 33097395 PMCID: PMC7749052 DOI: 10.1016/j.ymgme.2020.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/25/2022]
Abstract
Leigh syndrome is a genetically heterogeneous disorder resulting from deficient oxidative energy biogenesis. The syndrome is characterized by subacute episodic decompensations, transiently elevated lactate, and necrotizing brain lesions most often in the striatum and brainstem. Acute decompensation is often triggered by viral infections. Sequalae from repeated episodes leads to progressive neurological deterioration and death. The severity of Leigh syndrome varies widely, from a rapid demise in childhood to rare adult presentations. Although the causes of Leigh syndrome include genes affecting a variety of different pathways, more than 75 of them are nuclear or mitochondrial encoded genes involved in the assembly and catalytic activity of mitochondrial respiratory complex I. Here we report the detailed clinical and molecular phenotype of two adults with mild presentations of NDUFS3 and NDUFAF6-related Leigh Syndrome. Mitochondrial assays revealed slightly reduced complex I activity in one proband and normal complex I activity in the other. The proband with NDUFS3-related Leigh syndrome was mildly affected and lived into adulthood with novel biallelic variants causing aberrant mRNA splicing (NM_004551.2:c.419G > A; p.Arg140Gln; NM_004551.2:c.381 + 6 T > C). The proband with NDUFAF6-related Leigh syndrome had biallelic variants that cause defects in mRNA splicing (NM_152416.3:c.371 T > C; p.Ile124Thr; NM_152416.3:c.420 + 2_420 + 3insTA). The mild phenotypes of these two individuals may be attributed to some residual production of normal NDUFS3 and NDUFAF6 proteins by NDUFS3 and NDUFAF6 mRNA isoforms alongside mutant transcripts. Taken together, these cases reported herein suggest that splice-regulatory variants to complex I proteins could result in milder phenotypes.
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Affiliation(s)
- Thomas Johnstone
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; United States Naval Academy, Annapolis, MD, USA
| | - Jennifer Wang
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA
| | - Daron Ross
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas Balanda
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA
| | - Yan Huang
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA
| | - Rena Godfrey
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Catherine Groden
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brandon R Barton
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - William Gahl
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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50
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Chennen K, Weber T, Lornage X, Kress A, Böhm J, Thompson J, Laporte J, Poch O. MISTIC: A prediction tool to reveal disease-relevant deleterious missense variants. PLoS One 2020; 15:e0236962. [PMID: 32735577 PMCID: PMC7394404 DOI: 10.1371/journal.pone.0236962] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/16/2020] [Indexed: 12/20/2022] Open
Abstract
The diffusion of next-generation sequencing technologies has revolutionized research and diagnosis in the field of rare Mendelian disorders, notably via whole-exome sequencing (WES). However, one of the main issues hampering achievement of a diagnosis via WES analyses is the extended list of variants of unknown significance (VUS), mostly composed of missense variants. Hence, improved solutions are needed to address the challenges of identifying potentially deleterious variants and ranking them in a prioritized short list. We present MISTIC (MISsense deleTeriousness predICtor), a new prediction tool based on an original combination of two complementary machine learning algorithms using a soft voting system that integrates 113 missense features, ranging from multi-ethnic minor allele frequencies and evolutionary conservation, to physiochemical and biochemical properties of amino acids. Our approach also uses training sets with a wide spectrum of variant profiles, including both high-confidence positive (deleterious) and negative (benign) variants. Compared to recent state-of-the-art prediction tools in various benchmark tests and independent evaluation scenarios, MISTIC exhibits the best and most consistent performance, notably with the highest AUC value (> 0.95). Importantly, MISTIC maintains its high performance in the specific case of discriminating deleterious variants from benign variants that are rare or population-specific. In a clinical context, MISTIC drastically reduces the list of VUS (<30%) and significantly improves the ranking of "causative" deleterious variants. Pre-computed MISTIC scores for all possible human missense variants are available at http://lbgi.fr/mistic.
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Affiliation(s)
- Kirsley Chennen
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory – CNRS, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Thomas Weber
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory – CNRS, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
| | - Xavière Lornage
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Arnaud Kress
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory – CNRS, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
| | - Johann Böhm
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Julie Thompson
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory – CNRS, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
| | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U1258, CNRS UMR7104, University of Strasbourg, Illkirch, France
| | - Olivier Poch
- Complex Systems and Translational Bioinformatics (CSTB), ICube laboratory – CNRS, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
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