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Türkyılmaz A, Cimbek EA, Kardeş H, Çebi AH, Acar Arslan E, Karagüzel G. A triple molecular diagnosis in a Turkish individual with hypotrichosis, deafness, and diabetes. Clin Dysmorphol 2024; 33:118-120. [PMID: 38818819 DOI: 10.1097/mcd.0000000000000499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Affiliation(s)
| | - Emine Ayça Cimbek
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
| | - Hakan Kardeş
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
| | | | - Elif Acar Arslan
- Department of Pediatric Neurology, Marmara University, Faculty of Medicine, İstanbul, Türkiye
| | - Gülay Karagüzel
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
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2
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Ilic N, Maric N, Maver A, Armengol L, Kravljanac R, Cirkovic J, Krstic J, Radivojevic D, Cirkovic S, Ostojic S, Krasic S, Paripovic A, Vukomanovic V, Peterlin B, Maric G, Sarajlija A. Reverse Phenotyping after Whole-Exome Sequencing in Children with Developmental Delay/Intellectual Disability-An Exception or a Necessity? Genes (Basel) 2024; 15:789. [PMID: 38927725 PMCID: PMC11203244 DOI: 10.3390/genes15060789] [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: 05/02/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
This study delves into the diagnostic yield of whole-exome sequencing (WES) in pediatric patients presenting with developmental delay/intellectual disability (DD/ID), while also exploring the utility of Reverse Phenotyping (RP) in refining diagnoses. A cohort of 100 pediatric patients underwent WES, yielding a diagnosis in 66% of cases. Notably, RP played a significant role in cases with negative prior genetic testing, underscoring its significance in complex diagnostic scenarios. The study revealed a spectrum of genetic conditions contributing to DD/ID, illustrating the heterogeneity of etiological factors. Despite challenges, WES demonstrated effectiveness, particularly in cases with metabolic abnormalities. Reverse phenotyping was indicated in half of the patients with positive WES findings. Neural network models exhibited moderate-to-exceptional predictive abilities for aiding in patient selection for WES and RP. These findings emphasize the importance of employing comprehensive genetic approaches and RP in unraveling the genetic underpinnings of DD/ID, thereby facilitating personalized management and genetic counseling for affected individuals and families. This research contributes insights into the genetic landscape of DD/ID, enhancing our understanding and guiding clinical practice in this particular field of clinical genetics.
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Affiliation(s)
- Nikola Ilic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Nina Maric
- Clinic for Children Diseases, University Clinical Center of the Republic of Srpska, Banja Luka 78000, Bosnia and Herzegovina;
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (B.P.)
| | - Lluis Armengol
- CIBER en Epidemiología y Salud Pública (CIBERESP), Genes and Disease Program, Center for Genomic Regulation (CRG-UPF), 08003 Barcelona, Spain;
| | - Ruzica Kravljanac
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (R.K.); (S.O.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
| | - Jana Cirkovic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Jovana Krstic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
| | - Danijela Radivojevic
- Laboratory of Medical Genetics, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (D.R.); (S.C.)
| | - Sanja Cirkovic
- Laboratory of Medical Genetics, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (D.R.); (S.C.)
| | - Slavica Ostojic
- Department of Neurology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (R.K.); (S.O.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
| | - Stasa Krasic
- Department of Cardiology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia;
| | - Aleksandra Paripovic
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
- Department of Nephrology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia
| | - Vladislav Vukomanovic
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
- Department of Cardiology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia;
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (B.P.)
| | - Gorica Maric
- Institute of Epidemiology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
| | - Adrijan Sarajlija
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.C.); (J.K.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (A.P.); (V.V.)
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3
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van Karnebeek CDM, Tarailo-Graovac M, Leen R, Meinsma R, Correard S, Jansen-Meijer J, Prykhozhij SV, Pena IA, Ban K, Schock S, Saxena V, Pras-Raves ML, Drögemöller BI, Grootemaat AE, van der Wel NN, Dobritzsch D, Roseboom W, Schomakers BV, Jaspers YRJ, Zoetekouw L, Roelofsen J, Ferreira CR, van der Lee R, Ross CJ, Kochan J, McIntyre RL, van Klinken JB, van Weeghel M, Kramer G, Weschke B, Labrune P, Willemsen MA, Riva D, Garavaglia B, Moeschler JB, Filiano JJ, Ekker M, Berman JN, Dyment D, Vaz FM, Wasserman WW, Houtkooper RH, van Kuilenburg ABP. CIAO1 and MMS19 deficiency: A lethal neurodegenerative phenotype caused by cytosolic Fe-S cluster protein assembly disorders. Genet Med 2024; 26:101104. [PMID: 38411040 DOI: 10.1016/j.gim.2024.101104] [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: 07/25/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024] Open
Abstract
PURPOSE The functionality of many cellular proteins depends on cofactors; yet, they have only been implicated in a minority of Mendelian diseases. Here, we describe the first 2 inherited disorders of the cytosolic iron-sulfur protein assembly system. METHODS Genetic testing via genome sequencing was applied to identify the underlying disease cause in 3 patients with microcephaly, congenital brain malformations, progressive developmental and neurologic impairments, recurrent infections, and a fatal outcome. Studies in patient-derived skin fibroblasts and zebrafish models were performed to investigate the biochemical and cellular consequences. RESULTS Metabolic analysis showed elevated uracil and thymine levels in body fluids but no pathogenic variants in DPYD, encoding dihydropyrimidine dehydrogenase. Genome sequencing identified compound heterozygosity in 2 patients for missense variants in CIAO1, encoding cytosolic iron-sulfur assembly component 1, and homozygosity for an in-frame 3-nucleotide deletion in MMS19, encoding the MMS19 homolog, cytosolic iron-sulfur assembly component, in the third patient. Profound alterations in the proteome, metabolome, and lipidome were observed in patient-derived fibroblasts. We confirmed the detrimental effect of deficiencies in CIAO1 and MMS19 in zebrafish models. CONCLUSION A general failure of cytosolic and nuclear iron-sulfur protein maturation caused pleiotropic effects. The critical function of the cytosolic iron-sulfur protein assembly machinery for antiviral host defense may well explain the recurrent severe infections occurring in our patients.
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Affiliation(s)
- Clara D M van Karnebeek
- Amsterdam UMC location University of Amsterdam, Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam, The Netherlands; Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands; Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; United for Metabolic Diseases, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Maja Tarailo-Graovac
- Departments of Medical Genetics and Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute (ACHRI), Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - René Leen
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Rutger Meinsma
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Solenne Correard
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Judith Jansen-Meijer
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Sergey V Prykhozhij
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Izabella A Pena
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology-MIT, Boston, MA
| | - Kevin Ban
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Sarah Schock
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Vishal Saxena
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Mia L Pras-Raves
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Britt I Drögemöller
- Rady Faculty of Health Sciences, Department of Biochemistry and Medical Genetics, Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anita E Grootemaat
- Amsterdam UMC Location University of Amsterdam, Department of Medical Biology, Amsterdam, The Netherlands
| | - Nicole N van der Wel
- Amsterdam UMC Location University of Amsterdam, Department of Medical Biology, Amsterdam, The Netherlands
| | - Doreen Dobritzsch
- Uppsala University, Department of Chemistry, Biomedical Center, Uppsala, Sweden
| | - Winfried Roseboom
- Swammerdam Institute for Life Sciences, University of Amsterdam, Laboratory for Mass Spectrometry of Biomolecules, Amsterdam, The Netherlands
| | - Bauke V Schomakers
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Yorrick R J Jaspers
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Lida Zoetekouw
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Jeroen Roelofsen
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Robin van der Lee
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Colin J Ross
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Jakub Kochan
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biochemistry, Kraków, Poland
| | - Rebecca L McIntyre
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Jan B van Klinken
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel van Weeghel
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Gertjan Kramer
- Swammerdam Institute for Life Sciences, University of Amsterdam, Laboratory for Mass Spectrometry of Biomolecules, Amsterdam, The Netherlands
| | - Bernhard Weschke
- Department of Neuropediatrics, Charité University Medicine Berlin, Berlin, Germany
| | - Philippe Labrune
- APHP-Université Paris-Saclay, Hôpital Antoine Béclère, Centre de Référence Maladies Héréditaires du Métabolisme Hépatique, Service de Pédiatrie, Clamart, and Paris-Saclay University, and INSERM U 1195, Clamart, France
| | - Michèl A Willemsen
- Department of Pediatric Neurology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daria Riva
- Neurogenetic Syndromes and Autism Spectrum Disorders Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta," Milan, Italy
| | - Barbara Garavaglia
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta," Milan, Italy
| | - John B Moeschler
- Geisel School of Medicine, Dartmouth College and Departments of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH
| | - James J Filiano
- Geisel School of Medicine, Dartmouth College and Departments of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH
| | - Marc Ekker
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jason N Berman
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - David Dyment
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Frédéric M Vaz
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Wyeth W Wasserman
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Riekelt H Houtkooper
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - André B P van Kuilenburg
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands.
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4
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Li L, Zhang Y, Zhou J, Wang J, Wang L. Single-cell metabolomics in rare disease: From technology to disease. Intractable Rare Dis Res 2024; 13:99-103. [PMID: 38836176 PMCID: PMC11145402 DOI: 10.5582/irdr.2023.01073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 05/12/2024] [Accepted: 05/22/2024] [Indexed: 06/06/2024] Open
Abstract
With the development of clinical experience and technology, rare diseases (RDs) are gradually coming into the limelight. As they often lead to poor prognosis, it is urgent to promote the accuracy and rapidity of diagnosis and promote the development of therapeutic drugs. In recent years, with the rapid improvement of single-cell sequencing technology, the advantages of multi-omics combined application in diseases have been continuously explored. Single-cell metabolomics represents a powerful tool for advancing our understanding of rare diseases, particularly metabolic RDs, and transforming clinical practice. By unraveling the intricacies of cellular metabolism at a single-cell resolution, this innovative approach holds the potential to revolutionize diagnosis, treatment, and management strategies, ultimately improving outcomes for RDs patients. Continued research and technological advancements in single-cell metabolomics are essential for realizing its full potential in the field of RDs diagnosis and therapeutics. It is expected that single-cell metabolomics can be better applied to RDs research in the future, for the benefit of patients and society.
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Affiliation(s)
- Lisha Li
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Yiqin Zhang
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Shanghai Key Laboratory Embryo Original Diseases, Shanghai, China
| | - Jing Zhou
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Jing Wang
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Ling Wang
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
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5
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Rodrigues Alves Barbosa V, Maroilley T, Diao C, Colvin-James L, Perrier R, Tarailo-Graovac M. Single variant, yet "double trouble": TSC and KBG syndrome because of a large de novo inversion. Life Sci Alliance 2024; 7:e202302115. [PMID: 38253421 PMCID: PMC10803213 DOI: 10.26508/lsa.202302115] [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: 04/26/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Despite the advances in high-throughput sequencing, many rare disease patients remain undiagnosed. In particular, the patients with well-defined clinical phenotypes and established clinical diagnosis, yet missing or partial genetic diagnosis, may hold a clue to more complex genetic mechanisms of a disease that could be missed by available clinical tests. Here, we report a patient with a clinical diagnosis of Tuberous sclerosis, combined with unusual secondary features, but negative clinical tests including TSC1 and TSC2 Short-read whole-genome sequencing combined with advanced bioinformatics analyses were successful in uncovering a de novo pericentric 87-Mb inversion with breakpoints in TSC2 and ANKRD11, which explains the TSC clinical diagnosis, and confirms a second underlying monogenic disorder, KBG syndrome. Our findings illustrate how complex variants, such as large inversions, may be missed by clinical tests and further highlight the importance of well-defined clinical diagnoses in uncovering complex molecular mechanisms of a disease, such as complex variants and "double trouble" effects.
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Affiliation(s)
- Victoria Rodrigues Alves Barbosa
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Tatiana Maroilley
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Catherine Diao
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Leslie Colvin-James
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Renee Perrier
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Maja Tarailo-Graovac
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
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6
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Regier DA, Loewen R, Chan B, Ehman M, Pollard S, Friedman JM, Stockler-Ipsiroglu S, van Karnebeek C, Race S, Elliott AM, Dragojlovic N, Lynd LD, Weymann D. Real-world diagnostic outcomes and cost-effectiveness of genome-wide sequencing for developmental and seizure disorders: Evidence from Canada. Genet Med 2024; 26:101069. [PMID: 38205742 DOI: 10.1016/j.gim.2024.101069] [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: 07/21/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
PURPOSE To determine real-world diagnostic rates, cost trajectories, and cost-effectiveness of exome sequencing (ES) and genome sequencing (GS) for children with developmental and/or seizure disorders in British Columbia, Canada. METHODS Based on medical records review, we estimated real-world costs and outcomes for 491 patients who underwent standard of care (SOC) diagnostic testing at British Columbia Children's Hospital. Results informed a state-transition Markov model examining cost-effectiveness of 3 competing diagnostic strategies: (1) SOC with last-tier access to ES, (2) streamlined ES access, and (3) first-tier GS. RESULTS Through SOC, 49.4% (95% CI: 40.6, 58.2) of patients were diagnosed at an average cost of C$11,683 per patient (95% CI: 9200, 14,166). Compared with SOC, earlier ES or GS access yielded similar or improved diagnostic rates and shorter times to genetic diagnosis, with 94% of simulations demonstrating cost savings for streamlined ES and 60% for first-tier GS. Net benefit from the perspective of the health care system was C$2956 (95% CI: -608, 6519) for streamlined ES compared with SOC. CONCLUSION Using real-world data, we found earlier access to ES may yield more rapid genetic diagnosis of childhood developmental and seizure disorders and cost savings compared with current practice in a Canadian health care system.
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Affiliation(s)
- Dean A Regier
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Rosalie Loewen
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Brandon Chan
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Morgan Ehman
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Samantha Pollard
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada; BC Children's Hospital Research Institute, Vancouver, Canada
| | - Sylvia Stockler-Ipsiroglu
- BC Children's Hospital Research Institute, Vancouver, Canada; Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Division of Biochemical Genetics, BC Children's Hospital, Vancouver, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Simone Race
- Division of Biochemical Genetics, BC Children's Hospital, Vancouver, Canada
| | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada; BC Children's Hospital Research Institute, Vancouver, Canada
| | - Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada; Centre for Health Evaluation and Outcomes Sciences, Providence Health Research Institute, Vancouver, Canada
| | - Deirdre Weymann
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada.
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7
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Yuan J, Li K, Peng H, Zhang Y, Yao Y, Qu J, Su J. Protocol for detecting rare and common genetic associations in whole-exome sequencing studies using MAGICpipeline. STAR Protoc 2024; 5:102806. [PMID: 38175747 PMCID: PMC10793169 DOI: 10.1016/j.xpro.2023.102806] [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: 07/30/2023] [Revised: 10/20/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
Whole-exome sequencing (WES) is a major approach to uncovering gene-disease associations and pinpointing effector genes. Here, we present a protocol for estimating genetic associations of rare and common variants in large-scale case-control WES studies using MAGICpipeline, an open-access analysis pipeline. We describe steps for assessing gene-based rare-variant association analyses by incorporating multiple variant pathogenic annotations and statistical techniques. We then detail procedures for identifying disease-related modules and hub genes using weighted correlation network analysis, a systems biology approach. For complete details on the use and execution of this protocol, please refer to Su et al. (2023).1.
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Affiliation(s)
- Jian Yuan
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Kai Li
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China
| | - Hui Peng
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yue Zhang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Jia Qu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China
| | - Jianzhong Su
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China.
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8
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Singh S, Hämäläinen RH. The Roles of Cystatin B in the Brain and Pathophysiological Mechanisms of Progressive Myoclonic Epilepsy Type 1. Cells 2024; 13:170. [PMID: 38247861 PMCID: PMC10814315 DOI: 10.3390/cells13020170] [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: 12/07/2023] [Revised: 01/03/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Progressive myoclonic epilepsy type 1 (EPM1) is an autosomal recessive disorder, also known as Unverricht-Lundborg disease (ULD). EPM1 patients suffer from photo-sensitive seizures, stimulus-sensitive myoclonus, nocturnal myoclonic seizures, ataxia and dysarthria. In addition, cerebral ataxia and impaired GABAergic inhibition are typically present. EPM1 is caused by mutations in the Cystatin B gene (CSTB). The CSTB protein functions as an intracellular thiol protease inhibitor and inhibits Cathepsin function. It also plays a crucial role in brain development and regulates various functions in neurons beyond maintaining cellular proteostasis. These include controlling cell proliferation and differentiation, synaptic functions and protection against oxidative stress, likely through regulation of mitochondrial function. Depending on the differentiation stage and status of neurons, the protein localizes either to the cytoplasm, nucleus, lysosomes or mitochondria. Further, CSTB can also be secreted to the extracellular matrix for interneuron rearrangement and migration. In this review, we will review the various functions of CSTB in the brain and discuss the putative pathophysiological mechanism underlying EPM1.
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Affiliation(s)
| | - Riikka H. Hämäläinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland;
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9
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Heinken A, El Kouche S, Guéant-Rodriguez RM, Guéant JL. Towards personalized genome-scale modeling of inborn errors of metabolism for systems medicine applications. Metabolism 2024; 150:155738. [PMID: 37981189 DOI: 10.1016/j.metabol.2023.155738] [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: 08/14/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023]
Abstract
Inborn errors of metabolism (IEMs) are a group of more than 1000 inherited diseases that are individually rare but have a cumulative global prevalence of 50 per 100,000 births. Recently, it has been recognized that like common diseases, patients with rare diseases can greatly vary in the manifestation and severity of symptoms. Here, we review omics-driven approaches that enable an integrated, holistic view of metabolic phenotypes in IEM patients. We focus on applications of Constraint-based Reconstruction and Analysis (COBRA), a widely used mechanistic systems biology approach, to model the effects of inherited diseases. Moreover, we review evidence that the gut microbiome is also altered in rare diseases. Finally, we outline an approach using personalized metabolic models of IEM patients for the prediction of biomarkers and tailored therapeutic or dietary interventions. Such applications could pave the way towards personalized medicine not just for common, but also for rare diseases.
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Affiliation(s)
- Almut Heinken
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France.
| | - Sandra El Kouche
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - Rosa-Maria Guéant-Rodriguez
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France; National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
| | - Jean-Louis Guéant
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France; National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
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10
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Piombarolo A, Ialongo C, Bizzarri M, Angeloni A. Systems Biology and Inborn Error of Metabolism: Analytical Strategy in Investigating Different Biochemical/Genetic Parameters. Methods Mol Biol 2024; 2745:191-210. [PMID: 38060187 DOI: 10.1007/978-1-0716-3577-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Inborn errors of metabolism (IEM) are a group of about 500 rare genetic diseases with large diversity and complexity due to number of metabolic pathways involved in. Establishing a correct diagnosis and identifying the specific clinical phenotype is consequently a difficult task. However, an inclusive diagnosis able in capturing the different clinical phenotypes is mandatory for successful treatment. However, in contrast with Garrod's basic assumption "one-gene one-disease," no "simple" correlation between genotype-phenotype can be vindicated in IEMs. An illustrative example of IEM is Phenylketonuria (PKU), an autosomal recessive inborn error of L-phenylalanine (Phe) metabolism, ascribed to variants of the phenylalanine hydroxylase (PAH) gene encoding for the enzyme complex phenylalanine-hydroxylase. Blood values of Phe allow classifying PKU into different clinical phenotypes, albeit the participation of other genetic/biochemical pathways in the pathogenetic mechanisms remains elusive. Indeed, it has been shown that the most serious complications, such as cognitive impairment, are not only related to the gene dysfunction but also to the patient's background and the participation of several nongenetic factors.Therefore, a Systems Biology-based strategy is required in addressing IEM complexity, and in identifying the interplay between different pathways in shaping the clinical phenotype. Such an approach should entail the concerted investigation of genomic, transcriptomics, proteomics, metabolomics profiles altogether with phenylalanine and amino acids metabolism. Noticeably, this "omic" perspective could be instrumental in planning personalized treatment, tailored accordingly to the disease profile and prognosis.
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Affiliation(s)
- Aurora Piombarolo
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Cristiano Ialongo
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Mariano Bizzarri
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Antonio Angeloni
- Department of Experimental Medicine, Sapienza University, Rome, Italy.
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11
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Balasar Ö, Başdemirci M. Assessment of whole-exome sequencing results in neurogenetic diseases. J Hum Genet 2023; 68:797-804. [PMID: 37524782 DOI: 10.1038/s10038-023-01185-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/22/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023]
Abstract
Neurogenetic diseases are rare genetic diseases in which neurological findings are prominent. Whole exome sequencing (WES) has led to great advances in the understanding of the causes of neurogenetic diseases. Etiological research ends with the WES method in many patients. This etiological research is called a "diagnostic odyssey" for many families. Here, we present the results of 168 patients who were previously undiagnosed and underwent WES with the suspicion of neurogenetic disease. A total of 168 cases, 94 males and 74 females, with suspected undiagnosed neurogenetic disease were included in the study. We presented the WES results of the patients. The mean age of patients at the time of WES request was 11 years (range 0.25-68 years). Seventy percent (n = 117) of the patients were born from consanguineous marriage. Most of the patients were children (n = 145). Patients were grouped according to age at the time of examination. Patients younger than 18 years of age at the time of examination were classified as children, otherwise adults. Seventy-eight patients had either a pathogenic variant or a likely pathogenic variant so the diagnostic rate for WES in our cohort was %46. Our experience showing the high diagnostic rate of WES, supports its use in undiagnosed neurogenetic diseases. It also affects medical treatment, prognosis and family planning by enabling early diagnosis in patients.
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Affiliation(s)
- Özgür Balasar
- Department of Medical Genetics, Konya City Hospital, Konya, Turkey.
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12
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Bulus AD, Yasartekin Y, Ceylan AC, Dirican O, Husseini AA. Cases of hypogonadotropic hypogonadism: A single-center experience. Niger J Clin Pract 2023; 26:1552-1556. [PMID: 37929534 DOI: 10.4103/njcp.njcp_244_23] [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] [Indexed: 11/07/2023]
Abstract
Background Delayed puberty (DP) affects approximately 2% of adolescents. In most patients of both genders, delayed puberty is due to constitutional delay in growth and puberty (CDGP); it is a self-limiting condition starting later than usual during puberty but progressing normally. Other causes of DP include permanent hypogonadotropic hypogonadism, functional hypogonadotropic hypogonadism, and gonadal insufficiency. Methods Nine patients admitted to the Ankara Atatürk Sanatoryum Training and Research Hospital Pediatric Endocrinology Department with hypogonadotropic hypogonadism between January 2012 and December 2022 were analyzed. Results Nine patients who applied to our pediatric endocrinology clinic with delayed puberty were analyzed. These nine patients were diagnosed and reported as hypogonadotropic hypogonadism with molecular methods. We aimed to determine the status of these cases from a molecular point of view, to emphasize the importance of hypogonadotropic hypogonadism in patients with delayed puberty, and to reveal the rarely encountered delayed puberty together with the clinical and laboratory data set of the patients. Conclusions To emphasize the importance of hypogonadotropic hypogonadism, which is a rare cause of delayed puberty, the molecular predispositions of our patients followed in our clinic are reviewed, and the data we have provided will contribute to the accumulation of data in this area.
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Affiliation(s)
- A D Bulus
- Pediatric Endocrinology, Ankara Atatürk Sanatorium Training and Research Hospital, University of Health Sciences, Ankara, Türkiye
| | - Y Yasartekin
- Pediatric Endocrinology, Ankara Atatürk Sanatorium Training and Research Hospital, University of Health Sciences, Ankara, Türkiye
| | - A C Ceylan
- Medical Genetics, Ankara Bilkent City Hospital, Ankara, Türkiye
| | - O Dirican
- Department of Pathology, Istanbul Gelisim University, Istanbul, Türkiye
| | - A A Husseini
- Department of Biomedical Device Technology, Istanbul Gelişim University, Istanbul, Türkiye
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13
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Smirnov D, Konstantinovskiy N, Prokisch H. Integrative omics approaches to advance rare disease diagnostics. J Inherit Metab Dis 2023; 46:824-838. [PMID: 37553850 DOI: 10.1002/jimd.12663] [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: 03/13/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023]
Abstract
Over the past decade high-throughput DNA sequencing approaches, namely whole exome and whole genome sequencing became a standard procedure in Mendelian disease diagnostics. Implementation of these technologies greatly facilitated diagnostics and shifted the analysis paradigm from variant identification to prioritisation and evaluation. The diagnostic rates vary widely depending on the cohort size, heterogeneity and disease and range from around 30% to 50% leaving the majority of patients undiagnosed. Advances in omics technologies and computational analysis provide an opportunity to increase these unfavourable rates by providing evidence for disease-causing variant validation and prioritisation. This review aims to provide an overview of the current application of several omics technologies including RNA-sequencing, proteomics, metabolomics and DNA-methylation profiling for diagnostics of rare genetic diseases in general and inborn errors of metabolism in particular.
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Affiliation(s)
- Dmitrii Smirnov
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| | - Nikita Konstantinovskiy
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
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14
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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15
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[Expert consensus on the diagnosis and treatment of neonatal hyperammonemia]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2023; 25:437-447. [PMID: 37272168 PMCID: PMC10247199 DOI: 10.7499/j.issn.1008-8830.2302140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/07/2023] [Indexed: 06/06/2023]
Abstract
Neonatal hyperammonemia is a disorder of ammonia metabolism that occurs in the neonatal period. It is a clinical syndrome characterized by abnormal accumulation of ammonia in the blood and dysfunction of the central nervous system. Due to its low incidence and lack of specificity in clinical manifestations, it is easy to cause misdiagnosis and missed diagnosis. In order to further standardize the diagnosis and treatment of neonatal hyperammonemia, the Youth Commission, Subspecialty Group of Neonatology, Society of Pediatrics, Chinese Medical Association formulated the expert consensus based on clinical evidence in China and overseas and combined with clinical practice experience,and put forward 18 recommendations for the diagnosis and treatment of neonatal hyperaminemia.
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16
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Sharma M, Leung D, Momenilandi M, Jones LC, Pacillo L, James AE, Murrell JR, Delafontaine S, Maimaris J, Vaseghi-Shanjani M, Del Bel KL, Lu HY, Chua GT, Di Cesare S, Fornes O, Liu Z, Di Matteo G, Fu MP, Amodio D, Tam IYS, Chan GSW, Sharma AA, Dalmann J, van der Lee R, Blanchard-Rohner G, Lin S, Philippot Q, Richmond PA, Lee JJ, Matthews A, Seear M, Turvey AK, Philips RL, Brown-Whitehorn TF, Gray CJ, Izumi K, Treat JR, Wood KH, Lack J, Khleborodova A, Niemela JE, Yang X, Liang R, Kui L, Wong CSM, Poon GWK, Hoischen A, van der Made CI, Yang J, Chan KW, Rosa Duque JSD, Lee PPW, Ho MHK, Chung BHY, Le HTM, Yang W, Rohani P, Fouladvand A, Rokni-Zadeh H, Changi-Ashtiani M, Miryounesi M, Puel A, Shahrooei M, Finocchi A, Rossi P, Rivalta B, Cifaldi C, Novelli A, Passarelli C, Arasi S, Bullens D, Sauer K, Claeys T, Biggs CM, Morris EC, Rosenzweig SD, O’Shea JJ, Wasserman WW, Bedford HM, van Karnebeek CD, Palma P, Burns SO, Meyts I, Casanova JL, Lyons JJ, Parvaneh N, Nguyen ATV, Cancrini C, Heimall J, Ahmed H, McKinnon ML, Lau YL, Béziat V, Turvey SE. Human germline heterozygous gain-of-function STAT6 variants cause severe allergic disease. J Exp Med 2023; 220:e20221755. [PMID: 36884218 PMCID: PMC10037107 DOI: 10.1084/jem.20221755] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/12/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
STAT6 (signal transducer and activator of transcription 6) is a transcription factor that plays a central role in the pathophysiology of allergic inflammation. We have identified 16 patients from 10 families spanning three continents with a profound phenotype of early-life onset allergic immune dysregulation, widespread treatment-resistant atopic dermatitis, hypereosinophilia with esosinophilic gastrointestinal disease, asthma, elevated serum IgE, IgE-mediated food allergies, and anaphylaxis. The cases were either sporadic (seven kindreds) or followed an autosomal dominant inheritance pattern (three kindreds). All patients carried monoallelic rare variants in STAT6 and functional studies established their gain-of-function (GOF) phenotype with sustained STAT6 phosphorylation, increased STAT6 target gene expression, and TH2 skewing. Precision treatment with the anti-IL-4Rα antibody, dupilumab, was highly effective improving both clinical manifestations and immunological biomarkers. This study identifies heterozygous GOF variants in STAT6 as a novel autosomal dominant allergic disorder. We anticipate that our discovery of multiple kindreds with germline STAT6 GOF variants will facilitate the recognition of more affected individuals and the full definition of this new primary atopic disorder.
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Affiliation(s)
- Mehul Sharma
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Daniel Leung
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Mana Momenilandi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris-Cité, Paris, France
| | - Lauren C.W. Jones
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Lucia Pacillo
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Academic Dept. of Pediatrics (DPUO), Unit of Clinical Immunology and Vaccinology, IRCCS Bambin Gesù Children Hospital, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Alyssa E. James
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jill R. Murrell
- Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Selket Delafontaine
- Dept. of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Pediatric Immunodeficiencies Division, University Hospitals Leuven, Leuven, Belgium
| | - Jesmeen Maimaris
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- Dept. of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Maryam Vaseghi-Shanjani
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Kate L. Del Bel
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Henry Y. Lu
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Dept. of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Gilbert T. Chua
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
- Allergy Centre, Union Hospital, Hong Kong, China
| | - Silvia Di Cesare
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
- Dept. of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Zhongyi Liu
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Gigliola Di Matteo
- Academic Dept. of Pediatrics (DPUO), Unit of Clinical Immunology and Vaccinology, IRCCS Bambin Gesù Children Hospital, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Maggie P. Fu
- Dept. of Medical Genetics, The University of British Columbia, Vancouver, Canada
- Genome Science and Technology Program, Faculty of Science, The University of British Columbia, Vancouver, Canada
| | - Donato Amodio
- Academic Dept. of Pediatrics (DPUO), Unit of Clinical Immunology and Vaccinology, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Issan Yee San Tam
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | | | | | - Joshua Dalmann
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Robin van der Lee
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
- Dept. of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Géraldine Blanchard-Rohner
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
- Unit of Immunology and Vaccinology, Division of General Pediatrics, Dept. of Woman, Child, and Adolescent Medicine, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Susan Lin
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris-Cité, Paris, France
| | - Phillip A. Richmond
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Jessica J. Lee
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, Canada
| | - Allison Matthews
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
- Dept. of Paediatrics, University of Toronto, Toronto, Canada
| | - Michael Seear
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Alexandra K. Turvey
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Rachael L. Philips
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Terri F. Brown-Whitehorn
- Dept. of Pediatrics, Division of Allergy and Immunology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christopher J. Gray
- Pediatrics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kosuke Izumi
- Pediatrics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - James R. Treat
- Pediatrics, Division of Pediatric Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen H. Wood
- Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, MD, USA
| | - Asya Khleborodova
- NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, MD, USA
| | | | - Xingtian Yang
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Rui Liang
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Lin Kui
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
- Dept. of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Christina Sze Man Wong
- Dept. of Medicine, Divison of Dermatology, The University of Hong Kong, Hong Kong, China
| | - Grace Wing Kit Poon
- Dept. of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong, China
| | - Alexander Hoischen
- Dept. of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Jing Yang
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Koon Wing Chan
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Jaime Sou Da Rosa Duque
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Pamela Pui Wah Lee
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Marco Hok Kung Ho
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
- Virtus Medical, Hong Kong, China
| | - Brian Hon Yin Chung
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Huong Thi Minh Le
- Pediatric Center, Vinmec Times City International General Hospital, Hanoi, Vietnam
| | - Wanling Yang
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Pejman Rohani
- Pediatrics, Pediatric Gastroenterology and Hepatology Research Center, Pediatrics Centre of Excellence, Children’s Medical Center, University of Medical Sciences, Tehran, Iran
| | - Ali Fouladvand
- Pediatrics, Allergy and Clinical Immunology, Lorestan University of Medical Sciences, Khoramabad, Iran
| | - Hassan Rokni-Zadeh
- Dept. of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Mohammad Miryounesi
- Dept. of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris-Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Mohammad Shahrooei
- Microbiology and Immunology, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, Leuven, Belgium
| | - Andrea Finocchi
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Paolo Rossi
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- DPUO, Research Unit of Infectivology and Pediatrics Drugs Development, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Beatrice Rivalta
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Academic Dept. of Pediatrics (DPUO), Unit of Clinical Immunology and Vaccinology, IRCCS Bambin Gesù Children Hospital, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Cristina Cifaldi
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Chiara Passarelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Stefania Arasi
- Allergy Unit, Area of Translational Research in Pediatric Specialities, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Dominique Bullens
- Dept. of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Pediatric Allergy Division, University Hospitals Leuven, Leuven, Belgium
| | - Kate Sauer
- Dept. of Pediatrics, Pediatric Pulmonology Division, AZ Sint-Jan Brugge, Brugge, Belgium
- Dept. of Pediatrics, Pediatric Pulmonology Division, University Hospitals Leuven, Leuven, Belgium
| | - Tania Claeys
- Dept. of Pediatrics, Pediatric Gastroenterology Division, AZ Sint-Jan Brugge, Brugge, Belgium
| | - Catherine M. Biggs
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Emma C. Morris
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- Dept. of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | | | - John J. O’Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Wyeth W. Wasserman
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
| | - H. Melanie Bedford
- Dept. of Paediatrics, University of Toronto, Toronto, Canada
- Genetics Program, North York General Hospital, Toronto, Canada
| | - Clara D.M. van Karnebeek
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
- Depts. of Pediatrics and Clinical Genetics, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Paolo Palma
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Academic Dept. of Pediatrics (DPUO), Unit of Clinical Immunology and Vaccinology, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Siobhan O. Burns
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- Dept. of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Isabelle Meyts
- Dept. of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Pediatric Immunodeficiencies Division, University Hospitals Leuven, Leuven, Belgium
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris-Cité, Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jonathan J. Lyons
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nima Parvaneh
- Department of Pediatrics, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Anh Thi Van Nguyen
- Dept. of Immunology, Allergy and Rheumatology, Division of Primary Immunodeficiency, Vietnam National Children’s Hospital, Hanoi, Vietnam
| | - Caterina Cancrini
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Jennifer Heimall
- Dept. of Pediatrics, Division of Allergy and Immunology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hanan Ahmed
- Faculty of Health Sciences, McMaster University, Hamilton, Canada
| | | | - Yu Lung Lau
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris-Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Stuart E. Turvey
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
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17
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Baalmann N, Spielmann M, Gillessen-Kaesbach G, Hanker B, Schmidt J, Lill CM, Hellenbroich Y, Greiten B, Lohmann K, Trinh J, Hüning I. Phenotypic specificity in patients with neurodevelopmental delay does not correlate with diagnostic yield of trio-exome sequencing. Eur J Med Genet 2023; 66:104774. [PMID: 37120078 DOI: 10.1016/j.ejmg.2023.104774] [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: 10/24/2022] [Revised: 03/12/2023] [Accepted: 04/26/2023] [Indexed: 05/01/2023]
Abstract
In this study, we aimed to examine the diagnostic yield achieved by applying a trio approach in exome sequencing (ES) and the interdependency between the clinical specificity in families with neurodevelopmental delay. Thirty-seven families were recruited and trio-ES as well as three criteria for estimating the clinical phenotypic specificity were suggested and applied to the underaged children. All our patients showed neurodevelopmental delay and most of them a large spectrum of congenital anomalies. Applying the pathogenicity guidelines of the American College of Medical Genetics (ACMG), likely pathogenic (29.7%) and pathogenic variants (8.1%) were found in 40,5% of our index patients. Additionally, we found four variants of uncertain significance (VUS; according to ACMG) and two genes of interest (GOI; going beyond ACMG classification) (GLRA4, NRXN2). Spastic Paraplegia 4 (SPG4) caused by a formerly known SPAST variant was diagnosed in a patient with a complex phenotype, in whom a second genetic disorder may be present. A potential pathogenic variant linked to severe intellectual disability in GLRA4 requires further investigation. No interdependency between the diagnostic yield and the clinical specificity of the phenotypes could be observed. In consequence, trio-ES should be used early in the diagnostic process, independently from the specificity of the patient.
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Affiliation(s)
- Nadja Baalmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
| | | | - Britta Hanker
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
| | - Julia Schmidt
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany; Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.
| | - Christina M Lill
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany; Institute of Neurogenetics, University of Lübeck, Lübeck, Germany; Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Germany; Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London, London, UK.
| | | | - Bianca Greiten
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
| | - Irina Hüning
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
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18
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Post MA, de Wit I, Zijlstra FSM, Engelke UFH, van Rooij A, Christodoulou J, Tan TY, Le Fevre A, Jin D, Yaplito-Lee J, Lee BH, Low KJ, Mallick AA, Õunap K, Pitt J, Reardon W, Vals MA, Wortmann SB, Wessels HJCT, Bärenfänger M, van Karnebeek CDM, Lefeber DJ. MOGS-CDG: Quantitative analysis of the diagnostic Glc 3 Man tetrasaccharide and clinical spectrum of six new cases. J Inherit Metab Dis 2023; 46:313-325. [PMID: 36651519 DOI: 10.1002/jimd.12588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
Congenital disorders of glycosylation (CDG) are a clinically and biochemically heterogeneous subgroup of inherited metabolic disorders. Most CDG with abnormal N-glycosylation can be detected by transferrin screening, however, MOGS-CDG escapes this routine screening. Combined with the clinical heterogeneity of reported cases, diagnosing MOGS-CDG can be challenging. Here, we clinically characterize ten MOGS-CDG cases including six previously unreported individuals, showing a phenotype characterized by dysmorphic features, global developmental delay, muscular hypotonia, and seizures in all patients and in a minority vision problems and hypogammaglobulinemia. Glycomics confirmed accumulation of a Glc3 Man7 GlcNAc2 glycan in plasma. For quantification of the diagnostic Glcα1-3Glcα1-3Glcα1-2Man tetrasaccharide in urine, we developed and validated a liquid chromatography-mass spectrometry method of 2-aminobenzoic acid (2AA) labeled urinary glycans. As an internal standard, isotopically labeled 13 C6 -2AA Glc3 Man was used, while labeling efficiency was controlled by use of 12 C6 -2AA and 13 C6 -2AA labeled laminaritetraose. Recovery, linearity, intra- and interassay coefficients of variability of these labeled compounds were determined. Furthermore, Glc3 Man was specifically identified by retention time matching against authentic MOGS-CDG urine and compared with Pompe urine. Glc3 Man was increased in all six analyzed cases, ranging from 34.1 to 618.0 μmol/mmol creatinine (reference <5 μmol). In short, MOGS-CDG has a broad manifestation of symptoms but can be diagnosed with the use of a quantitative method for analysis of urinary Glc3 Man excretion.
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Affiliation(s)
- Merel A Post
- Department of Neurology, Donders institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Isis de Wit
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- On behalf of United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Fokje S M Zijlstra
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Udo F H Engelke
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arno van Rooij
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - John Christodoulou
- Genomic Medicine Research Theme, Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Melbourne, Australia
| | - Tiong Yang Tan
- Genomic Medicine Research Theme, Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Anna Le Fevre
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Danqun Jin
- Pediatric Intensive Care Unit, Anhui Provincial Children's Hospital, Hefei, China
| | - Joy Yaplito-Lee
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Metabolic Medicine, The Royal Children's Hospital Melbourne, Parkville, Australia
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
| | - Karen J Low
- School of Clinical Sciences, University of Bristol, Bristol, UK
- Clinical Genetics, St. Michael's Hospital, University Hospitals NHS Trust, Bristol, UK
| | - Andrew A Mallick
- Department of Pediatric Neurology, Bristol Royal Hospital for Children, Bristol, UK
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - James Pitt
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - William Reardon
- Clinical Genetics, Children's Health Ireland (CHI), Crumlin, Ireland
| | - Mari-Anne Vals
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Children's Clinic, Tartu University Hospital, Tartu, Estonia
| | - Saskia B Wortmann
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Melissa Bärenfänger
- Department of Neurology, Donders institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- Division of Bioanalytical Chemistry, VU Amsterdam, Amsterdam, The Netherlands
| | - Clara D M van Karnebeek
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- On behalf of United for Metabolic Diseases, Amsterdam, The Netherlands
- Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Dirk J Lefeber
- Department of Neurology, Donders institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- On behalf of United for Metabolic Diseases, Amsterdam, The Netherlands
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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19
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Lee NC. The incorporation of next-generation sequencing into pediatric care. Pediatr Neonatol 2023; 64 Suppl 1:S30-S34. [PMID: 36456424 DOI: 10.1016/j.pedneo.2022.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic condition is one of the major etiologies causing morbidity and mortality in infants and children. More and more etiologies can be solved using next-generation sequencing (NGS) as it develops. Currently, whole-exome sequencing (WES) and whole-genome sequencing (WGS) have been highly integrated into clinical practice. The average diagnostic yield of WES/WGS in pediatric patients with genetic condition was around 40% (range: 21%-80%), with acceptable turnaround time and cost. The higher diagnostic yield categories are deafness, ophthalmic, neurological, skeletal conditions, and inborn error of metabolism. Positive results provide benefit with those for actionable diseases, next pregnancy planning, and family members. For those in critical condition, with the emergence of sequencing technology and bioinformatics analysis tools, provisional diagnosis can be made as short as 13.5 h using ultrarapid WGS. We believe this powerful tool has changed pediatric daily practice.
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Affiliation(s)
- Ni-Chung Lee
- Department of Pediatrics and Medical Genetics, National Taiwan University Hospital, 8 Chung-Shan South Road, Taipei 10041, Taiwan.
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20
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Salman DO, Mahfouz R, Bitar ER, Samaha J, Karam PE. Challenges of genetic diagnosis of inborn errors of metabolism in a major tertiary care center in Lebanon. Front Genet 2022; 13:1029947. [PMID: 36468010 PMCID: PMC9715967 DOI: 10.3389/fgene.2022.1029947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/08/2022] [Indexed: 01/25/2023] Open
Abstract
Background: Inborn errors of metabolism are rare genetic disorders; however, these are prevalent in countries with high consanguinity rates, like Lebanon. Patients are suspected, based on a combination of clinical and biochemical features; however, the final confirmation relies on genetic testing. Using next generation sequencing, as a new genetic investigational tool, carries several challenges for the physician, the geneticist, and the families. Methods: In this retrospective study, we analyzed the clinical, biochemical, and genetic profile of inborn errors of metabolism suspected patients, seen at a major tertiary care center in Lebanon, between 2015 and 2018. Genetic testing was performed using next generation sequencing. Genotype-phenotype correlation and diagnostic yield of each testing modality were studied. Results: Out of 211 patients genetically tested, 126 were suspected to have an inborn error of metabolism. The diagnostic yield of next generation sequencing reached 64.3%. Single gene testing was requested in 53%, whole exome sequencing in 36% and gene panels in 10%. Aminoacid disorders were mostly diagnosed followed by storage disorders, organic acidemias and mitochondrial diseases. Targeted testing was performed in 77% of aminoacid and organic acid disorders and half of suspected storage disorders. Single gene sequencing was positive in 75%, whereas whole exome sequencing diagnostic yield for complex cases, like mitochondrial disorders, reached 49%. Good clinical and biochemical correlation allowed the interpretation of variants of unknown significance and negative mutations as well as therapeutic management of most patients. Conclusion: Tailoring the choice of test modality, by next generation sequencing, to the category of suspected inborn errors of metabolism may lead to rapid diagnosis, shortcutting the cost of repeated testing. Whole exome sequencing as a first-tier investigation may be considered mainly for suspected mitochondrial diseases, whereas targeted sequencing can be offered upon suspicion of a specific enzyme deficiency. Timing and modality of gene test remain challenging, in view of the cost incurred by families.
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Affiliation(s)
- Doaa O. Salman
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Elio R. Bitar
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Jinane Samaha
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Beirut, Lebanon,Inherited Metabolic Diseases Program, American University of Beirut Medical Center, Beirut, Lebanon
| | - Pascale E. Karam
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Beirut, Lebanon,Inherited Metabolic Diseases Program, American University of Beirut Medical Center, Beirut, Lebanon,*Correspondence: Pascale E. Karam,
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21
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Oldoni E, Saunders G, Bietrix F, Garcia Bermejo ML, Niehues A, ’t Hoen PAC, Nordlund J, Hajduch M, Scherer A, Kivinen K, Pitkänen E, Mäkela TP, Gut I, Scollen S, Kozera Ł, Esteller M, Shi L, Ussi A, Andreu AL, van Gool AJ. Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report. Front Mol Biosci 2022; 9:974799. [PMID: 36310597 PMCID: PMC9608444 DOI: 10.3389/fmolb.2022.974799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Personalised medicine (PM) presents a great opportunity to improve the future of individualised healthcare. Recent advances in -omics technologies have led to unprecedented efforts characterising the biology and molecular mechanisms that underlie the development and progression of a wide array of complex human diseases, supporting further development of PM. This article reflects the outcome of the 2021 EATRIS-Plus Multi-omics Stakeholder Group workshop organised to 1) outline a global overview of common promises and challenges that key European stakeholders are facing in the field of multi-omics research, 2) assess the potential of new technologies, such as artificial intelligence (AI), and 3) establish an initial dialogue between key initiatives in this space. Our focus is on the alignment of agendas of European initiatives in multi-omics research and the centrality of patients in designing solutions that have the potential to advance PM in long-term healthcare strategies.
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Affiliation(s)
- Emanuela Oldoni
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
- *Correspondence: Gary Saunders, ; Emanuela Oldoni,
| | - Gary Saunders
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
- *Correspondence: Gary Saunders, ; Emanuela Oldoni,
| | - Florence Bietrix
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Maria Laura Garcia Bermejo
- Biomarkers and Therapeutic Targets Group, Ramon and Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Anna Niehues
- Translational Metabolomic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Peter A. C. ’t Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czechia
| | - Andreas Scherer
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Katja Kivinen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Esa Pitkänen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Tomi Pekka Mäkela
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Łukasz Kozera
- Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), Graz, Austria
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Anton Ussi
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Antonio L. Andreu
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Alain J. van Gool
- Translational Metabolomic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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22
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Zhang H, Wang Y, Qiu Y, Zhang C. Expanded newborn screening for inherited metabolic disorders by tandem mass spectrometry in a northern Chinese population. Front Genet 2022; 13:801447. [PMID: 36246604 PMCID: PMC9562093 DOI: 10.3389/fgene.2022.801447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Tandem mass spectrometry (MS/MS) has been developed as one of the most important diagnostic platforms for the early detection and screening of inherited metabolic disorders (IMDs). To determine the disease spectrum and genetic characteristics of IMDs in Suqian city of Jiangsu province in the northern Chinese population, dried blood spots from 2,04,604 newborns, were assessed for IMDs by MS/MS from January 2016 to November 2020. Suspected positive patients were diagnosed through next-generation sequencing (NGS) and validated by Sanger sequencing. One hundred patients with IMDs were diagnosed, resulting in an overall incidence of 1/2,046, of which 56 (1/3,653), 22 (1/9,300), and 22 (1/9,300) were confirmed amino acids disorders (AAs), organic acids disorders (OAs), fatty acid oxidation disorders (FAODs) positive cases, respectively. The highest incidence of IMDs is phenylalanine hydroxylase deficiency (PAHD) (45 cases), with a total incidence of 1:4,546. Hot spot mutations in phenylalanine hydroxylase (PAH)-related genes are c.158G > A (24.44%), c.728G > A (16.67%), c.611A > G (7.78%), and c.331C>T (7.78%). The related hot spot mutation of the MMACHC gene is c.609G > A (45.45%). Short-chain acyl-CoA dehydrogenase deficiency (SCAD)-related ACADS gene hotspot mutations are c.164C > T (33.33%) and c.1031A > G (33.33%). Our work indicated that the overall incidence of IMDs is high, and the mutations in PAH, ACADS, and MMACHC genes are the leading causes of IMDs in Suqian city. The incidence of AAs in Suqian city is higher than in other Chinese areas. The disease spectrum and genetic backgrounds were elucidated, contributing to the treatment and prenatal genetic counseling of these disorders in this region.
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Affiliation(s)
- Hong Zhang
- Suqian Maternal and Child Health Care Hospital, Suqian, China
| | - Yanyun Wang
- Nanjing Maternal and Child Health Care Hospital, Nanjing, China
| | - Yali Qiu
- Suqian Maternal and Child Health Care Hospital, Suqian, China
| | - Chao Zhang
- Suqian Maternal and Child Health Care Hospital, Suqian, China
- *Correspondence: Chao Zhang,
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23
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Tebani A, Bekri S. [The promise of omics in the precision medicine era]. Rev Med Interne 2022; 43:649-660. [PMID: 36041909 DOI: 10.1016/j.revmed.2022.07.009] [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: 06/10/2022] [Accepted: 07/12/2022] [Indexed: 10/15/2022]
Abstract
The rise of omics technologies that simultaneously measure thousands of molecules in a complex biological sample represents the core of systems biology. These technologies have profoundly impacted biomarkers and therapeutic targets discovery in the precision medicine era. Systems biology aims to perform a systematic probing of complex interactions in biological systems. Powered by high-throughput omics technologies and high-performance computing, systems biology provides relevant, resolving, and multi-scale overviews from cells to populations. Precision medicine takes advantage of these conceptual and technological developments and is based on two main pillars: the generation of multimodal data and their subsequent modeling. High-throughput omics technologies enable the comprehensive and holistic extraction of biological information, while computational capabilities enable multidimensional modeling and, as a result, offer an intuitive and intelligible visualization. Despite their promise, translating these technologies into clinically actionable tools has been slow. In this contribution, we present the most recent multi-omics data generation and analysis strategies and their clinical deployment in the post-genomic era. Furthermore, medical application challenges of omics-based biomarkers are discussed.
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Affiliation(s)
- A Tebani
- UNIROUEN, Inserm U1245, Department of Metabolic Biochemistry, Normandie University, CHU Rouen, 76000 Rouen, France.
| | - S Bekri
- UNIROUEN, Inserm U1245, Department of Metabolic Biochemistry, Normandie University, CHU Rouen, 76000 Rouen, France
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24
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Suzuki H, Nozaki M, Yoshihashi H, Imagawa K, Kajikawa D, Yamada M, Yamaguchi Y, Morisada N, Eguchi M, Ohashi S, Ninomiya S, Seto T, Tokutomi T, Hida M, Toyoshima K, Kondo M, Inui A, Kurosawa K, Kosaki R, Ito Y, Okamoto N, Kosaki K, Takenouchi T. Genome Analysis in Sick Neonates and Infants: High-yield Phenotypes and Contribution of Small Copy Number Variations. J Pediatr 2022; 244:38-48.e1. [PMID: 35131284 DOI: 10.1016/j.jpeds.2022.01.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/25/2021] [Accepted: 01/18/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To delineate the diagnostic efficacy of medical exome, whole exome, and whole genome sequencing according to primary symptoms, the contribution of small copy number variations, and the impact of molecular diagnosis on clinical management. STUDY DESIGN This was a prospective study of 17 tertiary care centers in Japan, conducted between April 2019 and March 2021. Critically ill neonates and infants less than 6 months of age were recruited in neonatal intensive care units and in outpatient clinics. The patients underwent medical exome, whole exome, or whole genome sequencing as the first tier of testing. Patients with negative results after medical exome or whole exome sequencing subsequently underwent whole genome sequencing. The impact of molecular diagnosis on clinical management was evaluated through contacting primary care physicians. RESULTS Of the 85 patients, 41 (48%) had positive results. Based on the primary symptoms, patients with metabolic phenotypes had the highest diagnostic yield (67%, 4/6 patients), followed by renal (60%, 3/5 patients), and neurologic phenotypes (58%, 14/24 patients). Among them, 4 patients had pathogenic small copy number variations identified using whole genome sequencing. In the 41 patients with a molecular diagnosis, 20 (49%) had changes in clinical management. CONCLUSIONS Genome analysis for critically ill neonates and infants had a high diagnostic yield for metabolic, renal, and neurologic phenotypes. Small copy number variations detected using whole genome sequencing contributed to the overall molecular diagnosis in 5% of all the patients. The resulting molecular diagnoses had a significant impact on clinical management.
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Affiliation(s)
- Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Masatoshi Nozaki
- Department of Neonatal Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Hiroshi Yoshihashi
- Department of Genetics, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Kazuo Imagawa
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Daigo Kajikawa
- Department of Neonatology, Ibaraki Children's Hospital, Ibaraki, Japan
| | - Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Yu Yamaguchi
- Department of Clinical Genetics, Gunma Children's Medical Center, Gunma, Japan
| | - Naoya Morisada
- Department of Clinical Genetics, Hyogo Prefectural Kobe Children's Hospital, Hyogo, Japan
| | - Mayuko Eguchi
- Department of Neonatology, Tokyo Metropolitan Bokutoh Hospital, Tokyo, Japan
| | - Shoko Ohashi
- Department of Neonatology, Tokyo Metropolitan Ohtsuka Hospital, Tokyo, Japan
| | - Shinsuke Ninomiya
- Department of Clinical Genetics, Kurashiki Central Hospital, Okayama, Japan
| | - Toshiyuki Seto
- Department of Medical Genetics, Osaka City University Hospital, Osaka, Japan
| | - Tomoharu Tokutomi
- Department of Clinical Genetics, Iwate Medical University, Iwate, Japan
| | - Mariko Hida
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Katsuaki Toyoshima
- Department of Neonatology, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Masatoshi Kondo
- Department of Neonatology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Ayano Inui
- Department of Pediatric Hepatology and Gastroenterology, Saiseikai Yokohama-shi Tobu Hospital, Kanagawa, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Yushi Ito
- Division of Neonatology, National Center for Child Health and Development, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.
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25
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Elliott AM, Adam S, du Souich C, Lehman A, Nelson TN, van Karnebeek C, Alderman E, Armstrong L, Aubertin G, Blood K, Boelman C, Boerkoel C, Bretherick K, Brown L, Chijiwa C, Clarke L, Couse M, Creighton S, Watts-Dickens A, Gibson WT, Gill H, Tarailo-Graovac M, Hamilton S, Heran H, Horvath G, Huang L, Hulait GK, Koehn D, Lee HK, Lewis S, Lopez E, Louie K, Niederhoffer K, Matthews A, Meagher K, Peng JJ, Patel MS, Race S, Richmond P, Rupps R, Salvarinova R, Seath K, Selby K, Steinraths M, Stockler S, Tang K, Tyson C, van Allen M, Wasserman W, Mwenifumbo J, Friedman JM. Genome-wide Sequencing and the Clinical Diagnosis of Genetic Disease: The CAUSES Study. HGG ADVANCES 2022; 3:100108. [PMID: 35599849 PMCID: PMC9117924 DOI: 10.1016/j.xhgg.2022.100108] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Genome-wide sequencing (GWS) is a standard of care for diagnosis of suspected genetic disorders, but the proportion of patients found to have pathogenic or likely pathogenic variants ranges from less than 30% to more than 60% in reported studies. It has been suggested that the diagnostic rate can be improved by interpreting genomic variants in the context of each affected individual’s full clinical picture and by regular follow-up and reinterpretation of GWS laboratory results. Trio exome sequencing was performed in 415 families and trio genome sequencing in 85 families in the CAUSES study. The variants observed were interpreted by a multidisciplinary team including laboratory geneticists, bioinformaticians, clinical geneticists, genetic counselors, pediatric subspecialists, and the referring physician, and independently by a clinical laboratory using standard American College of Medical Genetics and Genomics (ACMG) criteria. Individuals were followed for an average of 5.1 years after testing, with clinical reassessment and reinterpretation of the GWS results as necessary. The multidisciplinary team established a diagnosis of genetic disease in 43.0% of the families at the time of initial GWS interpretation, and longitudinal follow-up and reinterpretation of GWS results produced new diagnoses in 17.2% of families whose initial GWS interpretation was uninformative or uncertain. Reinterpretation also resulted in rescinding a diagnosis in four families (1.9%). Of the families studied, 33.6% had ACMG pathogenic or likely pathogenic variants related to the clinical indication. Close collaboration among clinical geneticists, genetic counselors, laboratory geneticists, bioinformaticians, and individuals’ primary physicians, with ongoing follow-up, reanalysis, and reinterpretation over time, can improve the clinical value of GWS.
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Affiliation(s)
- Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Women's Health Research Institute, Vancouver, BC, Canada
| | - Shelin Adam
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Christèle du Souich
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Tanya N Nelson
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
- Department of Pediatrics, Emma Children's Hospital, Amsterdam, University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Emily Alderman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Gudrun Aubertin
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Katherine Blood
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Cyrus Boelman
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Cornelius Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Karla Bretherick
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Lindsay Brown
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Chieko Chijiwa
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Lorne Clarke
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Madeline Couse
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Susan Creighton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Abby Watts-Dickens
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Harinder Gill
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Sara Hamilton
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Harindar Heran
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Gabriella Horvath
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Lijia Huang
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Gurdip K Hulait
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - David Koehn
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Hyun Kyung Lee
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Elena Lopez
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kristal Louie
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Karen Niederhoffer
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Allison Matthews
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Kirsten Meagher
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Junran J Peng
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Millan S Patel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Simone Race
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Phillip Richmond
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Rosemarie Rupps
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ramona Salvarinova
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Kimberly Seath
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kathryn Selby
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Michelle Steinraths
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sylvia Stockler
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Kaoru Tang
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Christine Tyson
- Division of Genome Diagnostics, Department of Pathology and Laboratory Medicine, BC Children's and Women's Hospitals, Vancouver, BC, Canada
| | - Margot van Allen
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Wyeth Wasserman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Pediatrics, Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Jill Mwenifumbo
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
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26
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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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27
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P. Fishler K, Euteneuer JC, Brunelli L. Ethical Considerations for Equitable Access to Genomic Sequencing for Critically Ill Neonates in the United States. Int J Neonatal Screen 2022; 8:ijns8010022. [PMID: 35323201 PMCID: PMC8950005 DOI: 10.3390/ijns8010022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Rare diseases impact all socio-economic, geographic, and racial groups indiscriminately. Newborn screening (NBS) is an exemplary international public health initiative that identifies infants with rare conditions early in life to reduce morbidity and mortality. NBS theoretically promotes equity through universal access, regardless of financial ability. There is however heterogeneity in access to newborn screening and conditions that are screened throughout the world. In the United States and some other developed countries, NBS is provided to all babies, subsidized by the local or federal government. Although NBS is an equitable test, infants admitted to neonatal intensive care units (NICUs) may not receive similar benefits to healthier infants. Newborns in the NICU may receive delayed and/or multiple newborn screens due to known limitations in interpreting the results with prematurity, total parenteral nutrition, blood transfusions, infection, and life support. Thus, genomic technologies might be needed in addition to NBS for equitable care of this vulnerable population. Whole exome (WES) and genome sequencing (WGS) have been recently studied in critically ill newborns across the world and have shown promising results in shortening diagnostic odysseys and providing clinical utility. However, in certain circumstances several barriers might limit access to these tests. Here, we discuss some of the existing barriers to genomic sequencing in NICUs in the United States, explore the ethical implications related to low access, consider ways to increase access to genomic testing, and offer some suggestions for future research in these areas.
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Affiliation(s)
- Kristen P. Fishler
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence:
| | | | - Luca Brunelli
- Division of Neonatology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA;
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28
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Herman I, Jolly A, Du H, Dawood M, Abdel-Salam GMH, Marafi D, Mitani T, Calame DG, Coban-Akdemir Z, Fatih JM, Hegazy I, Jhangiani SN, Gibbs RA, Pehlivan D, Posey JE, Lupski JR. Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. Am J Med Genet A 2022; 188:735-750. [PMID: 34816580 PMCID: PMC8837671 DOI: 10.1002/ajmg.a.62565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 12/19/2022]
Abstract
Genomic sequencing and clinical genomics have demonstrated that substantial subsets of atypical and/or severe disease presentations result from multilocus pathogenic variation (MPV) causing blended phenotypes. In an infant with a severe neurodevelopmental disorder, four distinct molecular diagnoses were found by exome sequencing (ES). The blended phenotype that includes brain malformation, dysmorphism, and hypotonia was dissected using the Human Phenotype Ontology (HPO). ES revealed variants in CAPN3 (c.259C > G:p.L87V), MUSK (c.1781C > T:p.A594V), NAV2 (c.1996G > A:p.G666R), and ZC4H2 (c.595A > C:p.N199H). CAPN3, MUSK, and ZC4H2 are established disease genes linked to limb-girdle muscular dystrophy (OMIM# 253600), congenital myasthenia (OMIM# 616325), and Wieacker-Wolff syndrome (WWS; OMIM# 314580), respectively. NAV2 is a retinoic-acid responsive novel disease gene candidate with biological roles in neurite outgrowth and cerebellar dysgenesis in mouse models. Using semantic similarity, we show that no gene identified by ES individually explains the proband phenotype, but rather the totality of the clinically observed disease is explained by the combination of disease-contributing effects of the identified genes. These data reveal that multilocus pathogenic variation can result in a blended phenotype with each gene affecting a different part of the nervous system and nervous system-muscle connection. We provide evidence from this n = 1 study that in patients with MPV and complex blended phenotypes resulting from multiple molecular diagnoses, quantitative HPO analysis can allow for dissection of phenotypic contribution of both established disease genes and novel disease gene candidates not yet proven to cause human disease.
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Affiliation(s)
- Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ghada M. H. Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Daniel G. Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ibrahim Hegazy
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030
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29
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Molecular Diagnostic Outcomes from 700 Cases: What Can We Learn from a Retrospective Analysis of Clinical Exome Sequencing? J Mol Diagn 2022; 24:274-286. [PMID: 35065284 PMCID: PMC9904168 DOI: 10.1016/j.jmoldx.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 11/29/2021] [Accepted: 12/10/2021] [Indexed: 01/19/2023] Open
Abstract
Clinical exome sequencing (CES) aids in the diagnosis of rare genetic disorders. Herein, we report the molecular diagnostic yield and spectrum of genetic alterations contributing to disease in 700 pediatric cases analyzed at the Children's Hospital of Philadelphia. The overall diagnostic yield was 23%, with three cases having more than one molecular diagnosis and 2.6% having secondary/additional findings. A candidate gene finding was reported in another 8.4% of cases. The clinical indications with the highest diagnostic yield were neurodevelopmental disorders (including seizures), whereas immune- and oncology-related indications were negatively associated with molecular diagnosis. The rapid expansion of knowledge regarding the genome's role in human disease necessitates reanalysis of CES samples. To capture these new discoveries, a subset of cases (n = 240) underwent reanalysis, with an increase in diagnostic yield. We describe our experience reporting CES results in a pediatric setting, including reporting of secondary findings, reporting newly discovered genetic conditions, and revisiting negative test results. Finally, we highlight the challenges associated with implementing critical updates to the CES workflow. Although these updates are necessary, they demand an investment of time and resources from the laboratory. In summary, these data demonstrate the clinical utility of exome sequencing and reanalysis, while highlighting the critical considerations for continuous improvement of a CES test in a clinical laboratory.
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30
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
AbstractRare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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31
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Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. Genes (Basel) 2022; 13:genes13020333. [PMID: 35205378 PMCID: PMC8871714 DOI: 10.3390/genes13020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.
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32
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Personalized medicine for rare neurogenetic disorders: can we make it happen? Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006200. [PMID: 35332073 PMCID: PMC8958924 DOI: 10.1101/mcs.a006200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rare neurogenetic disorders are collectively common, affecting 3% of the population, and often manifest with complex multiorgan comorbidity. With advances in genetic, -omics, and computational analysis, more children can be diagnosed and at an earlier age. Innovations in translational research facilitate the identification of treatment targets and development of disease-modifying drugs such as gene therapy, nutraceuticals, and drug repurposing. This increasingly allows targeted therapy to prevent the often devastating manifestations of rare neurogenetic disorders. In this perspective, successes in diagnosis, prevention, and treatment are discussed with a focus on inherited disorders of metabolism. Barriers for the identification, development, and implementation of rare disease-specific therapies are discussed. New methodologies, care networks, and collaborative frameworks are proposed to optimize the potential of personalized genomic medicine to decrease morbidity and improve lives of these vulnerable patients.
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33
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Le Guennec L, Marois C, Demeret S, Wijdicks EFM, Weiss N. Toxic-metabolic encephalopathy in adults: Critical discussion and pragmatical diagnostic approach. Rev Neurol (Paris) 2022; 178:93-104. [PMID: 34996631 DOI: 10.1016/j.neurol.2021.11.007] [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: 08/02/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
Toxic-metabolic encephalopathy (TME) results from an acute cerebral dysfunction due to different metabolic disturbances including medications or illicit-drugs. It can lead to altered consciousness, going from delirium to coma, which may require intensive care and invasive mechanical ventilation. Even if it is a life-threatening condition, TME might have an excellent prognosis if its etiology is rapidly identified and treated adequately. This review summarizes the main etiologies, their differential diagnosis, and diagnostic strategy and management of TME with a critical discussion on the definition of TME.
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Affiliation(s)
- L Le Guennec
- Sorbonne Université, AP-HP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière, département de neurologie, unité de Médecine Intensive Réanimation à orientation neurologique, Paris, France; Groupe de Recherche Clinique en REanimation et Soins intensifs du Patient en Insuffisance Respiratoire aiguE (GRC-RESPIRE) Sorbonne Université, Sorbonne, France
| | - C Marois
- Sorbonne Université, AP-HP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière, département de neurologie, unité de Médecine Intensive Réanimation à orientation neurologique, Paris, France
| | - S Demeret
- Sorbonne Université, AP-HP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière, département de neurologie, unité de Médecine Intensive Réanimation à orientation neurologique, Paris, France
| | - E F M Wijdicks
- Mayo Clinic, Department of Neurology, 200 First Street SW, Rochester, MN 55905, USA
| | - N Weiss
- Groupe de Recherche Clinique en REanimation et Soins intensifs du Patient en Insuffisance Respiratoire aiguE (GRC-RESPIRE) Sorbonne Université, Sorbonne, France; Sorbonne Université, AP-HP, Sorbonne Université, Hôpital de la Pitié-Salpêtrière, département de neurologie, unité de Médecine Intensive Réanimation à orientation neurologique, Paris, France; Brain Liver Pitié-Salpêtrière (BLIPS) Study Group, INSERM UMR_S 938, Centre de recherche Saint-Antoine, Maladies métaboliques, biliaires et fibro-inflammatoire du foie, Institute of Cardiometabolism and Nutrition (ICAN), Paris, France.
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34
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Tackling healthcare access barriers for individuals with autism from diagnosis to adulthood. Pediatr Res 2022; 91:1028-1035. [PMID: 33767375 PMCID: PMC7993081 DOI: 10.1038/s41390-021-01465-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/21/2020] [Accepted: 02/23/2021] [Indexed: 02/04/2023]
Abstract
Most individuals with autism spectrum disorder (ASD)-a complex, life-long developmental disorder-do not have access to the care required to address their diverse health needs. Here, we review: (1) common barriers to healthcare access (shortage/cost of services; physician awareness; stigma); (2) barriers encountered primarily during childhood (limited screening/diagnosis; unclear referral pathways), transition to adulthood (insufficient healthcare transition services; suboptimal physician awareness of healthcare needs) and adulthood (shortage of services/limited insurance; communication difficulties with physicians; limited awareness of healthcare needs of aging adults); and (3) advances in research/program development for better healthcare access. A robust understanding of barriers to accessing healthcare across the lifespan of autistic individuals is critical to ensuring the best use of healthcare resources to improve social, physical, and mental health outcomes. Stakeholders must strengthen healthcare service provision by coming together to: better understand healthcare needs of underserved populations; strengthen medical training on care of autistic individuals; increase public awareness of ASD; promote research into/uptake of tools for ASD screening, diagnosis, and treatment; understand specific healthcare needs of autistic individuals in lower resource countries; and conduct longitudinal studies to understand the lifetime health, social, and economic impacts of ASD and enable the evaluation of novel approaches to increasing healthcare access. IMPACT: Despite the growing body of evidence, our understanding of barriers to healthcare encountered by individuals with ASD remains limited, particularly beyond childhood and in lower resource countries. We describe current and emerging barriers to healthcare access encountered by individuals with ASD across the lifespan. We recommend that stakeholders develop evidence-informed policies, programs, and technologies that address barriers to healthcare access for individuals with ASD and consider broad, equitable implementation to maximize impact.
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35
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Abstract
PURPOSE OF REVIEW A single genetic diagnosis, especially from the analysis of a limited number of genes, may not signal the end of a diagnostic odyssey. When a patient with a genetic syndrome presents with symptoms that are not usually associated with their disease phenotype, additional genetic testing is warranted. RECENT FINDINGS Although multiple co-existing genetic diagnoses may sound unlikely, many recent studies and case reports have demonstrated that this scenario is more common than expected. Studies involving whole exome and genome sequencing have identified a frequency of multiple genetic diagnoses and have identified clinical findings that make a second diagnosis more likely, which we have seen reflected in recent cases from our own clinic and consult service. These include multisystem disease, consanguinity, well described aneuploidies with rare or new symptoms, and complex structural chromosomal anomalies which may include multiple chromosomes and breakpoints that disrupt gene function. SUMMARY Identifying a second diagnosis can have vast implications for patient management and counseling. Patients can be followed with appropriate medical screening and early interventions to support optimal child development. Furthermore, the patient's family can be impacted by ending the diagnostic odyssey, providing testing for other at-risk family members, and offering prenatal options.
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Affiliation(s)
- Kristin B Linscott
- Department of Genetics
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jennifer A Cassady
- Department of Genetics
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nathaniel H Robin
- Department of Genetics
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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36
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Buphamalai P, Kokotovic T, Nagy V, Menche J. Network analysis reveals rare disease signatures across multiple levels of biological organization. Nat Commun 2021; 12:6306. [PMID: 34753928 PMCID: PMC8578255 DOI: 10.1038/s41467-021-26674-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/19/2021] [Indexed: 01/26/2023] Open
Abstract
Rare genetic diseases are typically caused by a single gene defect. Despite this clear causal relationship between genotype and phenotype, identifying the pathobiological mechanisms at various levels of biological organization remains a practical and conceptual challenge. Here, we introduce a network approach for evaluating the impact of rare gene defects across biological scales. We construct a multiplex network consisting of over 20 million gene relationships that are organized into 46 network layers spanning six major biological scales between genotype and phenotype. A comprehensive analysis of 3,771 rare diseases reveals distinct phenotypic modules within individual layers. These modules can be exploited to mechanistically dissect the impact of gene defects and accurately predict rare disease gene candidates. Our results show that the disease module formalism can be applied to rare diseases and generalized beyond physical interaction networks. These findings open up new venues to apply network-based tools for cross-scale data integration.
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Affiliation(s)
- Pisanu Buphamalai
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna BioCenter 5, 1030, Vienna, Austria
| | - Tomislav Kokotovic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Department of Neurology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Vanja Nagy
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Department of Neurology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria.
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna BioCenter 5, 1030, Vienna, Austria.
- Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, 1090, Vienna, Austria.
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37
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Yang K, Shi Y, Du X, Wang J, Zhang Y, Shan S, Yuan Y, Wang R, Zhou C, Liu Y, Cai Z, Wang Y, Fan L, Xu H, Yu J, Cheng J, Li F, Qiu Z. SENP1 in the retrosplenial agranular cortex regulates core autistic-like symptoms in mice. Cell Rep 2021; 37:109939. [PMID: 34731627 DOI: 10.1016/j.celrep.2021.109939] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 08/26/2021] [Accepted: 10/12/2021] [Indexed: 12/23/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder, causing defects of social interaction and repetitive behaviors. Here, we identify a de novo heterozygous gene-truncating mutation of the Sentrin-specific peptidase1 (SENP1) gene in people with ASD without neurodevelopmental delay. We find that Senp1+/- mice exhibit core autistic-like symptoms such as social deficits and repetitive behaviors but normal learning and memory ability. Moreover, we find that inhibitory and excitatory synaptic functions are severely affected in the retrosplenial agranular (RSA) cortex of Senp1+/- mice. Lack of Senp1 leads to increased SUMOylation and degradation of fragile X mental retardation protein (FMRP), also implicated in syndromic ASD. Importantly, re-introducing SENP1 or FMRP specifically in RSA fully rescues the defects of synaptic function and autistic-like symptoms of Senp1+/- mice. Together, these results demonstrate that disruption of the SENP1-FMRP regulatory axis in the RSA causes autistic symptoms, providing a candidate region for ASD pathophysiology.
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Affiliation(s)
- Kan Yang
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yuhan Shi
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiujuan Du
- Department of Developmental and Behavioural Pediatric & Child Primary Care, Brain and Behavioural Research Unit of Shanghai Institute for Pediatric Research and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200049, China
| | - Jincheng Wang
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuefang Zhang
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shifang Shan
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yiting Yuan
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ruoqing Wang
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Zhiyuan College, School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chenhuan Zhou
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuting Liu
- Zhiyuan College, School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zilin Cai
- Zhiyuan College, School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanzhi Wang
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liu Fan
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Huatai Xu
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Juehua Yu
- Department of Developmental and Behavioural Pediatric & Child Primary Care, Brain and Behavioural Research Unit of Shanghai Institute for Pediatric Research and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200049, China; NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Jinke Cheng
- Department of Molecular Cellular Biology, College of Basic Medical Sciences, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Fei Li
- Department of Developmental and Behavioural Pediatric & Child Primary Care, Brain and Behavioural Research Unit of Shanghai Institute for Pediatric Research and MOE-Shanghai Key Laboratory for Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200049, China.
| | - Zilong Qiu
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
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38
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Delanne J, Bruel AL, Huet F, Moutton S, Nambot S, Grisval M, Houcinat N, Kuentz P, Sorlin A, Callier P, Jean-Marcais N, Mosca-Boidron AL, Mau-Them FT, Denommé-Pichon AS, Vitobello A, Lehalle D, El Chehadeh S, Francannet C, Lebrun M, Lambert L, Jacquemont ML, Gerard-Blanluet M, Alessandri JL, Willems M, Thevenon J, Chouchane M, Darmency V, Fatus-Fauconnier C, Gay S, Bournez M, Masurel A, Leguy V, Duffourd Y, Philippe C, Feillet F, Faivre L, Thauvin-Robinet C. The diagnostic rate of inherited metabolic disorders by exome sequencing in a cohort of 547 individuals with developmental disorders. Mol Genet Metab Rep 2021; 29:100812. [PMID: 34712575 PMCID: PMC8528787 DOI: 10.1016/j.ymgmr.2021.100812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/07/2021] [Accepted: 10/09/2021] [Indexed: 11/24/2022] Open
Abstract
Considering that some Inherited Metabolic Disorders (IMDs) can be diagnosed in patients with no distinctive clinical features of IMDs, we aimed to evaluate the power of exome sequencing (ES) to diagnose IMDs within a cohort of 547 patients with unspecific developmental disorders (DD). IMDs were diagnosed in 12% of individuals with causative diagnosis (177/547). There are clear benefits of using ES in DD to diagnose IMD, particularly in cases where biochemical studies are unavailable. Synopsis Exome sequencing and diagnostic rate of Inherited Metabolic Disorders in individuals with developmental disorders.
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Affiliation(s)
- Julian Delanne
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Ange-Line Bruel
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Frédéric Huet
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | - Sébastien Moutton
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Sophie Nambot
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Margot Grisval
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | - Nada Houcinat
- CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Paul Kuentz
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France.,Biologie moléculaire, CHU Besançon, Besançon, France
| | - Arthur Sorlin
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Patrick Callier
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Laboratoire de cytogénétique et génétique moléculaire, CHU Dijon Bourgogne, France
| | - Nolwenn Jean-Marcais
- CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | | | - Frédéric Tran Mau-Them
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Anne-Sophie Denommé-Pichon
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Antonio Vitobello
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Daphné Lehalle
- CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Salima El Chehadeh
- CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Christine Francannet
- Service de Génétique Médicale, Centre de Référence Déficiences Intellectuelles de causes rares, CHU Clermont Ferrand, France
| | - Marine Lebrun
- Laboratoire de génétique, CHU de Saint-Etienne, Saint-Etienne, France
| | | | - Marie-Line Jacquemont
- Unité de Génétique Médicale, Pole Femme-Mère-Enfant, Groupe Hospitalier Sud Réunion, CHU de La Réunion, La Réunion, France
| | | | - Jean-Luc Alessandri
- Service de Réanimation Néonatale, Pole Femme-Mère-Enfant, CH Felix Guyon, CHU de La Réunion, Saint-Denis, La Réunion, France
| | - Marjolaine Willems
- Department of Medical Genetics, Reference Center for Rare Diseases, Developmental Disorders and Multiple Congenital Anomalies, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Julien Thevenon
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Mondher Chouchane
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | - Véronique Darmency
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | | | - Sébastien Gay
- Service de Pédiatrie, CH William Morey, Chalon-Sur-Saône, France
| | - Marie Bournez
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | - Alice Masurel
- CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
| | - Vanessa Leguy
- Centre de Compétence Maladies Héréditaires du Métabolisme, CHU Dijon Bourgogne, France
| | - Yannis Duffourd
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Christophe Philippe
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - François Feillet
- Department of Medical Genetics, Reference Center for Rare Diseases, Developmental Disorders and Multiple Congenital Anomalies, Arnaud de Villeneuve Hospital, Montpellier, France
| | - Laurence Faivre
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,CHU Dijon, Centre de référence maladies rares Anomalies du Développement et Syndromes Malformatifs, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France
| | - Christel Thauvin-Robinet
- INSERM - University of Bourgogne Franche-Comté, UMR 1231 GAD Team, Genetics of Developmental Disorders, FHU TRANSLAD, CHU Dijon Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique dans les maladies rares, Laboratoire de Génétique chromosomique moléculaire, CHU Dijon Bourgogne, France.,Centre de référence maladies rares Déficiences Intellectuelles de causes rares, Centre de Génétique, FHU TRANSLAD, CHU Dijon Bourgogne, France
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39
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Tran Mau-Them F, Duffourd Y, Vitobello A, Bruel AL, Denommé-Pichon AS, Nambot S, Delanne J, Moutton S, Sorlin A, Couturier V, Bourgeois V, Chevarin M, Poe C, Mosca-Boidron AL, Callier P, Safraou H, Faivre L, Philippe C, Thauvin-Robinet C. Interest of exome sequencing trio-like strategy based on pooled parental DNA for diagnosis and translational research in rare diseases. Mol Genet Genomic Med 2021; 9:e1836. [PMID: 34716697 PMCID: PMC8683640 DOI: 10.1002/mgg3.1836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/22/2021] [Accepted: 10/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Exome sequencing (ES) has become the most powerful and cost‐effective molecular tool for deciphering rare diseases with a diagnostic yield approaching 30%–40% in solo‐ES and 50% in trio‐ES. We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio‐ES. Methods We pooled six (Agilent‐CRE‐v2–100X) or five parental DNA (TWIST‐HCE–70X) aiming to detect allelic balance around 8–10% for heterozygous status. The strategies were applied as second‐tier (74 individuals after negative solo‐ES) and first‐tier approaches (324 individuals without previous ES). Results The allelic balance of parental‐pool variants was around 8.97%. Sanger sequencing uncovered false positives in 1.5% of sporadic variants. In the second‐tier approach, we evaluated than two thirds of the Sanger validations performed after solo‐ES (41/59–69%) would have been saved if the parental‐pool segregations had been available from the start. The parental‐pool strategy identified a causative diagnosis in 18/74 individuals (24%) in the second‐tier and in 116/324 individuals (36%) in the first‐tier approaches, including 19 genes newly associated with human disorders. Conclusions Parental‐pooling is an efficient alternative to trio‐ES. It provides rapid segregation and extension to translational research while reducing the cost of parental and Sanger sequencing.
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Affiliation(s)
- Frederic Tran Mau-Them
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Yannis Duffourd
- Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,FHU-TRANSLAD, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Julian Delanne
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Sebastien Moutton
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Arthur Sorlin
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
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- FHU-TRANSLAD, Dijon, France
| | - Victor Couturier
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Valentin Bourgeois
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Martin Chevarin
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Charlotte Poe
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | | | - Patrick Callier
- Laboratoire de Génétique Chromosomique et Moléculaire, CHU de Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Laurence Faivre
- Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares «Déficiences Intellectuelles de Causes Rares», Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
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40
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Cook CB, Armstrong L, Boerkoel CF, Clarke LA, du Souich C, Demos MK, Gibson WT, Gill H, Lopez E, Patel MS, Selby K, Abu-Sharar Z, Elliott AM, Friedman JM. Somatic mosaicism detected by genome-wide sequencing in 500 parent-child trios with suspected genetic disease: clinical and genetic counseling implications. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006125. [PMID: 34697084 PMCID: PMC8751411 DOI: 10.1101/mcs.a006125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 01/28/2023] Open
Abstract
Identifying genetic mosaicism is important in establishing a diagnosis, assessing recurrence risk, and providing accurate genetic counseling. Next-generation sequencing has allowed for the identification of mosaicism at levels below those detectable by conventional Sanger sequencing or chromosomal microarray analysis. The CAUSES Clinic was a pediatric translational trio-based genome-wide (exome or genome) sequencing study of 500 families (531 children) with suspected genetic disease at BC Children's and Women's Hospitals. Here we present 12 cases of apparent mosaicism identified in the CAUSES cohort: nine cases of parental mosaicism for a disease-causing variant found in a child and three cases of mosaicism in the proband for a de novo variant. In six of these cases, there was no evidence of mosaicism on Sanger sequencing—the variant was not detected on Sanger sequencing in three cases, and it appeared to be heterozygous in three others. These cases are examples of six clinical manifestations of mosaicism: a proband with classical clinical features of mosaicism (e.g., segmental abnormalities of skin pigmentation or asymmetrical growth of bilateral body parts), a proband with unusually mild manifestations of a disease, a mosaic proband who is clinically indistinguishable from the constitutive phenotype, a mosaic parent with no clinical features of the disease, a mosaic parent with mild manifestations of the disease, and a family in which both parents are unaffected and two siblings have the same disease-causing constitutional mutation. Our data demonstrate the importance of considering the possibility of mosaicism whenever exome or genome sequencing is performed and that its detection via genome-wide sequencing can permit more accurate genetic counseling.
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Affiliation(s)
- Courtney B Cook
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Linlea Armstrong
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Cornelius F Boerkoel
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Lorne A Clarke
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Christèle du Souich
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Michelle K Demos
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | - William T Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Harinder Gill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Elena Lopez
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Millan S Patel
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Kathryn Selby
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | - Ziad Abu-Sharar
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | | | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4.,Women's Health Research Institute, Vancouver, British Columbia, Canada V6H 2N9
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
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41
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Mergnac JP, Wiedemann A, Chery C, Ravel JM, Namour F, Guéant JL, Feillet F, Oussalah A. Diagnostic yield of clinical exome sequencing as a first-tier genetic test for the diagnosis of genetic disorders in pediatric patients: results from a referral center study. Hum Genet 2021; 141:1269-1278. [PMID: 34495415 DOI: 10.1007/s00439-021-02358-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/28/2021] [Indexed: 12/29/2022]
Abstract
The emergence of next-generation sequencing enabled a cost-effective and straightforward diagnostic approach to genetic disorders using clinical exome sequencing (CES) panels. We performed a retrospective observational study to assess the diagnostic yield of CES as a first-tier genetic test in 128 consecutive pediatric patients addressed to a referral center in the North-East of France for a suspected genetic disorder, mainly an inborn error of metabolism between January 2016 and August 2020. CES was performed using the TruSight One (4811 genes) or the TruSight One expanded (6699 genes) panel on an Illumina sequencing platform. The median age was 6.5 years (IQR 2.0-12.0) with 43% of males (55/128), and the median disease duration was 7 months (IQR 1-47). In the whole analysis, the CES diagnostic yield was 55% (70/128). The median test-to-report time was 5 months (IQR 4-7). According to CES indications, the CES diagnostic yields were 81% (21/26) for hyperlipidemia, 75% (6/8) for osteogenesis imperfecta, 64% (25/39) for metabolic disorders, 39% (10/26) for neurological disorders, and 28% (8/29) for the subgroup of patients with miscellaneous conditions. Our results demonstrate the usefulness of a CES-based diagnosis as a first-tier genetic test to establish a molecular diagnosis in pediatric patients with a suspected genetic disorder with a median test-to-report time of 5 months. It highlights the importance of a close interaction between the pediatrician with expertise in genetic disorders and the molecular medicine physician to optimize both CES indication and interpretation. Diagnostic yield of clinical exome sequencing (CES) as a first-tier genetic test for diagnosing genetic disorders in 128 consecutive pediatric patients referred to a reference center in the North-East of France for a suspected genetic disorder, mainly an inborn error of metabolism between January 2016 and August 2020. The CES diagnostic yields are reported in the whole population and patients' subgroups (hyperlipidemia, osteogenesis imperfecta, metabolic diseases, neurological disorders, miscellaneous conditions) (Icons made by Flaticon, flaticon.com; CC-BY-3.0).
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Affiliation(s)
- Jean-Philippe Mergnac
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Department of Pediatrics, University Hospital of Nancy, 54000, Nancy, France
| | - Arnaud Wiedemann
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Pediatric Intensive Care Unit, University Hospital of Nancy, 54000, Nancy, France.,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France
| | - Céline Chery
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France.,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, University Hospital of Nancy, 54000, Nancy, France
| | - Jean-Marie Ravel
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France
| | - Farès Namour
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France.,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, University Hospital of Nancy, 54000, Nancy, France
| | - Jean-Louis Guéant
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France.,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, University Hospital of Nancy, 54000, Nancy, France
| | - François Feillet
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.,Department of Pediatrics, University Hospital of Nancy, 54000, Nancy, France.,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France
| | - Abderrahim Oussalah
- Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France. .,Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, INSERM UMR_S 1256, 54000, Nancy, France. .,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, University Hospital of Nancy, 54000, Nancy, France.
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42
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Extended Phenotyping and Functional Validation Facilitate Diagnosis of a Complex Patient Harboring Genetic Variants in MCCC1 and GNB5 Causing Overlapping Phenotypes. Genes (Basel) 2021; 12:genes12091352. [PMID: 34573334 PMCID: PMC8469011 DOI: 10.3390/genes12091352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
Identifying multiple ultra-rare genetic syndromes with overlapping phenotypes is a diagnostic conundrum in clinical genetics. This study investigated the pathogenicity of a homozygous missense variant in GNB5 (GNB5L; NM_016194.4: c.920T > G (p. Leu307Arg); GNB5S; NM_006578.4: c.794T > G (p. Leu265Arg)) identified through exome sequencing in a female child who also had 3-methylcrotonyl-CoA carboxylase (3-MCC) deficiency (newborn screening positive) and hemoglobin E trait. The proband presented with early-onset intellectual disability, the severity of which was more in keeping with GNB5-related disorder than 3-MCC deficiency. She later developed bradycardia and cardiac arrest, and upon re-phenotyping showed cone photo-transduction recovery deficit, all known only to GNB5-related disorders. Patient-derived fibroblast assays showed preserved GNB5S expression, but bioluminescence resonance energy transfer assay showed abolished function of the variant reconstituted Gβ5S containing RGS complexes for deactivation of D2 dopamine receptor activity, confirming variant pathogenicity. This study highlights the need for precise phenotyping and functional assays to facilitate variant classification and clinical diagnosis in patients with complex medical conditions.
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43
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Shickh S, Mighton C, Uleryk E, Pechlivanoglou P, Bombard Y. The clinical utility of exome and genome sequencing across clinical indications: a systematic review. Hum Genet 2021; 140:1403-1416. [PMID: 34368901 DOI: 10.1007/s00439-021-02331-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022]
Abstract
Exome sequencing and genome sequencing have the potential to improve clinical utility for patients undergoing genetic investigations. However, evidence of clinical utility is limited to pediatric populations; we aimed to fill this gap by conducting a systematic review of the literature on the clinical utility of exome/genome sequencing across disease indications in pediatric and adult populations. MEDLINE, EMBASE and Cochrane Library were searched between 2016 and 2020. Quantitative studies evaluating diagnostic yield were included; other measures of clinical utility such as changes to clinical management were documented if reported. Two reviewers screened, extracted data, and appraised risk of bias. Fifty studies met our inclusion criteria. All studies reported diagnostic yield, which ranged from 3 to 70%, with higher range of yields reported for neurological indications and acute illness ranging from 22 to 68% and 37-70%, respectively. Diagnoses triggered a range of clinical management changes including surveillance, reproductive-risk counseling, and identifying at-risk relatives in 4-100% of patients, with higher frequencies reported for acute illness ranging from 67 to 95%. The frequency of variants of uncertain significance ranged from 5 to 85% across studies with a potential trend of decreasing frequency over time and higher rates identified in patients of non-European ancestry. This review provides evidence for a higher range of diagnostic yield of exome/genome sequencing compared to standard genetic tests, particularly in neurological and acute indications. However, we identified significant heterogeneity in study procedures and outcomes, precluding a meaningful meta-analysis and certainty in the evidence available for decision-making. Future research that incorporates a comprehensive and consistent approach in capturing clinical utility of exome/genome sequencing across broader ancestral groups is necessary to improve diagnostic accuracy and yield and allow for analysis of trends over time.Prospero registration CRD42019094101.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | | | - Petros Pechlivanoglou
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada. .,Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada. .,Li Ka Shing Knowledge Institute of St. Michael's Hospital, University of Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
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44
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Rajasekaran S, Bupp CP, Leimanis-Laurens M, Shukla A, Russell C, Junewick J, Gleason E, VanSickle EA, Edgerly Y, Wittmann BM, Prokop JW, Bachmann AS. Repurposing eflornithine to treat a patient with a rare ODC1 gain-of-function variant disease. eLife 2021; 10:67097. [PMID: 34282722 PMCID: PMC8291972 DOI: 10.7554/elife.67097] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/16/2021] [Indexed: 01/17/2023] Open
Abstract
Background: Polyamine levels are intricately controlled by biosynthetic, catabolic enzymes and antizymes. The complexity suggests that minute alterations in levels lead to profound abnormalities. We described the therapeutic course for a rare syndrome diagnosed by whole exome sequencing caused by gain-of-function variants in the C-terminus of ornithine decarboxylase (ODC), characterized by neurological deficits and alopecia. Methods: N-acetylputrescine levels with other metabolites were measured using ultra-performance liquid chromatography paired with mass spectrometry and Z-scores established against a reference cohort of 866 children. Results: From previous studies and metabolic profiles, eflornithine was identified as potentially beneficial with therapy initiated on FDA approval. Eflornithine normalized polyamine levels without disrupting other pathways. She demonstrated remarkable improvement in both neurological symptoms and cortical architecture. She gained fine motor skills with the capacity to feed herself and sit with support. Conclusions: This work highlights the strategy of repurposing drugs to treat a rare disease. Funding: No external funding was received for this work.
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Affiliation(s)
- Surender Rajasekaran
- Pediatric Critical Care Medicine, Helen DeVos Children's Hospital, Grand Rapids, United States.,Spectrum Health Office of Research and Education, Grand Rapids, United States.,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, United States
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, United States.,Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, United States
| | - Mara Leimanis-Laurens
- Pediatric Critical Care Medicine, Helen DeVos Children's Hospital, Grand Rapids, United States.,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, United States
| | - Ankit Shukla
- Department of Pharmacy, Helen DeVos Children's Hospital, Grand Rapids, United States
| | - Christopher Russell
- Spectrum Health Office of Research and Education, Grand Rapids, United States
| | - Joseph Junewick
- Department of Diagnostic Radiology, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, United States
| | - Emily Gleason
- Spectrum Health Office of Research and Education, Grand Rapids, United States
| | - Elizabeth A VanSickle
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, United States
| | - Yvonne Edgerly
- Spectrum Health Office of Research and Education, Grand Rapids, United States
| | | | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, United States.,Department of Pharmacology and Toxicology, College of Human Medicine, Michigan State University, East Lansing, United States
| | - André S Bachmann
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, United States
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45
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van Karnebeek CD, Blydt-Hansen I, Matthews AM, Avramovic V, Price M, Drogemoller B, Shyr C, Lee J, Mwenifumbo J, Ghani A, Stockler S, Friedman JM, Lehman A, Ross CJ, Wasserman WW, Tarailo-Graovac M, Horvath GA. Secondary biogenic amine deficiencies: genetic etiology, therapeutic interventions, and clinical effects. Neurogenetics 2021; 22:251-262. [PMID: 34213677 DOI: 10.1007/s10048-021-00652-7] [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: 09/14/2020] [Accepted: 06/08/2021] [Indexed: 11/25/2022]
Abstract
Monoamine neurotransmitter disorders present predominantly with neurologic features, including dystonic or dyskinetic cerebral palsy and movement disorders. Genetic conditions that lead to secondary defects in the synthesis, catabolism, transport, and metabolism of biogenic amines can lead to neurotransmitter abnormalities, which can present with similar features. Eleven patients with secondary neurotransmitter abnormalities were enrolled between 2011 and 2015. All patients underwent research-based whole exome and/or whole genome sequencing (WES/WGS). A trial of treatment with levodopa/carbidopa and 5-hydroxytryptophan was initiated. In six families with abnormal neurotransmitter profiles and neurological phenotypes, variants in known disease-causing genes (KCNJ6, SCN2A, CSTB in 2 siblings, NRNX1, KIF1A and PAK3) were identified, while one patient had a variant of uncertain significance in a candidate gene (DLG4) that may explain her phenotype. In 3 patients, no compelling candidate genes were identified. A trial of neurotransmitter replacement therapy led to improvement in motor and behavioral symptoms in all but two patients. The patient with KCNJ6 variant did not respond to L-dopa therapy, but rather experienced increased dyskinetic movements even at low dose of medication. The patient's symptoms harboring the NRNX1 deletion remained unaltered. This study demonstrates the utility of genome-wide sequencing in further understanding the etiology and pathophysiology of neurometabolic conditions, and the potential of secondary neurotransmitter deficiencies to serve as novel therapeutic targets. As there was a largely favorable response to therapy in our case series, a careful trial of neurotransmitter replacement therapy should be considered in patients with cerebrospinal fluid (CSF) monoamines below reference range.
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Affiliation(s)
- Clara D van Karnebeek
- BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada.,Department of Pediatrics, Amsterdam University Medical Centre, Amsterdam, the Netherlands.,Department of Pediatrics, Radboud University Medical Center, Nijmegen, the Netherlands.,United for Metabolic Diseases', Amsterdam, the Netherlands
| | | | - Allison M Matthews
- BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Vladimir Avramovic
- Department of Biochemistry, Molecular Biology, and Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Magda Price
- BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Casper Shyr
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Jessica Lee
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Jill Mwenifumbo
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Aisha Ghani
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Sylvia Stockler
- BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Jan M Friedman
- BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Adult Metabolic Diseases Clinic, Vancouver General Hospital, Vancouver, Canada
| | | | - Colin J Ross
- BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wyeth W Wasserman
- BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Maja Tarailo-Graovac
- Department of Biochemistry, Molecular Biology, and Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
| | - Gabriella A Horvath
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada. .,Adult Metabolic Diseases Clinic, Vancouver General Hospital, Vancouver, Canada. .,Biochemical Genetics, BC Children's Hospital, 4480 Oak Street, Vancouver, BC, V6H 3V4, Canada.
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Exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:2029-2037. [PMID: 34211152 DOI: 10.1038/s41436-021-01242-6] [Citation(s) in RCA: 229] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE To develop an evidence-based clinical practice guideline for the use of exome and genome sequencing (ES/GS) in the care of pediatric patients with one or more congenital anomalies (CA) with onset prior to age 1 year or developmental delay (DD) or intellectual disability (ID) with onset prior to age 18 years. METHODS The Pediatric Exome/Genome Sequencing Evidence-Based Guideline Work Group (n = 10) used the Grading of Recommendations Assessment, Development and Evaluation (GRADE) evidence to decision (EtD) framework based on the recent American College of Medical Genetics and Genomics (ACMG) systematic review, and an Ontario Health Technology Assessment to develop and present evidence summaries and health-care recommendations. The document underwent extensive internal and external peer review, and public comment, before approval by the ACMG Board of Directors. RESULTS The literature supports the clinical utility and desirable effects of ES/GS on active and long-term clinical management of patients with CA/DD/ID, and on family-focused and reproductive outcomes with relatively few harms. Compared with standard genetic testing, ES/GS has a higher diagnostic yield and may be more cost-effective when ordered early in the diagnostic evaluation. CONCLUSION We strongly recommend that ES/GS be considered as a first- or second-tier test for patients with CA/DD/ID.
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Andolfo I, Martone S, Rosato BE, Marra R, Gambale A, Forni GL, Pinto V, Göransson M, Papadopoulou V, Gavillet M, Elalfy M, Panarelli A, Tomaiuolo G, Iolascon A, Russo R. Complex Modes of Inheritance in Hereditary Red Blood Cell Disorders: A Case Series Study of 155 Patients. Genes (Basel) 2021; 12:genes12070958. [PMID: 34201899 PMCID: PMC8304671 DOI: 10.3390/genes12070958] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 12/19/2022] Open
Abstract
Hereditary erythrocytes disorders include a large group of conditions with heterogeneous molecular bases and phenotypes. We analyzed here a case series of 155 consecutive patients with clinical suspicion of hereditary erythrocyte defects referred to the Medical Genetics Unit from 2018 to 2020. All of the cases followed a diagnostic workflow based on a targeted next-generation sequencing panel of 86 genes causative of hereditary red blood cell defects. We obtained an overall diagnostic yield of 84% of the tested patients. Monogenic inheritance was seen for 69% (107/155), and multi-locus inheritance for 15% (23/155). PIEZO1 and SPTA1 were the most mutated loci. Accordingly, 16/23 patients with multi-locus inheritance showed dual molecular diagnosis of dehydrated hereditary stomatocytosis/xerocytosis and hereditary spherocytosis. These dual inheritance cases were fully characterized and were clinically indistinguishable from patients with hereditary spherocytosis. Additionally, their ektacytometry curves highlighted alterations of dual inheritance patients compared to both dehydrated hereditary stomatocytosis and hereditary spherocytosis. Our findings expand the genotypic spectrum of red blood cell disorders and indicate that multi-locus inheritance should be considered for analysis and counseling of these patients. Of note, the genetic testing was crucial for diagnosis of patients with a complex mode of inheritance.
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Affiliation(s)
- Immacolata Andolfo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
| | - Stefania Martone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
| | - Barbara Eleni Rosato
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
| | - Roberta Marra
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
| | - Antonella Gambale
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
- Department of Laboratory Medicine (DAIMedLab), UOC Medical Genetics, ‘Federico II’ University Hospital, 80131 Naples, Italy
| | - Gian Luca Forni
- Centro della Microcitemia e delle Anemie Congenite, Ospedale Galliera, 16128 Genoa, Italy; (G.L.F.); (V.P.)
| | - Valeria Pinto
- Centro della Microcitemia e delle Anemie Congenite, Ospedale Galliera, 16128 Genoa, Italy; (G.L.F.); (V.P.)
| | - Magnus Göransson
- Department of Paediatrics, The Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, 41345 Gothenburg, Sweden;
| | - Vasiliki Papadopoulou
- Service and Central Laboratory of Haematology, Department of Oncology and Department of Laboratory Medicine and Pathology, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; (V.P.); (M.G.)
| | - Mathilde Gavillet
- Service and Central Laboratory of Haematology, Department of Oncology and Department of Laboratory Medicine and Pathology, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; (V.P.); (M.G.)
| | - Mohsen Elalfy
- Thalassemia Centre, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt;
| | | | - Giovanna Tomaiuolo
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
- Department of Chemical Engineering, Materials and Industrial Production, ‘Federico II’ University of Naples, 80125 Naples, Italy
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
- Correspondence:
| | - Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
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Seaby EG, Rehm HL, O’Donnell-Luria A. Strategies to Uplift Novel Mendelian Gene Discovery for Improved Clinical Outcomes. Front Genet 2021; 12:674295. [PMID: 34220947 PMCID: PMC8248347 DOI: 10.3389/fgene.2021.674295] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/12/2021] [Indexed: 01/31/2023] Open
Abstract
Rare genetic disorders, while individually rare, are collectively common. They represent some of the most severe disorders affecting patients worldwide with significant morbidity and mortality. Over the last decade, advances in genomic methods have significantly uplifted diagnostic rates for patients and facilitated novel and targeted therapies. However, many patients with rare genetic disorders still remain undiagnosed as the genetic etiology of only a proportion of Mendelian conditions has been discovered to date. This article explores existing strategies to identify novel Mendelian genes and how these discoveries impact clinical care and therapeutics. We discuss the importance of data sharing, phenotype-driven approaches, patient-led approaches, utilization of large-scale genomic sequencing projects, constraint-based methods, integration of multi-omics data, and gene-to-patient methods. We further consider the health economic advantages of novel gene discovery and speculate on potential future methods for improved clinical outcomes.
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Affiliation(s)
- Eleanor G. Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Genomic Informatics Group, University Hospital Southampton, Southampton, United Kingdom
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, United States
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, United States
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
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49
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Should we respect parents' views about which results to return from genomic sequencing? Hum Genet 2021; 141:1059-1068. [PMID: 33987713 DOI: 10.1007/s00439-021-02293-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/06/2021] [Indexed: 01/22/2023]
Abstract
Genomic sequencing (GS) is now well embedded in clinical practice. However, guidelines issued by professional bodies disagree about whether unsolicited findings (UF)-i.e., disease-causing changes found in the DNA unrelated to the reason for testing-should be reported if they are identified inadvertently during data analysis. This extends to a lack of clarity regarding parents' ability to decide about receiving UF for their children. To address this, I use an ethical framework, the Zone of Parental Discretion (ZPD), to consider which UF parents should be allowed to choose (not) to receive and examine how well this assessment aligns with existing professional recommendations. Assessment of guidelines shows recommendations ranging from leaving the decision to the discretion of laboratories through to mandatory reporting for UF for childhood onset, treatable/preventable conditions. The ZPD suggests that parents' decisions should be respected, even where there is no expected benefit, provided that there is not sufficient evidence of serious harm. Using this lens, parents should be able to choose whether or not to know UF for adult-onset conditions in their children, but only insofar as there is insufficient evidence that this knowledge will cause harm or benefit. In contrast, parents should not be allowed to refuse receiving UF for childhood-onset medically actionable conditions. The ZPD is a helpful tool for assessing where it is appropriate to offer parents the choice of receiving UF for their children. This has implications for refinement of policy and laboratory reporting practices, development of consent forms, and genetic counselling practice.
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50
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Modi BP, Khan HN, van der Lee R, Wasim M, Haaxma CA, Richmond PA, Drögemöller B, Shah S, Salomons G, van der Kloet FM, Vaz FM, van der Crabben SN, Ross CJ, Wasserman WW, van Karnebeek CD, Awan FR. Adult GAMT deficiency: A literature review and report of two siblings. Mol Genet Metab Rep 2021; 27:100761. [PMID: 33996490 PMCID: PMC8093930 DOI: 10.1016/j.ymgmr.2021.100761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 04/18/2021] [Indexed: 11/02/2022] Open
Abstract
Guanidinoacetate methyltransferase (GAMT) deficiency is a creatine deficiency disorder and an inborn error of metabolism presenting with progressive intellectual and neurological deterioration. As most cases are identified and treated in early childhood, adult phenotypes that can help in understanding the natural history of the disorder are rare. We describe two adult cases of GAMT deficiency from a consanguineous family in Pakistan that presented with a history of global developmental delay, cognitive impairments, excessive drooling, behavioral abnormalities, contractures and apparent bone deformities initially presumed to be the reason for abnormal gait. Exome sequencing identified a homozygous nonsense variant in GAMT: NM_000156.5:c.134G>A (p.Trp45*). We also performed a literature review and compiled the genetic and clinical characteristics of all adult cases of GAMT deficiency reported to date. When compared to the adult cases previously reported, the musculoskeletal phenotype and the rapidly progressive nature of neurological and motor decline seen in our patients is striking. This study presents an opportunity to gain insights into the adult presentation of GAMT deficiency and highlights the need for in-depth evaluation and reporting of clinical features to expand our understanding of the phenotypic spectrum.
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Affiliation(s)
- Bhavi P. Modi
- Centre for Molecular Medicine and Therapeutics, Dept. of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
- Correspondence to: B. P. Modi, University of British Columbia, BC Children's Hospital Research Institute, 938 W 28 Ave, Vancouver, BC V5Z 4H4, Canada.
| | - Haq Nawaz Khan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Robin van der Lee
- Centre for Molecular Medicine and Therapeutics, Dept. of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Muhammad Wasim
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Charlotte A. Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Phillip A. Richmond
- Centre for Molecular Medicine and Therapeutics, Dept. of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Britt Drögemöller
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Suleman Shah
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Gajja Salomons
- Laboratory for Genetic Metabolic Diseases, Amsterdam University Medical Centres, Amsterdam, the Netherlands
| | - Frans M. van der Kloet
- Laboratory for Genetic Metabolic Diseases, Amsterdam University Medical Centres, Amsterdam, the Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, the Netherlands
| | - Fred M. Vaz
- Laboratory for Genetic Metabolic Diseases, Amsterdam University Medical Centres, Amsterdam, the Netherlands
- Dept. of Clinical Chemistry and Pediatrics, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, the Netherlands
| | | | - Colin J. Ross
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wyeth W. Wasserman
- Centre for Molecular Medicine and Therapeutics, Dept. of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Clara D.M. van Karnebeek
- Centre for Molecular Medicine and Therapeutics, Dept. of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
- Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Centres, Amsterdam, Netherlands
- Department of Pediatric Metabolic Diseases, Amalia Children's Hospital, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
- United for Metabolic Diseases, the Netherlands
| | - Fazli Rabbi Awan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
- Correspondence to: F. R. Awan, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan.
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