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Ferreira EA, Buijs MJN, Wijngaard R, Daams JG, Datema MR, Engelen M, van Karnebeek CDM, Oud MM, Vaz FM, Wamelink MMC, van der Crabben SN, Langeveld M. Inherited metabolic disorders in adults: systematic review on patient characteristics and diagnostic yield of broad sequencing techniques (exome and genome sequencing). Front Neurol 2023; 14:1206106. [PMID: 37560457 PMCID: PMC10408679 DOI: 10.3389/fneur.2023.1206106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/26/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND/OBJECTIVES The timely diagnosis of inherited metabolic disorders (IMD) is essential for initiating treatment, prognostication and genetic testing of relatives. Recognition of IMD in adults is difficult, because phenotypes are different from those in children and influenced by symptoms from acquired conditions. This systematic literature review aims to answer the following questions: (1) What is the diagnostic yield of exome/genome sequencing (ES/GS) for IMD in adults with unsolved phenotypes? (2) What characteristics do adult patients diagnosed with IMD through ES/GS have? METHODS A systematic search was conducted using the following search terms (simplified): "Whole exome sequencing (WES)," "Whole genome sequencing (WGS)," "IMD," "diagnostics" and the 1,450 known metabolic genes derived from ICIMD. Data from 695 articles, including 27,702 patients, were analyzed using two different methods. First, the diagnostic yield for IMD in patients presenting with a similar phenotype was calculated. Secondly, the characteristics of patients diagnosed with IMD through ES/GS in adulthood were established. RESULTS The diagnostic yield of ES and/or GS for adult patients presenting with unexplained neurological symptoms is 11% and for those presenting with dyslipidemia, diabetes, auditory and cardiovascular symptoms 10, 9, 8 and 7%, respectively. IMD patients diagnosed in adulthood (n = 1,426), most frequently portray neurological symptoms (65%), specifically extrapyramidal/cerebellar symptoms (57%), intellectual disability/dementia/psychiatric symptoms (41%), pyramidal tract symptoms/myelopathy (37%), peripheral neuropathy (18%), and epileptic seizures (16%). The second most frequently observed symptoms were ophthalmological (21%). In 47% of the IMD diagnosed patients, symptoms from multiple organ systems were reported. On average, adult patients are diagnosed 15 years after first presenting symptoms. Disease-related abnormalities in metabolites in plasma, urine or cerebral spinal fluid were identified in 40% of all patients whom underwent metabolic screening. In 52% the diagnosis led to identification of affected family members with the same IMD. CONCLUSION ES and/or GS is likely to yield an IMD diagnosis in adult patients presenting with an unexplained neurological phenotype, as well as in patients with a phenotype involving multiple organ systems. If a gene panel does not yield a conclusive diagnosis, it is worthwhile to analyze all known disease genes. Further prospective research is needed to establish the best diagnostic approach (type and sequence of metabolic and genetic test) in adult patients presenting with a wide range of symptoms, suspected of having an IMD. SYSTEMATIC REVIEW REGISTRATION https://www.crd.york.ac.uk/prospero/, identifier: CRD42021295156.
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Affiliation(s)
- Elise A. Ferreira
- Department of Paediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- United for Metabolic Diseases, Amsterdam, Netherlands
| | - Mark J. N. Buijs
- United for Metabolic Diseases, Amsterdam, Netherlands
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Robin Wijngaard
- United for Metabolic Diseases, Amsterdam, Netherlands
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Joost G. Daams
- Medical Library (J.G.D.), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Mareen R. Datema
- Department of Endocrinology and Metabolism, Amsterdam UMC, Research Institute Gastroenterology, Endocrinology and Metabolism (AGEM), University of Amsterdam, Amsterdam, Netherlands
| | - Marc Engelen
- Department of Pediatric Neurology/Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Clara D. M. van Karnebeek
- Department of Paediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- United for Metabolic Diseases, Amsterdam, Netherlands
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Machteld M. Oud
- United for Metabolic Diseases, Amsterdam, Netherlands
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frédéric M. Vaz
- Department of Paediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, Gastroenterology, Endocrinology & Metabolism (AGEM), University of Amsterdam, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Mirjam M. C. Wamelink
- Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, Gastroenterology, Endocrinology & Metabolism (AGEM), University of Amsterdam, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Saskia N. van der Crabben
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Mirjam Langeveld
- Department of Endocrinology and Metabolism, Amsterdam UMC, Research Institute Gastroenterology, Endocrinology and Metabolism (AGEM), University of Amsterdam, Amsterdam, Netherlands
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Quaio CRDC, Obando MJR, Perazzio SF, Dutra AP, Chung CH, Moreira CM, Novo Filho GM, Sacramento-Bobotis PR, Penna MG, Souza RRFD, Cintra VP, Carnavalli JEP, Silva RAD, Santos MNP, Paixão D, Baratela WADR, Olivati C, Spolador GM, Pintao MC, Fornari ARDS, Burger M, Ramalho RF, Pereira OJE, Ferreira ENE, Mitne-Neto M, Kim CA. Exome sequencing and targeted gene panels: a simulated comparison of diagnostic yield using data from 158 patients with rare diseases. Genet Mol Biol 2021; 44:20210061. [PMID: 34609444 PMCID: PMC8485181 DOI: 10.1590/1678-4685-gmb-2021-0061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/09/2021] [Indexed: 11/21/2022] Open
Abstract
Next-generation sequencing (NGS) has altered clinical genetic testing by widening the access to molecular diagnosis of genetically determined rare diseases. However, physicians may face difficulties selecting the best diagnostic approach. Our goal is to estimate the rate of possible molecular diagnoses missed by different targeted gene panels using data from a cohort of patients with rare genetic diseases diagnosed with exome sequencing (ES). For this purpose, we simulated a comparison between different targeted gene panels and ES: the list of genes harboring clinically relevant variants from 158 patients was used to estimate the theoretical rate of diagnoses missed by NGS panels from 53 different NGS panels from eight different laboratories. Panels presented a mean rate of missed diagnoses of 64% (range 14%-100%) compared to ES, representing an average predicted sensitivity of 36%. Metabolic abnormalities represented the group with highest mean of missed diagnoses (86%), while seizure represented the group with lowest mean (46%). Focused gene panels are restricted in covering select sets of genes implicated in specific diseases and they may miss molecular diagnoses of rare diseases compared to ES. However, their role in genetic diagnosis remains important especially for well-known genetic diseases with established genetic locus heterogeneity.
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Affiliation(s)
- Caio Robledo D'Angioli Costa Quaio
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas (HCFMUSP), Instituto da Criança, São Paulo, SP, Brazil.,Fleury Medicina e Saúde, São Paulo, SP, Brazil.,Hospital Israelita Albert Einstein, Laboratório Clínico, São Paulo, SP, Brazil
| | - María José Rivadeneira Obando
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas (HCFMUSP), Instituto da Criança, São Paulo, SP, Brazil
| | - Sandro Felix Perazzio
- Fleury Medicina e Saúde, São Paulo, SP, Brazil.,Universidade Federal de São Paulo, Divisão de Reumatologia, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | | | | | - Rafael Alves da Silva
- Fleury Medicina e Saúde, São Paulo, SP, Brazil.,Universidade Federal de São Paulo, Escola Paulista de Medicina, Laboratório de Hepatologia Molecular Aplicada (LHeMA), São Paulo, SP, Brazil
| | | | | | | | | | - Gustavo Marquezani Spolador
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas (HCFMUSP), Instituto da Criança, São Paulo, SP, Brazil.,Fleury Medicina e Saúde, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | - Chong Ae Kim
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas (HCFMUSP), Instituto da Criança, São Paulo, SP, Brazil
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