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Chengyan L, Chupeng X, You W, Yinhui C, Binglong H, Dang A, Ling L, Chuan T. Identification of genetic causes in children with unexplained epilepsy based on trio-whole exome sequencing. Clin Genet 2024; 106:140-149. [PMID: 38468460 DOI: 10.1111/cge.14519] [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: 11/03/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
Genotype and clinical phenotype analyses of 128 children were performed based on whole exome sequencing (WES), providing a reference for the provision of genetic counseling and the precise diagnosis and treatment of epilepsy. A total of 128 children with unexplained epilepsy were included in this study, and all their clinical data were analyzed. The children's treatments, epilepsy control, and neurodevelopmental levels were regularly followed up every 3 months. The genetic diagnostic yield of the 128 children with epilepsy is 50.8%, with an SNV diagnostic yield of 39.8% and a CNV diagnostic yield of 12.5%. Among the 128 children with epilepsy, 57.0% had onset of epilepsy in infancy, 25.8% have more than two clinical seizure forms, 62.5% require two or more anti-epileptic drug treatments, and 72.7% of the children have varying degrees of psychomotor development retardation. There are significant differences between ages of onset, neurodevelopmental levels and the presence of drug resistance in the genetic diagnostic yield (all p < 0.05). The 52 pathogenic/likely pathogenic SNVs involve 31 genes, with genes encoding ion channels having the largest number of mutations (30.8%). There were 16 cases of pathogenic/possibly pathogenic CNVs, among which the main proportions of CNVs were located in chromosome 15 and chromosome 16. Trio-WES is an essential tool for the genetic diagnosis of unexplained epilepsy, with a genetic diagnostic yield of up to 50.8%. Early genetic testing can provide an initiate appropriate therapies and accurate molecular diagnosis.
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Affiliation(s)
- Li Chengyan
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Xue Chupeng
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
- Department of Pediatrics, Shantou Central Hospital, Shantou, People's Republic of China
| | - Wang You
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Chen Yinhui
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Huang Binglong
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Ao Dang
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Liu Ling
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Tian Chuan
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
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Tolezano GC, Bastos GC, da Costa SS, Scliar MDO, de Souza CFM, Van Der Linden H, Fernandes WLM, Otto PA, Vianna-Morgante AM, Haddad LA, Honjo RS, Yamamoto GL, Kim CA, Rosenberg C, Jorge AADL, Bertola DR, Krepischi ACV. Clinical Characterization and Underlying Genetic Findings in Brazilian Patients with Syndromic Microcephaly Associated with Neurodevelopmental Disorders. Mol Neurobiol 2024; 61:5230-5247. [PMID: 38180615 DOI: 10.1007/s12035-023-03894-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
Microcephaly is characterized by an occipitofrontal circumference at least two standard deviations below the mean for age and sex. Neurodevelopmental disorders (NDD) are commonly associated with microcephaly, due to perturbations in brain development and functioning. Given the extensive genetic heterogeneity of microcephaly, managing patients is hindered by the broad spectrum of diagnostic possibilities that exist before conducting molecular testing. We investigated the genetic basis of syndromic microcephaly accompanied by NDD in a Brazilian cohort of 45 individuals and characterized associated clinical features, as well as evaluated the effectiveness of whole-exome sequencing (WES) as a diagnostic tool for this condition. Patients previously negative for pathogenic copy number variants underwent WES, which was performed using a trio approach for isolated index cases (n = 31), only the index in isolated cases with parental consanguinity (n = 8) or affected siblings in familial cases (n = 3). Pathogenic/likely pathogenic variants were identified in 19 families (18 genes) with a diagnostic yield of approximately 45%. Nearly 86% of the individuals had global developmental delay/intellectual disability and 51% presented with behavioral disturbances. Additional frequent clinical features included facial dysmorphisms (80%), brain malformations (67%), musculoskeletal (71%) or cardiovascular (47%) defects, and short stature (54%). Our findings unraveled the underlying genetic basis of microcephaly in half of the patients, demonstrating a high diagnostic yield of WES for microcephaly and reinforcing its genetic heterogeneity. We expanded the phenotypic spectrum associated with the condition and identified a potentially novel gene (CCDC17) for congenital microcephaly.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Giovanna Civitate Bastos
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Marília de Oliveira Scliar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Carolina Fischinger Moura de Souza
- Postgraduate Program in Child and Adolescent Health, Universidade Federal do Rio Grande do Sul, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | | | | | - Paulo Alberto Otto
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Angela M Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Luciana Amaral Haddad
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Guilherme Lopes Yamamoto
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
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Mazzonetto PC, Villela D, Krepischi ACV, Pierry PM, Bonaldi A, Almeida LGD, Paula MG, Bürger MC, de Oliveira AG, Fonseca GGG, Giugliani R, Riegel-Giugliani M, Bertola D, Yamamoto GL, Passos-Bueno MR, Campos GDS, Machado ACD, Mazzeu JF, Perrone E, Zechi-Ceide RM, Kokitsu-Nakata NM, Vieira TP, Steiner CE, Gil-da-Silva-Lopes VL, Vieira DKR, Boy R, de Pina-Neto JM, Scapulatempo-Neto C, Milanezi F, Rosenberg C. Low-pass whole genome sequencing as a cost-effective alternative to chromosomal microarray analysis for low- and middle-income countries. Am J Med Genet A 2024:e63802. [PMID: 38924610 DOI: 10.1002/ajmg.a.63802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Low-pass whole genome sequencing (LP-WGS) has been applied as alternative method to detect copy number variants (CNVs) in the clinical setting. Compared with chromosomal microarray analysis (CMA), the sequencing-based approach provides a similar resolution of CNV detection at a lower cost. In this study, we assessed the efficiency and reliability of LP-WGS as a more affordable alternative to CMA. A total of 1363 patients with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies were enrolled. Those patients were referred from 15 nonprofit organizations and university centers located in different states in Brazil. The analysis of LP-WGS at 1x coverage (>50kb) revealed a positive testing result in 22% of the cases (304/1363), in which 219 and 85 correspond to pathogenic/likely pathogenic (P/LP) CNVs and variants of uncertain significance (VUS), respectively. The 16% (219/1363) diagnostic yield observed in our cohort is comparable to the 15%-20% reported for CMA in the literature. The use of commercial software, as demonstrated in this study, simplifies the implementation of the test in clinical settings. Particularly for countries like Brazil, where the cost of CMA presents a substantial barrier to most of the population, LP-WGS emerges as a cost-effective alternative for investigating copy number changes in cytogenetics.
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Affiliation(s)
- Patricia C Mazzonetto
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | | | - Roberto Giugliani
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Casa dos Raros - House of Rares, Centro de Atenção Integral e Treinamento em Doenças Raras, Porto Alegre, Brazil
- INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Mariluce Riegel-Giugliani
- Casa dos Raros - House of Rares, Centro de Atenção Integral e Treinamento em Doenças Raras, Porto Alegre, Brazil
- INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Débora Bertola
- Instituto da Criança, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Guilherme Lopes Yamamoto
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Instituto da Criança, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Gabriele da Silva Campos
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Claudia Dantas Machado
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana F Mazzeu
- Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Eduardo Perrone
- Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Roseli M Zechi-Ceide
- Department of Clinical Genetics and Molecular Biology, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, São Paulo, Brazil
| | - Nancy M Kokitsu-Nakata
- Department of Clinical Genetics and Molecular Biology, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, São Paulo, Brazil
| | - Társis Paiva Vieira
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Carlos Eduardo Steiner
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Daniela Koeller Rodrigues Vieira
- Municipal Secretary of Health of Angra dos Reis, Rio de Janeiro, Brazil
- National Institute of Women, Children and Adolescents Health Fernandes Figueira/Oswaldo Cruz Foundation (IFF/FIOCRUZ), Rio de Janeiro, Brazil
| | - Raquel Boy
- State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
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Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [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] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
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Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
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Chi CS, Tsai CR, Lee HF. Resolving unsolved whole-genome sequencing data in paediatric neurological disorders: a cohort study. Arch Dis Child 2024:archdischild-2024-326985. [PMID: 38789118 DOI: 10.1136/archdischild-2024-326985] [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: 02/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
OBJECTIVE To resolve unsolved whole-genome sequencing (WGS) data in individuals with paediatric neurological disorders. DESIGN A cohort study method using updated bioinformatic tools, new analysis targets, clinical information and literature databases was employed to reanalyse existing unsolved genome data. PARTICIPANTS From January 2016 to September 2023, a total of 615 individuals who aged under 18 years old, exhibited neurological disorders and received singleton WGS were recruited. 364 cases were unsolved during initial WGS analysis, in which 102 consented to reanalyse existing singleton WGS data. RESULTS Median duration for reanalysis after initial negative WGS results was 2 years and 4 months. The diagnostic yield was 29 of 102 individuals (28.4%) through reanalysis. New disease gene discovery and new target acquisitions contributed to 13 of 29 solved cases (44.8%). The reasons of non-detected causative variants during initial WGS analysis were variant reclassification in 9 individuals (31%), analytical issue in 9 (31%), new emerging disease-gene association in 8 (27.6%) and clinical update in 3 (10.3%). The 29 new diagnoses increased the cumulative diagnostic yield of clinical WGS in the entire study cohort to 45.5% after reanalysis. CONCLUSIONS Unsolved paediatric WGS individuals with neurological disorders could obtain molecular diagnoses through reanalysis within a timeframe of 2-2.5 years. New disease gene, structural variations and deep intronic splice variants make a significant contribution to diagnostic yield. This approach can provide precise genetic counselling to positive reanalysis results and end a diagnostic odyssey.
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Affiliation(s)
- Ching-Shiang Chi
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Ren Tsai
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Hsiu-Fen Lee
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
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Modelhart A, Sturz D, Kremslehner L, Prainsack B. Lived experiences of genetic diagnosis for rare disease patients: a qualitative interview study. Orphanet J Rare Dis 2024; 19:68. [PMID: 38355619 PMCID: PMC10868115 DOI: 10.1186/s13023-024-03058-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Genetic diagnosis is often understood as a single event within the care pathway of rare disease patients. Legal, policy and ethical scholarship focusing on rare diseases and genetic information discusses questions of how to best deal with the process of genetic diagnosis and the communication of genetic information within a given health system. We co-created a research design with rare disease patients and their families in Austria to explore in-depth the experiences of genetic diagnosis for people affected by rare diseases. Our objective was to trace the whole pathway of genetic testing and understand how rare disease patients experience genetic diagnosis as part of their care pathway in the healthcare system. RESULTS Data was collected through in-depth semi-structured qualitative interviews with 14 patients with a suspected or diagnosed rare disease or their parents, focusing on their perception of the pathway of genetic diagnosis in Austria. This pathway included the initial triggering of genetic diagnosis, the process of testing and its immediate (communication of results, counselling) and long-term, wider aftermath. Patients missed a clear link to already established forms of care such as their primary care/treating physicians. They also advocate for an integrated and interdisciplinary care pathway. CONCLUSIONS Our study underscores the importance of a continuous care and communication pathway spanning from the initial genetic diagnosis process to post-test phases. It further shows the importance of exploring patients' perspectives through qualitative research methods to understand the intricate workings of public health policies and tools. Integrating genetic diagnosis into a broader care trajectory is crucial for a holistic approach to care for rare disease patients who often rely on regular interactions with the healthcare system. Achieving this holistic approach requires collaboration between experts in specific rare disease areas, primary care physicians, and support networks.
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Affiliation(s)
- Antonia Modelhart
- Department of Political Science, University of Vienna, Universitätsstraße 1, 1010, Vienna, Austria.
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.
| | - Dominique Sturz
- Pro Rare Austria - Austrian Rare Disease Alliance, Vienna, Austria
- ePAG (European Patient Advocacy Group) ERN-Eye, Strasbourg, FR, France
- Retina International Usher Syndrome Committee and Genetic Diagnosis Task Force, Dublin, Ireland
- Usher Initiative Austria, Vienna, Austria
| | | | - Barbara Prainsack
- Department of Political Science, University of Vienna, Universitätsstraße 1, 1010, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
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Lin X, Hu J, Zhou B, Zhang Q, Jiang Y, Wang O, Xia W, Xing X, Li M. Genotype-phenotype relationship and comparison between eastern and western patients with osteogenesis imperfecta. J Endocrinol Invest 2024; 47:67-77. [PMID: 37270749 PMCID: PMC10776744 DOI: 10.1007/s40618-023-02123-2] [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: 03/16/2023] [Accepted: 05/26/2023] [Indexed: 06/05/2023]
Abstract
PURPOSE To evaluate the genotypic and phenotypic relationship in a large cohort of OI patients and to compare the differences between eastern and western OI cohorts. METHODS A total of 671 OI patients were included. Pathogenic mutations were identified, phenotypic information was collected, and relationships between genotypes and phenotypes were analyzed. Literature about western OI cohorts was searched, and differences were compared between eastern and western OI cohorts. RESULTS A total of 560 OI patients were identified as carrying OI pathogenic mutations, and the positive detection rate of disease-causing gene mutations was 83.5%. Mutations in 15 OI candidate genes were identified, with COL1A1 (n = 308, 55%) and COL1A2 (n = 164, 29%) being the most common mutations, and SERPINF1 and WNT1 being the most common biallelic variants. Of the 414 probands, 48.8, 16.9, 29.2 and 5.1% had OI types I, III, IV and V, respectively. Peripheral fracture was the most common phenotype (96.6%), and femurs (34.7%) were most commonly affected. Vertebral compression fracture was observed in 43.5% of OI patients. Biallelic or COL1A2 mutation led to more bone deformities and poorer mobility than COL1A1 mutation (all P < 0.05). Glycine substitution of COL1A1 or COL1A2 or biallelic variants led to more severe phenotypes than haploinsufficiency of collagen type I α chains, which induced the mildest phenotypes. Although the gene mutation spectrum varied among countries, the fracture incidence was similar between eastern and western OI cohorts. CONCLUSION The findings are valuable for accurate diagnosis and treatment of OI, mechanism exploration and prognosis judgment. Genetic profiles of OI may vary among races, but the mechanism needs to be explored.
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Affiliation(s)
- X Lin
- Department of Endocrinology, National Health Commission Key Laboratory of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - J Hu
- Department of Endocrinology, National Health Commission Key Laboratory of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - B Zhou
- Department of Endocrinology, National Health Commission Key Laboratory of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Q Zhang
- Department of Endocrinology, National Health Commission Key Laboratory of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Y Jiang
- Department of Endocrinology, National Health Commission Key Laboratory of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - O Wang
- Department of Endocrinology, National Health Commission Key Laboratory of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - W Xia
- Department of Endocrinology, National Health Commission Key Laboratory of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - X Xing
- Department of Endocrinology, National Health Commission Key Laboratory of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - M Li
- Department of Endocrinology, National Health Commission Key Laboratory of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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8
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Shreeve N, Sproule C, Choy KW, Dong Z, Gajewska-Knapik K, Kilby MD, Mone F. Incremental yield of whole-genome sequencing over chromosomal microarray analysis and exome sequencing for congenital anomalies in prenatal period and infancy: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:15-23. [PMID: 37725747 DOI: 10.1002/uog.27491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/08/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
OBJECTIVES First, to determine the incremental yield of whole-genome sequencing (WGS) over quantitative fluorescence polymerase chain reaction (QF-PCR)/chromosomal microarray analysis (CMA) with and without exome sequencing (ES) in fetuses, neonates and infants with a congenital anomaly that was or could have been detected on prenatal ultrasound. Second, to evaluate the turnaround time (TAT) and quantity of DNA required for testing using these pathways. METHODS This review was registered prospectively in December 2022. Ovid MEDLINE, EMBASE, MEDLINE (Web of Science), The Cochrane Library and ClinicalTrials.gov databases were searched electronically (January 2010 to December 2022). Inclusion criteria were cohort studies including three or more fetuses, neonates or infants with (i) one or more congenital anomalies; (ii) an anomaly which was or would have been detectable on prenatal ultrasound; and (iii) negative QF-PCR and CMA. In instances in which the CMA result was unavailable, all cases of causative pathogenic copy number variants > 50 kb were excluded, as these would have been detectable on standard prenatal CMA. Pooled incremental yield was determined using a random-effects model and heterogeneity was assessed using Higgins' I2 test. Subanalyses were performed based on pre- or postnatal cohorts, cases with multisystem anomalies and those meeting the NHS England prenatal ES inclusion criteria. RESULTS A total of 18 studies incorporating 902 eligible cases were included, of which eight (44.4%) studies focused on prenatal cohorts, incorporating 755 cases, and the remaining studies focused on fetuses undergoing postmortem testing or neonates/infants with congenital structural anomalies, constituting the postnatal cohort. The incremental yield of WGS over QF-PCR/CMA was 26% (95% CI, 18-36%) (I2 = 86%), 16% (95% CI, 9-24%) (I2 = 85%) and 39% (95% CI, 27-51%) (I2 = 53%) for all, prenatal and postnatal cases, respectively. The incremental yield increased in cases in which sequencing was performed in line with the NHS England prenatal ES criteria (32% (95% CI, 22-42%); I2 = 70%) and in those with multisystem anomalies (30% (95% CI, 19-43%); I2 = 65%). The incremental yield of WGS for variants of uncertain significance (VUS) was 18% (95% CI, 7-33%) (I2 = 74%). The incremental yield of WGS over QF-PCR/CMA and ES was 1% (95% CI, 0-4%) (I2 = 47%). The pooled median TAT of WGS was 18 (range, 1-912) days, and the quantity of DNA required was 100 ± 0 ng for WGS and 350 ± 50 ng for QF-PCR/CMA and ES (P = 0.03). CONCLUSION While WGS in cases with congenital anomaly holds great promise, its incremental yield over ES is yet to be demonstrated. However, the laboratory pathway for WGS requires less DNA with a potentially faster TAT compared with sequential QF-PCR/CMA and ES. There was a relatively high rate of VUS using WGS. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- N Shreeve
- Department of Obstetrics & Gynaecology, University of Cambridge, Cambridge, UK
| | - C Sproule
- Department of Obstetrics & Gynaecology, South Eastern Health and Social Care Trust, Belfast, UK
| | - K W Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Z Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - K Gajewska-Knapik
- Department of Obstetrics & Gynaecology, Cambridge University Hospitals, Cambridge, UK
| | - M D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's Foundation Trust, Birmingham, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Medical Genomics Research Group, Illumina, Cambridge, UK
| | - F Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
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9
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Guo F, Liu R, Pan Y, Collins C, Bean L, Ma Z, Mathur A, Da Silva C, Nallamilli B, Guruju N, Chen-Deutsch X, Yousaf R, Chin E, Balciuniene J, Hegde M. Evidence from 2100 index cases supports genome sequencing as a first-tier genetic test. Genet Med 2024; 26:100995. [PMID: 37838930 DOI: 10.1016/j.gim.2023.100995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023] Open
Abstract
PURPOSE Genome sequencing (GS) is one of the most comprehensive assays that interrogate single-nucleotide variants, copy number variants, mitochondrial variants, repeat expansions, and structural variants in a single assay. Despite the clear technical superiority, the full clinical utility of GS has yet to be determined. METHODS We systematically evaluated 2100 clinical GS index cases performed in our laboratory to explore the diagnostic yield of GS as first-tier and as follow-up testing. RESULTS The overall diagnostic yield was 28% (585/2100). The diagnostic yield for GS as the first-tier test was 26% (294/1146). Among cases with prior non-diagnostic genetic tests, GS provided a diagnosis for 27% (247/910) of cases, including 56 cases with prior exome sequencing (ES). Although re-analysis of previous ES might have resolved the diagnosis in 29 cases, diagnoses for 27 cases would have been missed because of the technical inferiority of ES. Moreover, GS further disclosed additional genetic etiology in 3 out of 44 cases with existing partial diagnosis. CONCLUSION We present the largest-to-date GS data set of a clinically heterogeneous cohort from a single clinical laboratory. Our data demonstrate that GS should be considered as the first-tier genetic test that has the potential to shorten the diagnostic odyssey.
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Affiliation(s)
- Fen Guo
- Revvity Omics, Pittsburgh, PA.
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10
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Pena SDJ, Tarazona-Santos E. Clinical genomics and precision medicine. Genet Mol Biol 2022; 45:e20220150. [PMID: 36218382 PMCID: PMC9555143 DOI: 10.1590/1678-4685-gmb-2022-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/12/2022] [Indexed: 11/04/2022] Open
Abstract
Precision Medicine emerges from the genomic paradigm of health and disease. For precise molecular diagnoses of genetic diseases, we must analyze the Whole Exome (WES) or the Whole Genome (WGS). By not needing exon capture, WGS is more powerful to detect single nucleotide variants and copy number variants. In healthy individuals, we can observe monogenic highly penetrant variants, which may be causally responsible for diseases, and also susceptibility variants, associated with common polygenic diseases. But there is the major problem of penetrance. Thus, there is the question of whether it is worthwhile to perform WGS in all healthy individuals as a step towards Precision Medicine. The genetic architecture of disease is consistent with the fact that they are all polygenic. Moreover, ancestry adds another layer of complexity. We are now capable of obtaining Polygenic Risk Scores for all complex diseases using only data from new generation sequencing. Yet, review of available evidence does not at present favor the idea that WGS analyses are sufficiently developed to allow reliable predictions of the risk components for monogenic and polygenic hereditary diseases in healthy individuals. Probably, it is still better for WGS to remain reserved for the diagnosis of pathogenic variants of Mendelian diseases.
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Affiliation(s)
- Sérgio D. J. Pena
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Bioquímica e Imunologia, Belo Horizonte, MG, Brazil. ,Núcleo de Genética Médica, Belo Horizonte, MG, Brazil
| | - Eduardo Tarazona-Santos
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte, MG, Brazil
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11
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A Formative Study of the Implementation of Whole Genome Sequencing in Northern Ireland. Genes (Basel) 2022; 13:genes13071104. [PMID: 35885887 PMCID: PMC9316942 DOI: 10.3390/genes13071104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
Background: The UK 100,000 Genomes Project was a transformational research project which facilitated whole genome sequencing (WGS) diagnostics for rare diseases. We evaluated experiences of introducing WGS in Northern Ireland, providing recommendations for future projects. Methods: This formative evaluation included (1) an appraisal of the logistics of implementing and delivering WGS, (2) a survey of participant self-reported views and experiences, (3) semi-structured interviews with healthcare staff as key informants who were involved in the delivery of WGS and (4) a workshop discussion about interprofessional collaboration with respect to molecular diagnostics. Results: We engaged with >400 participants, with detailed reflections obtained from 74 participants including patients, caregivers, key National Health Service (NHS) informants, and researchers (patient survey n = 42; semi-structured interviews n = 19; attendees of the discussion workshop n = 13). Overarching themes included the need to improve rare disease awareness, education, and support services, as well as interprofessional collaboration being central to an effective, mainstreamed molecular diagnostic service. Conclusions: Recommendations for streamlining precision medicine for patients with rare diseases include administrative improvements (e.g., streamlining of the consent process), educational improvements (e.g., rare disease training provided from undergraduate to postgraduate education alongside genomics training for non-genetic specialists) and analytical improvements (e.g., multidisciplinary collaboration and improved computational infrastructure).
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