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Azuelos C, Marquis MA, Laberge AM. A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility. Eur J Med Genet 2024; 68:104925. [PMID: 38432472 DOI: 10.1016/j.ejmg.2024.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/31/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients. METHODS Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility. RESULTS Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members). CONCLUSION Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.
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Affiliation(s)
- Claudia Azuelos
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| | - Marc-Antoine Marquis
- Palliative Care, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Anne-Marie Laberge
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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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: 15] [Impact Index Per Article: 15.0] [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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Tan Y, Chen H, Gong S, Zou Y, Shen Y, Luo L, Jin G, Liu Z. Evolution and trends of childhood cataract research in the past 10 years: A scientometric analysis. Heliyon 2023; 9:e17590. [PMID: 37416629 PMCID: PMC10320269 DOI: 10.1016/j.heliyon.2023.e17590] [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: 02/11/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023] Open
Abstract
Purpose To present a panoramic review of childhood cataract knowledge networks, hotspots and trends. Methods The Web of Science Core Collection was used to retrieve the global literature on childhood cataract published between 2012 and 2021. Scientometric data were analyzed and visualized using VOSviewer and CiteSpace for metrics including publication count, citation count, country, journal, author, cited reference, subject category and their temporal trends. Results A total of 3395 analyzed publications showed an inconsistent annual increasing trend. The USA (n = 939) was the leading contributor among countries. The Journal of American Association for Pediatric Ophthalmology and Strabismus (n = 113) had the highest number of publications among journals. Eight clusters of author collaboration network including 183 authors were identified. Gene mutation, cataract surgery management, intraocular lens implantation complications, prevalence, and glaucoma were identified as the research hotspots. Pediatric cataract surgery, new mutations, artificial intelligence, and cerebrotendinous xanthomatosis were identified as frontier research topics. "Biochemistry and molecular biology", "neurosciences", and "radiology, nuclear medicine and medical imaging" had the highest betweenness centrality values (0.38, 0.32, and 0.22). Multidisciplinary (burst years: 2020 to 2021; strength = 4.32) had the greatest strength as of 2021. Conclusions Childhood cataract research intensely focuses on revealing the genetic background and pheno-spectrum of the diseases, innovating and/or optimizing surgical techniques, and preventing and treating postoperative complications. Artificial intelligence has shed light on the diagnosis and treatment of childhood cataracts. The advance in the research on molecular mechanisms of childhood cataracts depends on multidisciplinary cooperation.
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Affiliation(s)
- Yuan Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Hui Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Shaoyi Gong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
- Zhongshan Medical School, Sun Yat-sen University, Guangzhou, China
| | - Yingshi Zou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Yanyu Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Lixia Luo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Guangming Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Zhenzhen Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
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Zhang D, Wang D, Tong Y, Li M, Meng L, Song Q, Xin Y. A novel c.64G > T (p.G22C) NR5A1 variant in a Chinese adolescent with 46,XY disorders of sex development: a case report. BMC Pediatr 2023; 23:182. [PMID: 37072715 PMCID: PMC10114376 DOI: 10.1186/s12887-023-03974-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/27/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Adolescents with 46,XY disorders of sex development (DSD) face additional medical and psychological challenges. To optimize management and minimize hazards, correct and early clinical and molecular diagnosis is necessary. CASE PRESENTATION We report a 13-year-old Chinese adolescent with absent Müllerian derivatives and suspected testis in the inguinal area. History, examinations, and assistant examinations were available for clinical diagnosis of 46,XY DSD. The subsequent targeting specific disease-causing genes, comprising 360 endocrine disease-causing genes, was employed for molecular diagnosis. A novel variation in nuclear receptor subfamily 5 group A member 1 (NR5A1) [c.64G > T (p.G22C)] was identified in the patient. In vitro functional analyses of the novel variant suggested no impairment to NR5A1 mRNA or protein expression relative to wild-type, and immunofluorescence confirmed similar localization of NR5A1 mutant to the cell nucleus. However, we observed decreased DNA-binding affinity by the NR5A1 variant, while dual-luciferase reporter assays showed that the mutant effectively downregulated the transactivation capacity of anti-Müllerian hormone. We described a novel NR5A1 variant and demonstrated its adverse effects on the functional integrity of the NR5A1 protein resulting in serious impairment of its modulation of gonadal development. CONCLUSIONS This study adds one novel NR5A1 variant to the pool of pathogenic variants and enriches the adolescents of information available about the mutation spectrum of this gene in Chinese population.
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Affiliation(s)
- Dan Zhang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Dajia Wang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Yajie Tong
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Mingyu Li
- Department of Clinical Laboratory, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Lingzhe Meng
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Qiutong Song
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Ying Xin
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
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Alix T, Chéry C, Josse T, Bronowicki JP, Feillet F, Guéant-Rodriguez RM, Namour F, Guéant JL, Oussalah A. Predictors of the utility of clinical exome sequencing as a first-tier genetic test in patients with Mendelian phenotypes: results from a referral center study on 603 consecutive cases. Hum Genomics 2023; 17:5. [PMID: 36740706 PMCID: PMC9899384 DOI: 10.1186/s40246-023-00455-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 01/28/2023] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Clinical exome sequencing (CES) provides a comprehensive and effective analysis of relevant disease-associated genes in a cost-effective manner compared to whole exome sequencing. Although several studies have focused on the diagnostic yield of CES, no study has assessed predictors of CES utility among patients with various Mendelian phenotypes. We assessed the effectiveness of CES as a first-level genetic test for molecular diagnosis in patients with a Mendelian phenotype and explored independent predictors of the clinical utility of CES. RESULTS Between January 2016 and December 2019, 603 patients (426 probands and 177 siblings) underwent CES at the Department of Molecular Medicine of the University Hospital of Nancy. The median age of the probands was 34 years (IQR, 12-48), and the proportion of males was 46.9% (200/426). Adults and children represented 64.8% (276/426) and 35.2% (150/426), respectively. The median test-to-report time was 5.6 months (IQR, 4.1-7.2). CES revealed 203 pathogenic or likely pathogenic variants in 160 patients, corresponding to a diagnostic yield of 37.6% (160/426). Independent predictors of CES utility were criteria strongly suggestive of an extreme phenotype, including pediatric presentation and patient phenotypes associated with an increased risk of a priori probability of a monogenic disorder, the inclusion of at least one family member in addition to the proband, and a CES prescription performed by an expert in the field of rare genetic disorders. CONCLUSIONS Based on a large dataset of consecutive patients with various Mendelian phenotypes referred for CES as a first-tier genetic test, we report a diagnostic yield of ~ 40% and several independent predictors of CES utility that might improve CES diagnostic efficiency.
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Affiliation(s)
- Tom Alix
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France
| | - Céline Chéry
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Thomas Josse
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France
| | - Jean-Pierre Bronowicki
- grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Department of Gastroenterology and Liver Diseases, University Hospital of Nancy, 54000 Nancy, France
| | - François Feillet
- grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Department of Pediatrics, University Hospital of Nancy, 54000 Nancy, France
| | - Rosa-Maria Guéant-Rodriguez
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Farès Namour
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Jean-Louis Guéant
- Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000, Nancy, France. .,INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France. .,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.
| | - Abderrahim Oussalah
- Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000, Nancy, France. .,INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France. .,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.
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Jia A, Lei Y, Liu DP, Pan L, Guan HZ, Yang B. A Retrospective Analysis of Clinically Focused Exome Sequencing Results of 372 Infants with Suspected Monogenic Disorders in China. Pharmgenomics Pers Med 2023; 16:81-97. [PMID: 36755623 PMCID: PMC9901461 DOI: 10.2147/pgpm.s387767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Objective The context was designed to optimize the diagnostic utility of clinically focused exome sequencing (CFES) and shorten the diagnostic odyssey among pediatric patients suspected of monogenic disorders (MDs). Methods Here, we retrospectively analyzed the clinical notes of 372 patients from different areas in the Jiangxi province that were referred for a diagnostic CFES and analysis from June 2018 to March 2022 with symptoms suggestive of MDs. In our study, preliminary tests using the proband-only clinical exome sequencing as a cost-effective first-tier diagnostic test for pediatric patients with unidentified MDs, supplemented by family segregation studies for targeted variants when indicated. Results Probands with confirmed diagnostic (CD) or likely diagnostic (LD) genetic influences accounted for 12% of all cases, whereas those with an uncertain diagnosis accounted for 48%. We also found that systemic primary carnitine deficiency (CDSP) (SLC22A5 gene) and phenylketonuria (PAH gene) were relatively more prevalent, and these patients with CDSP had the most frequent c.1400C > G variant (p.S467C) and c.51C > G variant (p. F17L) in this study. In addition, statistical analysis revealed that the estimates of diagnostic yields varied across certain phenotypic features of patients, and patients with specific phenotypic traits tended to benefit more from CFES. Conclusion The CFES may be a first-line genetic test for diagnosing young children with suspected genetic conditions, as it validates the identification of molecular genetics alterations and facilitates comprehensive medical management. Moreover, we found that infants exhibiting metabolism/homeostasis abnormalities, craniofacial /otolaryngology/ ophthalmologic abnormalities, and/or the integument were significantly more likely to receive a genetic diagnosis via CFES than infants without such features. However, due to the current study's low diagnostic yield and inherent limitations, high-quality clinical studies with larger sample sizes are still needed to provide more likely results and confirm our findings.
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Affiliation(s)
- An Jia
- Medical School, Huanghe Science and Technology College, Zhengzhou, People’s Republic of China
| | - Yi Lei
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Dan-Ping Liu
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Lu Pan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Hui-Zhen Guan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Bicheng Yang
- Medical School, Huanghe Science and Technology College, Zhengzhou, People’s Republic of China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China,Correspondence: Bicheng Yang, Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, People’s Republic of China, Tel +86 15350402147, Email
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7
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Walsh M, West K, Taylor JA, Thompson BA, Hopkins A, Sexton A, Ragunathan A, Verma KP, Panetta J, Matotek E, Fahey MC, Christie M, Winship IM, Trainer AH, James PA. Real world outcomes and implementation pathways of exome sequencing in an adult genetic department. Genet Med 2022; 24:1536-1544. [PMID: 35416776 DOI: 10.1016/j.gim.2022.03.010] [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: 11/17/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE This study aimed to correlate the indications and diagnostic yield of exome sequencing (ES) in adult patients across various clinical settings. The secondary aim was to examine the clinical utility of ES in adult patients. METHODS Data on demographics, clinical indications, results, management changes, and cascade testing were collected for 250 consecutive patients who underwent ES through an adult genetics department between 2016 and 2021. Data were analyzed using descriptive and inferential statistics. Testing in which traditional gene panels were in standard use, such as in heritable cancers, was excluded. RESULTS The average age at testing was 43 years (range = 17-80 years). A molecular diagnosis was identified in 29% of patients. Older age at symptom onset did not pre-exclude a substantial diagnostic yield. Patients with syndromic intellectual disability and multiple system disorders had the highest yield. In >50% of patients with an exome diagnosis, the results changed management. Cascade testing occured in at least one family member for 30% of patients with a diagnosis. Diagnostic results had reproductive implications for 26% of patients and 31% of patients' relatives. CONCLUSION ES has a robust diagnostic yield and clear clinical utility in adult patients across a range of ages and phenotypes.
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Affiliation(s)
- Maie Walsh
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Kirsty West
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Jessica A Taylor
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Adelaide Hopkins
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Adrienne Sexton
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Abiramy Ragunathan
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Kunal P Verma
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Julie Panetta
- Metabolic Diseases Unit (MDU), The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ebony Matotek
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael C Fahey
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael Christie
- Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia; Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Alison H Trainer
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul A James
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
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8
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Huang L, Zhang L, Li X, Lu J, Sun L, Chen L, Ding X, Li Z. Ocular manifestations of Chinese patients with copy number variants in the NDP gene. Mol Vis 2022; 28:29-38. [PMID: 35656167 PMCID: PMC9108013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 03/23/2022] [Indexed: 12/04/2022] Open
Abstract
PURPOSE Familial exudative vitreoretinopathy (FEVR) and Norrie disease (ND) are genetic disorders that can be caused by mutations in the NDP gene and affect retinal vasculature growth and development. This study aimed to describe the copy number variations (CNVs) in the NDP gene in Chinese FEVR families and the associated phenotypes. METHODS This study recruited 651 FEVR families. SeqCNV was used to analyze the CNVs in the families without mutations in known FEVR-associated genes. Multiplex ligation-dependent probe amplification and semiquantitative multiplex PCR were performed to verify the NDP CNVs. The probands and family members underwent complete ocular examinations. RESULTS NDP CNVs were identified in four patients from three unrelated families, accounting for 15% of the patients with NDP mutations and 0.46% of the entire FEVR cohort. Exon 2 deletions were detected in two families, and whole gene deletion was identified in one family. The affected individuals were born blind with total retinal detachment. CONCLUSIONS The findings confirm that CNVs are a common NDP mutation type. The CNV-associated phenotype is congenital blindness with total retinal detachment. Antenatal genetic analyses and fetal ultrasound can facilitate early diagnosis and interventions in patients with NDP mutations.
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Affiliation(s)
- Li Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Linyan Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyu Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jinglin Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Limei Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Limei Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhan Li
- Zhuhai Women and Children's Hospital, Zhuhai, China
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9
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Yang L, Wei Z, Chen X, Hu L, Peng X, Wang J, Lu C, Kong Y, Dong X, Ni Q, Lu Y, Wu B, Wang H, Meirelles K, Tian X, Zhang J, Chang F, Liu L, Li C, You W, Cheng G, Wang L, Cao Y, Chen C, Fang P, Tang S, Zhou W. Use of medical exome sequencing for identification of underlying genetic defects in NICU: Experience in a cohort of 2303 neonates in China. Clin Genet 2021; 101:101-109. [PMID: 34671977 DOI: 10.1111/cge.14075] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 12/17/2022]
Abstract
Emerging evidence demonstrates the clinical utility of genomic applications in newborn intensive care unit (NICU) patients with strong indications of Mendelian etiology. However, such applications' diagnostic yield and utility remain unclear for NICU cohorts with minimal phenotype selection. In this study, focused medical exome sequencing was used as a first-tier, singleton-focused diagnostic tool for 2303 unrelated sick neonates. Integrated analysis of single nucleotide variants (SNVs), small insertions and deletions (Indels), and large copy number variants (CNVs) was performed. The diagnostic rate in this NICU cohort is 12.3% (284/2303), with 190 probands with molecular diagnoses made from SNV/Indel analyses (66.9%), 93 patients with diagnostic aneuploidy/CNVs findings (32.8%), and 1 patient with both SNV and CNV (0.4%). In addition, 54 (2.3%) of patients had a reportable incidental finding. Multiple organ involvements, craniofacial abnormalities, and dermatologic abnormalities were the strongest positive predictors for a molecular diagnosis. Among the 190 cases with SNV/Indel defects, direct impacts on medical management were observed in 46.8% of patients after the results were reported. In this study, we demonstrate that focused medical exome sequencing is a powerful first-line diagnostic tool for NICU patients. Significant number of diagnosed NICU patients can benefit from more focused medical management and long-term care.
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Affiliation(s)
- Lin Yang
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Zejun Wei
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Xiang Chen
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaomin Peng
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Wang
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Chunmei Lu
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Yanting Kong
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Qi Ni
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, China
| | | | - Xia Tian
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | | | - Liu Liu
- Sema4, Branford, Connecticut, USA
| | | | - Wesley You
- Google LLC, Mountain View, California, USA
| | - Guoqiang Cheng
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Chao Chen
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Ping Fang
- KingMed Diagnostics, Guangzhou, China
| | - Sha Tang
- KingMed Diagnostics, Guangzhou, China
| | - Wenhao Zhou
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China.,Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Shanghai, China
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10
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Diagnosing newborns with suspected mitochondrial disorders: an economic evaluation comparing early exome sequencing to current typical care. Genet Med 2021; 23:1854-1863. [PMID: 34040192 DOI: 10.1038/s41436-021-01210-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/03/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To determine the value of early exome sequencing (eES) relative to the current typical care (TC) in the diagnosis of newborns with suspected severe mitochondrial disorders (MitD). METHODS We used a decision tree-Markov hybrid to model neonatal intensive care unit (NICU)-related outcomes and costs, lifetime costs and quality-adjusted life-years among patients with MitD. Probabilities, costs, and utilities were populated using published literature, expert opinion, and the Pediatric Health Information System database. Incremental cost-effectiveness ratios (ICER) and net monetary benefits (NMB) were calculated from lifetime costs and quality-adjusted life-years for singleton and trio eES, and TC. Robustness was assessed using univariate and probabilistic sensitivity analyses (PSA). Scenario analyses were also conducted. RESULTS Findings indicate trio eES is a cost-minimizing and cost-effective alternative to current TC. Diagnostic probabilities and NICU length-of-stay were the most sensitive model parameters. Base case analysis demonstrates trio eES has the highest incremental NMB, and PSA demonstrates trio eES had the highest likelihood of being cost-effective at a willingness-to-pay (WTP) of $200,000 relative to TC, singleton eES, and no ES. CONCLUSION Trio and singleton eES are cost-effective and cost-minimizing alternatives to current TC in diagnosing newborns suspected of having a severe MitD.
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11
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Hong S, Wang L, Zhao D, Zhang Y, Chen Y, Tan J, Liang L, Zhu T. Clinical utility in infants with suspected monogenic conditions through next-generation sequencing. Mol Genet Genomic Med 2019; 7:e684. [PMID: 30968598 PMCID: PMC6565546 DOI: 10.1002/mgg3.684] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/06/2019] [Accepted: 03/04/2019] [Indexed: 12/14/2022] Open
Abstract
Background Rare diseases are complex disorders with huge variability in clinical manifestations. Decreasing cost of next‐generation sequencing (NGS) tests in recent years made it affordable. We witnessed the diagnostic yield and clinical use of different NGS strategies on a myriad of monogenic disorders in a pediatric setting. Methods Next‐generation sequencing tests are performed for 98 unrelated Chinese patients within their first year of life, who were admitted to Xin Hua Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, during a 2‐year period. Results Clinical indications for NGS tests included a range of medical concerns. The mean age was 4.4 ± 4.2 months of age for infants undergoing targeting specific (known) disease‐causing genes (TRS) analysis, and 4.4 ± 4.3 months of age for whole‐exome sequencing (WES) (p > 0.05). A molecular diagnosis is done in 72 infants (73.47%), which finds a relatively high yield with phenotypes of metabolism/homeostasis abnormality (HP: 0001939) (odds ratio, 1.83; 95% CI, 0.56–6.04; p = 0.32) and a significantly low yield with atypical symptoms (without a definite HPO term) (odds ratio, 0.08; 95% CI, 0.01–0.73; p = 0.03). TRS analysis provides molecular yields higher than WES (p = 0.01). Ninety‐eight different mutations are discovered in 72 patients. Twenty‐seven of them have not been reported previously. Nearly half (43.06%, 31/72) of the patients are found to carry 11 common disorders, mostly being inborn errors of metabolism (IEM) and neurogenetic disorders and all of them are observed through TRS analysis. Eight positive cases are identified through WES, and all of them are sporadic, of highly variable phenotypes and severity. There are 26 patients with negative findings in this study. Conclusion This study provides evidence that NGS can yield high success rates in a tertiary pediatric setting, but suggests that the scope of known Mendelian conditions may be considerably broader than currently recognized.
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Affiliation(s)
- Sha Hong
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Wang
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongying Zhao
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yonghong Zhang
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Chen
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jintong Tan
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lili Liang
- Department of Endocrinology and Genetic Metabolism, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianwen Zhu
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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