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Maver A, Lohmann K, Borovečki F, Wolstenholme N, Taylor RL, Spielmann M, Haack TB, Gerberding M, Peterlin B, Graessner H. Quality assurance for next-generation sequencing diagnostics of rare neurological diseases in the European Reference Network. Eur J Hum Genet 2024; 32:1014-1021. [PMID: 38839988 PMCID: PMC11292006 DOI: 10.1038/s41431-024-01639-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/26/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024] Open
Abstract
In the past decade, next-generation sequencing (NGS) has revolutionised genetic diagnostics for rare neurological disorders (RND). However, the lack of standardised technical, interpretative, and reporting standards poses a challenge for ensuring consistent and high-quality diagnostics globally. To address this, the European Reference Network for Rare Neurological Diseases (ERN-RND) collaborated with the European Molecular Genetics Quality Network (EMQN) to establish an external quality assessment scheme for NGS-based diagnostics in RNDs. The scheme, initiated in 2021 with a pilot involving 29 labs and followed by a second round in 2022 with 42 labs, aimed to evaluate the performance of laboratories in genetic testing for RNDs. Each participating lab analysed genetic data from three hypothetical cases, assessing genotyping, interpretation, and clerical accuracy. Despite a majority of labs using exome or genome sequencing, there was considerable variability in gene content, sequencing quality, adherence to standards, and clinical guidance provision. Results showed that while most labs provided correct molecular diagnoses, there was significant variability in reporting technical quality, adherence to interpretation standards, reporting strategies, and clinical commentary. Notably, some labs returned results with the potential for adverse medical outcomes. This underscores the need for further harmonisation, guideline development, and external quality assessment in the evolving landscape of genomic diagnostics for RNDs. Overall, the experience with the scheme highlighted the generally good quality of participating labs but emphasised the imperative for ongoing improvement in data analysis, interpretation, and reporting to enhance patient safety.
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Affiliation(s)
- Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katja Lohmann
- Institute of Neurogenetics, University of Luebeck, Luebeck, Germany
| | - Fran Borovečki
- Department of Neurology, University Hospital Centre Zagreb, Zagreb, Croatia
| | | | - Rachel L Taylor
- EMQN CIC, Unit 4 Enterprise Hse, Manchester Science Park, Manchester, UK
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Matthias Gerberding
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany.
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2
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Berkalieva A, Kelly NR, Fisher A, Hohmann SF, Sebastin M, Di Biase M, Bonini KE, Marathe P, Odgis JA, Suckiel SA, Ramos MA, Rhodes R, Abul-Husn NS, Greally JM, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD, Ferket BS. Physician services and costs after disclosure of diagnostic sequencing results in the NYCKidSeq program. Genet Med 2024; 26:101011. [PMID: 37897232 PMCID: PMC10842442 DOI: 10.1016/j.gim.2023.101011] [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: 06/30/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
PURPOSE To better understand the effects of returning diagnostic sequencing results on clinical actions and economic outcomes for pediatric patients with suspected genetic disorders. METHODS Longitudinal physician claims data after diagnostic sequencing were obtained for patients aged 0 to 21 years with neurologic, cardiac, and immunologic disorders with suspected genetic etiology. We assessed specialist consultation rates prompted by primary diagnostic results, as well as marginal effects on overall 18-month physician services and costs. RESULTS We included data on 857 patients (median age: 9.6 years) with a median follow-up of 17.3 months after disclosure of diagnostic sequencing results. The likelihood of having ≥1 recommendation for specialist consultation in 155 patients with positive findings was high (72%) vs 23% in 443 patients with uncertain findings and 21% in 259 patients with negative findings (P < .001). Follow-through consultation occurred in 30%. Increases in 18-month physician services and costs following a positive finding diminished after multivariable adjustment. Also, no significant differences between those with uncertain and negative findings were demonstrated. CONCLUSION Our study did not provide evidence for significant increases in downstream physician services and costs after returning positive or uncertain diagnostic sequencing findings. More large-scale longitudinal studies are needed to confirm these findings.
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Affiliation(s)
- Asem Berkalieva
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R Kelly
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Monisha Sebastin
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Miranda Di Biase
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katherine E Bonini
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Priya Marathe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jacqueline A Odgis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sabrina A Suckiel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michelle A Ramos
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Rosamond Rhodes
- Department of Education, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; 23andMe Inc, Sunnyvale, CA
| | - John M Greally
- Division of Genomics, Department of Genetics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Carol R Horowitz
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY; Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa P Wasserstein
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Division for Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Bart S Ferket
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY.
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3
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Cole JJ, Sellitto AD, Baratta LR, Huecker JB, Balls-Berry JE, Gurnett CA. Social Determinants of Genetics Referral and Completion Rates Among Child Neurology Patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295450. [PMID: 37745339 PMCID: PMC10516043 DOI: 10.1101/2023.09.12.23295450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Objective To investigate clinical, social, and systems-level determinants predictive of genetics clinic referral and completion of genetics clinic visits among child neurology patients. Methods Electronic health record data were extracted from patients 0-18 years old who were evaluated in child neurology clinics at a single tertiary care institution between July 2018 to January 2020. Variables aligned with the Health Equity Implementation Framework. Referral and referral completion rates to genetics and cardiology clinics were compared among Black vs White patients using bivariate analysis. Demographic variables associated with genetics clinic referral and visit completion were identified using logistic regressions. Results In a cohort of 11,371 child neurology patients, 304 genetics clinic referrals and 82 cardiology clinic referrals were placed. In multivariate analysis of patients with Black or White ethnoracial identity (n=10,601), genetics clinic referral rates did not differ by race, but were significantly associated with younger age, rural address, neurodevelopmental disorder diagnosis, number of neurology clinic visits, and provider type. The only predictors of genetics clinic visit completion number of neurology clinic visits and race/ethnicity, with White patients being twice as likely as Black patients to complete the visit. Cardiology clinic referrals and visit completion did not differ by race/ethnicity. Interpretation Although race/ethnicity was not associated with differences in genetics clinic referral rates, White patients were twice as likely as Black patients to complete a genetics clinic visit after referral. Further work is needed to determine whether this is due to systemic/structural racism, differences in attitudes toward genetic testing, or other factors.
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Affiliation(s)
- Jordan J Cole
- Washington University in St. Louis, Department of Neurology
- University of Colorado, Department of Pediatrics
| | | | | | - Julia B Huecker
- Washington University in St. Louis, Center for Biostatistics & Data Science
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4
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Fishler KP, Steber HS, Brunelli L, Shope RJ. Exploring collaboration models between geneticists and intensivists for implementing rapid genome sequencing in critical care settings. Am J Med Genet A 2023; 191:2290-2299. [PMID: 37318250 DOI: 10.1002/ajmg.a.63318] [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: 02/16/2023] [Revised: 04/13/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023]
Abstract
The availability of rapid genome sequencing (rGS) for children in a critical-care setting is increasing. This study explored the perspectives of geneticists and intensivists on optimal collaboration and division of roles when implementing rGS in neonatal and pediatric intensive care units (ICUs). We conducted an explanatory mixed methods study involving a survey embedded within an interview with 13 genetics and intensive care providers. Interviews were recorded, transcribed, and coded. Geneticists endorsed higher confidence in performing a physical exam and interpreting/communicating positive results. Intensivists endorsed highest confidence in determining whether genetic testing was appropriate, communicating negative results, and consenting. Major qualitative themes that emerged were: (1) concerns with both "genetics-led" and "intensivist-led" models with workflows and sustainability (2) shift the role of determining rGS eligibility to ICU medical professionals, (3) continued role of geneticists to assess phenotype, and (4) include genetic counselors (GCs) and neonatal nurse practitioners to enhance workflow and care. All geneticists supported shifting decisions regarding eligibility for rGS to the ICU team to minimize time cost for the genetics workforce. Exploring models of geneticist-led phenotyping, intensivist-led phenotyping for some indications, and/or inclusion of a dedicated inpatient GC may help offset the time burden of consenting and other tasks associated with rGS.
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Affiliation(s)
- Kristen P Fishler
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Hannah S Steber
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Luca Brunelli
- Division of Neonatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Ronald J Shope
- College of Allied Health Professions, University of Nebraska Medical Center, Omaha, Nebraska, USA
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5
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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6
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Evaluation of Individuals with Non-Syndromic Global Developmental Delay and Intellectual Disability. CHILDREN 2023; 10:children10030414. [PMID: 36979972 PMCID: PMC10047567 DOI: 10.3390/children10030414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/11/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Global Developmental Delay (GDD) and Intellectual Disability (ID) are two of the most common presentations encountered by physicians taking care of children. GDD/ID is classified into non-syndromic GDD/ID, where GDD/ID is the sole evident clinical feature, or syndromic GDD/ID, where there are additional clinical features or co-morbidities present. Careful evaluation of children with GDD and ID, starting with detailed history followed by a thorough examination, remain the cornerstone for etiologic diagnosis. However, when initial history and examination fail to identify a probable underlying etiology, further genetic testing is warranted. In recent years, genetic testing has been shown to be the single most important diagnostic modality for clinicians evaluating children with non-syndromic GDD/ID. In this review, we discuss different genetic testing currently available, review common underlying copy-number variants and molecular pathways, explore the recent evidence and recommendations for genetic evaluation and discuss an approach to the diagnosis and management of children with non-syndromic GDD and ID.
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7
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Lee G, Yu L, Suarez CJ, Stevenson DA, Ling A, Killer L. Factors associated with the time to complete clinical exome sequencing in a pediatric patient population. Genet Med 2022; 24:2028-2033. [PMID: 35951015 DOI: 10.1016/j.gim.2022.06.006] [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: 01/21/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
PURPOSE Exome sequencing (ES) is becoming increasingly important for diagnosing rare genetic disorders. Patients and clinicians face several barriers when attempting to obtain ES. This study is aimed to describe factors associated with a longer time interval between provider recommendation of testing and sample collection for ES. METHODS A retrospective chart review was conducted for insurance-authorized, completed pediatric ES in which initial requests were reviewed by Stanford's Genetic Testing Optimization Service between November 2018 and December 2019. Regression analysis was used to determine the association between the geocoded median household income and 3 different time point intervals defined as time to test, insurance decision, and scheduling/consent. RESULTS Of the 281 charts reviewed, 115 cases were included in the final cohort. The average time from provider preauthorization request to sample collection took 104.4 days, and income was negatively correlated with the length of the insurance decision interval. CONCLUSION Pediatric patients undergo a lengthy, uncertain process when attempting to obtain ES, some of which is associated with income. More research and clinician interventions are required to clarify specific socioeconomic factors that influence the ability to obtain timely ES and develop optimal protocols.
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Affiliation(s)
- Gabriella Lee
- Human Genetics and Genetic Counseling Master's Program, Stanford Medicine, Stanford, CA
| | - Linbo Yu
- Stanford Hospitals and Clinics Genetic Testing Optimization Service, Stanford Medicine, Stanford, CA
| | - Carlos J Suarez
- Stanford Hospitals and Clinics Genetic Testing Optimization Service, Stanford Medicine, Stanford, CA; Department of Pathology, Stanford University, Stanford, CA
| | - David A Stevenson
- Stanford Hospitals and Clinics Genetic Testing Optimization Service, Stanford Medicine, Stanford, CA; Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA
| | - Albee Ling
- Quantitative Sciences Unit, Stanford University, Palo Alto, CA
| | - Lindsay Killer
- Stanford Hospitals and Clinics Genetic Testing Optimization Service, Stanford Medicine, Stanford, CA.
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8
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Wang Q, Tang X, Yang K, Huo X, Zhang H, Ding K, Liao S. Deep phenotyping and whole-exome sequencing improved the diagnostic yield for nuclear pedigrees with neurodevelopmental disorders. Mol Genet Genomic Med 2022; 10:e1918. [PMID: 35266334 PMCID: PMC9034680 DOI: 10.1002/mgg3.1918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 02/18/2022] [Accepted: 02/25/2022] [Indexed: 12/21/2022] Open
Abstract
Background Neurodevelopmental disorders, a group of early‐onset neurological disorders with significant clinical and genetic heterogeneity, remain a diagnostic challenge for clinical genetic evaluation. Therefore, we assessed the diagnostic yield by combining standard phenotypes and whole‐exome sequencing in families with these disorders that were “not yet diagnosed” by the traditional testing methods. Methods Using a standardized vocabulary of phenotypic abnormalities from human phenotype ontology (HPO), we performed deep phenotyping for 45 “not yet diagnosed” pedigrees to characterize multiple clinical features extracted from Chinese electronic medical records (EMRs). By matching HPO terms with known human diseases and phenotypes from model organisms, together with whole‐exome sequencing data, we prioritized candidate mutations/genes. We made probable genetic diagnoses for the families. Results We obtained a diagnostic yield of 29% (13 out of 45) with probably genetic diagnosis, of which compound heterozygosity and de novo mutations accounted for 77% (10/13) of the diagnosis. Of note, these pedigrees are accompanied by a more significant number of non‐neurological features. Conclusions Deep phenotyping and whole‐exome sequencing improve the etiological evaluation for neurodevelopmental disorders in the clinical setting.
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Affiliation(s)
- Qingqing Wang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Xia Tang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Ke Yang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Xiaodong Huo
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Hui Zhang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Keyue Ding
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.,NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, China
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9
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P. Fishler K, Euteneuer JC, Brunelli L. Ethical Considerations for Equitable Access to Genomic Sequencing for Critically Ill Neonates in the United States. Int J Neonatal Screen 2022; 8:ijns8010022. [PMID: 35323201 PMCID: PMC8950005 DOI: 10.3390/ijns8010022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Rare diseases impact all socio-economic, geographic, and racial groups indiscriminately. Newborn screening (NBS) is an exemplary international public health initiative that identifies infants with rare conditions early in life to reduce morbidity and mortality. NBS theoretically promotes equity through universal access, regardless of financial ability. There is however heterogeneity in access to newborn screening and conditions that are screened throughout the world. In the United States and some other developed countries, NBS is provided to all babies, subsidized by the local or federal government. Although NBS is an equitable test, infants admitted to neonatal intensive care units (NICUs) may not receive similar benefits to healthier infants. Newborns in the NICU may receive delayed and/or multiple newborn screens due to known limitations in interpreting the results with prematurity, total parenteral nutrition, blood transfusions, infection, and life support. Thus, genomic technologies might be needed in addition to NBS for equitable care of this vulnerable population. Whole exome (WES) and genome sequencing (WGS) have been recently studied in critically ill newborns across the world and have shown promising results in shortening diagnostic odysseys and providing clinical utility. However, in certain circumstances several barriers might limit access to these tests. Here, we discuss some of the existing barriers to genomic sequencing in NICUs in the United States, explore the ethical implications related to low access, consider ways to increase access to genomic testing, and offer some suggestions for future research in these areas.
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Affiliation(s)
- Kristen P. Fishler
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence:
| | | | - Luca Brunelli
- Division of Neonatology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA;
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10
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AlQudairy H, AlDhalaan H, AlRuways S, AlMutairi N, AlNakiyah M, AlGhofaili R, AlBakheet A, Alomrani A, Alharbi OA, Tous E, AlSayed M, AlZaidan H, AlRasheed MM, AlOdaib A, Kaya N. Clinical, radiological, and genetic characterization of SLC13A5 variants in Saudi families: Genotype phenotype correlation and brief review of the literature. Front Pediatr 2022; 10:1051534. [PMID: 36923948 PMCID: PMC10008858 DOI: 10.3389/fped.2022.1051534] [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: 09/22/2022] [Accepted: 12/14/2022] [Indexed: 03/03/2023] Open
Abstract
Background SLC13A5 (solute carrier family 13, member 5) encodes sodium/citrate cotransporter, which mainly localizes in cellular plasma membranes in the frontal cortex, retina, and liver. Pathogenic variants of the gene cause an autosomal recessive syndrome known as "developmental and epileptic encephalopathy 25 with amelogenesis imperfecta." Results Here, we have investigated six patients from three different consanguineous Saudi families. The affected individuals presented with neonatal seizures, developmental delay, and significant defects in tooth development. Some patients showed other clinical features such as muscle weakness, motor difficulties, intellectual disability, microcephaly, and speech problems in addition to additional abnormalities revealed by electroencephalography (EEGs) and magnetic resonance imaging (MRI). One of the MRI findings was related to cortical thickening in the frontal lobe. To diagnose and study the genetic defects of the patients, whole exome sequencing (WES) coupled with confirmatory Sanger sequencing was utilized. Iterative filtering identified two variants of SLC13A5, one of which is novel, in the families. Families 1 and 2 had the same insertion (a previously reported mutation), leading to a frameshift and premature stop codon. The third family had a novel splice site variant. Confirmatory Sanger sequencing corroborated WES results and indicated full segregation of the variants in the corresponding families. The patients' conditions were poorly controlled by multiple antiepileptics as they needed constant care. Conclusion Considering that recessive mutations are common in the Arab population, SLC13A5 screening should be prioritized in future patients harboring similar symptoms including defects in molar development.
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Affiliation(s)
- Hanan AlQudairy
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia
| | | | - Sarah AlRuways
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Nouf AlMutairi
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Maha AlNakiyah
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | - Reema AlGhofaili
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia.,College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia
| | | | | | - Omar A Alharbi
- Department of Neurosciences, KFSHRC, Riyadh, Saudi Arabia
| | - Ehab Tous
- Department of Neurosciences, KFSHRC, Riyadh, Saudi Arabia
| | - Moeen AlSayed
- Department of Medical Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Hamad AlZaidan
- Department of Medical Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Maha M AlRasheed
- College of Pharmacy, King Saud University (KSU), Riyadh, Saudi Arabia.,Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali AlOdaib
- Training and Education Department, Research Centre, KFSHRC, Riyadh, Saudi Arabia
| | - Namik Kaya
- Translational Genomic Department, Center for Genomic Medicine, King Faisal Specialist Hospital, and Research Centre (KFSHRC), Riyadh, Saudi Arabia
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11
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Olde Keizer RACM, Henneman L, Ploos van Amstel JK, Vissers LELM, Frederix GWJ. Economic evaluations of exome and genome sequencing in pediatric genetics: considerations towards a consensus strategy. J Med Econ 2021; 24:60-70. [PMID: 34915793 DOI: 10.1080/13696998.2021.2009725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Next Generation Sequencing (NGS) is increasingly used for the diagnosis of rare genetic disorders. The aim of this study is to review the different approaches for economic evaluations of Next Generation Sequencing (NGS) in pediatric care used to date, to identify all costs, effects, and time horizons taken into account. METHODS A systematic literature review was conducted to identify published economic evaluations of NGS applications in pediatric diagnostics, i.e. exome sequencing (ES) and/or genome sequencing (GS). Information regarding methodological approach, costs, effects, and time horizon was abstracted from these publications. RESULTS Twenty-eight economic evaluations of ES/GS within pediatrics were identified. Costs included were mainly restricted to direct in-hospital healthcare costs and varied widely in inclusion of sort of costs and time-horizon. Nineteen studies included diagnostic yield and eight studies included cost-effectiveness as outcome measures. Studies varied greatly in terms of included sort of costs data, effects, and time horizon. CONCLUSION Large differences in inclusion of cost and effect parameters were identified between studies. Validity of outcomes can therefore be questioned, which hinders valid comparison and widespread generalization of conclusions. In addition to current health economic guidance, specific guidance for evaluations in pediatric care is therefore necessary to improve the validity of outcomes and furthermore facilitate comparable decision-making for implementing novel NGS-based diagnostic modalities in pediatric genetics and beyond.
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Affiliation(s)
- Richelle A C M Olde Keizer
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Lidewij Henneman
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Gerardus W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
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12
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Exome Sequencing in 200 Intellectual Disability/Autistic Patients: New Candidates and Atypical Presentations. Brain Sci 2021; 11:brainsci11070936. [PMID: 34356170 PMCID: PMC8303733 DOI: 10.3390/brainsci11070936] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 01/07/2023] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) belong to neurodevelopmental disorders and occur in ~1% of the general population. Due to disease heterogeneity, identifying the etiology of ID and ASD remains challenging. Exome sequencing (ES) offers the opportunity to rapidly identify variants associated with these two entities that often co-exist. Here, we performed ES in a cohort of 200 patients: 84 with isolated ID and 116 with ID and ASD. We identified 41 pathogenic variants with a detection rate of 22% (43/200): 39% in ID patients (33/84) and 9% in ID/ASD patients (10/116). Most of the causative genes are genes responsible for well-established genetic syndromes that have not been recognized for atypical phenotypic presentations. Two genes emerged as new candidates: CACNA2D1 and GPR14. In conclusion, this study reinforces the importance of ES in the diagnosis of ID/ASD and underlines that “reverse phenotyping” is fundamental to enlarge the phenotypic spectra associated with specific genes.
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13
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Exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:2029-2037. [PMID: 34211152 DOI: 10.1038/s41436-021-01242-6] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE To develop an evidence-based clinical practice guideline for the use of exome and genome sequencing (ES/GS) in the care of pediatric patients with one or more congenital anomalies (CA) with onset prior to age 1 year or developmental delay (DD) or intellectual disability (ID) with onset prior to age 18 years. METHODS The Pediatric Exome/Genome Sequencing Evidence-Based Guideline Work Group (n = 10) used the Grading of Recommendations Assessment, Development and Evaluation (GRADE) evidence to decision (EtD) framework based on the recent American College of Medical Genetics and Genomics (ACMG) systematic review, and an Ontario Health Technology Assessment to develop and present evidence summaries and health-care recommendations. The document underwent extensive internal and external peer review, and public comment, before approval by the ACMG Board of Directors. RESULTS The literature supports the clinical utility and desirable effects of ES/GS on active and long-term clinical management of patients with CA/DD/ID, and on family-focused and reproductive outcomes with relatively few harms. Compared with standard genetic testing, ES/GS has a higher diagnostic yield and may be more cost-effective when ordered early in the diagnostic evaluation. CONCLUSION We strongly recommend that ES/GS be considered as a first- or second-tier test for patients with CA/DD/ID.
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14
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Grant P, Langlois S, Lynd LD, Austin JC, Elliott AM. Out-of-pocket and private pay in clinical genetic testing: A scoping review. Clin Genet 2021; 100:504-521. [PMID: 34080181 DOI: 10.1111/cge.14006] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/19/2022]
Abstract
Full coverage of the cost of clinical genetic testing is not always available through public or private insurance programs, or a public healthcare system. Consequently, some patients may be faced with the decision of whether to finance testing out-of-pocket (OOP), meet OOP expenses required by their insurer, or not proceed with testing. A scoping review was conducted to identify literature associated with patient OOP and private pay in clinical genetic testing. Seven databases (EMBASE, MEDLINE, CINAHL, PsychINFO, PAIS, the Cochrane Database of Systematic Reviews, and the JBI Evidence-Based Practice database) were searched, resulting in 83 unique publications included in the review. The presented evidence includes a descriptive analysis, followed by a narrative account of the extracted data. Results were divided into four groups according to clinical indication: (1) hereditary breast and ovarian cancer, (2) other hereditary cancers, (3) prenatal testing, (4) other clinical indications. The majority of studies focused on hereditary cancer and prenatal genetic testing. Overall trends indicated that OOP costs have fallen and payer coverage has improved, but OOP expenses continue to present a barrier to patients who do not qualify for full coverage.
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Affiliation(s)
- Peter Grant
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia (BC), Canada
| | - Sylvie Langlois
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia (BC), Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Jehannine C Austin
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia (BC), Canada.,Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.,BC Mental Health and Substance Use Services Research Institute, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia (BC), Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Women's Health Research Institute, Vancouver, British Columbia, Canada
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15
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Hiraide T, Yamoto K, Masunaga Y, Asahina M, Endoh Y, Ohkubo Y, Matsubayashi T, Tsurui S, Yamada H, Yanagi K, Nakashima M, Hirano K, Sugimura H, Fukuda T, Ogata T, Saitsu H. Genetic and phenotypic analysis of 101 patients with developmental delay or intellectual disability using whole-exome sequencing. Clin Genet 2021; 100:40-50. [PMID: 33644862 DOI: 10.1111/cge.13951] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 12/20/2022]
Abstract
Whole-exome sequencing (WES) enables identification of pathogenic variants, including copy number variants (CNVs). In this study, we performed WES in 101 Japanese patients with unexplained developmental delay (DD) or intellectual disability (ID) (63 males and 38 females), 98 of them with trio-WES. Pathogenic variants were identified in 54 cases (53.5%), including four cases with pathogenic CNVs. In one case, a pathogenic variant was identified by reanalysis of exome data; and in two cases, two molecular diagnoses were identified. Among 58 pathogenic variants, 49 variants occurred de novo in 48 patients, including two somatic variants. The accompanying autism spectrum disorder and external ear anomalies were associated with detection of pathogenic variants with odds ratios of 11.88 (95% confidence interval [CI] 2.52-56.00) and 3.46 (95% CI 1.23-9.73), respectively. These findings revealed the importance of reanalysis of WES data and detection of CNVs and somatic variants in increasing the diagnostic yield for unexplained DD/ID. In addition, genetic testing is recommended when patients suffer from the autism spectrum disorder or external ear anomalies, which potentially suggests the involvement of genetic factors associated with gene expression regulation.
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Affiliation(s)
- Takuya Hiraide
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kaori Yamoto
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yohei Masunaga
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Miki Asahina
- Department of Pediatrics, Hamamatsu City Welfare and Medical Center for Development, Hamamatsu, Japan
| | - Yusaku Endoh
- Department of Pediatrics, Hamamatsu City Welfare and Medical Center for Development, Hamamatsu, Japan
| | - Yumiko Ohkubo
- Department of Pediatrics, Shizuoka Saiseikai Hospital, Shizuoka, Japan
| | - Tomoko Matsubayashi
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Pediatric Neurology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Satoshi Tsurui
- Department of Pediatrics, Seirei-Numazu Hospital, Numazu, Japan
| | - Hidetaka Yamada
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kouichi Hirano
- Department of Pediatrics, Hamamatsu City Welfare and Medical Center for Development, Hamamatsu, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tokiko Fukuda
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
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16
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Abstract
Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.
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Affiliation(s)
- Juliann M. Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States
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17
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Atli EI, Atli E, Yalcintepe S, Demir S, Kalkan R, Eker D, Gurkan H. Customized Targeted Massively Parallel Sequencing Enables More Precisely Diagnosis of Patients with Epilepsy. Intern Med J 2021; 52:1174-1184. [PMID: 33528079 DOI: 10.1111/imj.15219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Advancement in genetic technology has led to the identification of an increasing number of genes in epilepsy. This will provide a huge information in clinical practice and improve diagnosis and treatment of epilepsy. METHODS this was a single-center retrospective cohort study of 80 patients who underwent NGS testing with customize epilepsy panel. RESULTS In total 54 out of 80 patients (67, 5%), pathogenic / likely pathogenic and variants of uncertain significance variants were identified according to ACMG criteria. Pathogenic or likely pathogenic variants (n=35) were identified in 29 out of 80 individuals (36.25%). Variants of uncertain significance (VOUS) (n=34) have identified in 28 out of 80 patients (35%). Pathogenic, likely pathogenic, and variants of uncertain significance (VOUS) were most frequently identified in TSC2 (n = 11), SCN1A (n = 6) and TSC1 (n = 5) genes. Other common genes were KCNQ2 (n = 3), AMT (n = 3), CACNA1H (n = 3), CLCN2 (n = 3), MECP2 (n = 2), ASAH1 (n = 2) and SLC2A1 (n = 2). CONCLUSIONS NGS based testing panels contributes the diagnosis of epilepsy and may change the clinical management by preventing unnecessary and potentially harmful diagnostic procedures and management in patients. Thus, our results highlighted the benefit of genetic testing in children suffered with epilepsy. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Emine Ikbal Atli
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Engin Atli
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Sinem Yalcintepe
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Selma Demir
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Rasime Kalkan
- Faculty of Medicine, Department of Medical Genetics, Near East University, Nicosia, Cyprus
| | - Damla Eker
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Hakan Gurkan
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
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18
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Schiavoni S, Spagnoli C, Rizzi S, Salerno GG, Frattini D, Pisani F, Fusco C. Paediatric-onset hereditary spastic paraplegias: a retrospective cohort study. Dev Med Child Neurol 2020; 62:1068-1074. [PMID: 32277485 DOI: 10.1111/dmcn.14547] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 12/12/2022]
Abstract
AIM To describe the clinical and neurogenetic spectrum of paediatric-onset hereditary spastic paraplegias (HSPs) diagnosed in our unit. METHOD We report on 47 patients (30 males, 17 females; mean [SD] age 12y 7mo [6y 2mo], range 4-34y) clinically diagnosed with an HSP at the Child Neurology Unit, IRCCS-ASMN (Reggio Emilia, Italy) between 1990 and 2018, who were genetically investigated by means of single-gene direct sequencing and/or next-generation sequencing technologies (targeted panels, whole-exome sequencing [WES]). RESULTS Complex forms prevailed slightly (n=26), autosomal dominant being the main inheritance pattern (n=11), followed by recessive (n=5) and X-linked (n=1). A definite genetic diagnosis was achieved in 17 patients. Spastic paraplegia 3A (n=4) was the most frequent cause of autosomal dominant HSP in our cohort, while no genetic variant prevailed in autosomal recessive forms and pathogenic/likely pathogenic variants were disclosed in a wide range of different genes. INTERPRETATION We found wide phenotypic and genetic heterogeneity. With increasing accessibility to WES, a higher number of patients receive a diagnosis, allowing detection of variants in ultra-rare disease-causing genes and refining genotype-phenotype correlations. WHAT THIS PAPER ADDS A genetic diagnosis of paediatric-onset hereditary spastic paraplegia was achieved in one-third of patients. Pathogenic/likely pathogenic variants in rare genes were found. Genotypic and phenotypic heterogeneity favours targeted panel/whole-exome sequencing for diagnosis.
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Affiliation(s)
- Silvia Schiavoni
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Carlotta Spagnoli
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Susanna Rizzi
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Grazia G Salerno
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Daniele Frattini
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Francesco Pisani
- Child Neuropsychiatry Unit, Neuroscience Division, Medicine & Surgery Department, University of Parma, Parma, Italy
| | - Carlo Fusco
- Child Neurology Unit, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy.,Paediatric Neurophysiology Laboratory, Department of Paediatrics, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
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19
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Michelson DJ, Clark RD. Optimizing Genetic Diagnosis of Neurodevelopmental Disorders in the Clinical Setting. Clin Lab Med 2020; 40:231-256. [PMID: 32718497 DOI: 10.1016/j.cll.2020.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Progress in medical genetics has changed the practice of medicine in general and child neurology in particular. A genetic diagnosis has become critically important in determining optimal management of many neurodevelopmental disorders, making genetic testing a routine consideration of patient care in outpatient and inpatient settings. Today's child neurologists should be familiar with various genetic testing modalities and their appropriate use. Molecular genetic testing of children with unexplained developmental delays and/or congenital anomalies has a 20% to 30% chance of identifying a causative etiology. Newer methods have made genetic testing more widely available and sensitive but also more likely to produce ambiguous results.
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Affiliation(s)
- David Joshua Michelson
- Division of Child Neurology, Department of Pediatrics, Loma Linda University School of Medicine, Coleman Pavilion Room A, 1175 Campus Street, Loma Linda, CA 92354, USA.
| | - Robin Dawn Clark
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Coleman Pavilion Room A, 1175 Campus Street, Loma Linda, CA 92354, USA
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20
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Painous C, van Os NJH, Delamarre A, Michailoviene I, Marti MJ, van de Warrenburg BP, Meissner WG, Utkus A, Reinhard C, Graessner H, Tijssen MA. Management of rare movement disorders in Europe: outcome of surveys of the European Reference Network for Rare Neurological Diseases. Eur J Neurol 2020; 27:1493-1500. [PMID: 32386078 PMCID: PMC7496702 DOI: 10.1111/ene.14302] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023]
Abstract
Background and purpose The diagnosis of rare movement disorders is difficult and specific management programmes are not well defined. Thus, in order to capture and assess care needs, the European Reference Network for Rare Neurological Diseases has performed an explorative care need survey across all European Union (EU) countries. Methods This is a multicentre, cross‐sectional study. A survey about the management of different rare movement disorders (group 1, dystonia, paroxysmal dyskinesia and neurodegeneration with brain iron accumulation; group 2, ataxias and hereditary spastic paraparesis; group 3, atypical parkinsonism; group 4, choreas) was sent to an expert in each group of disorders from each EU country. Results Some EU countries claimed for an increase of teaching courses. Genetic testing was not readily available in a significant number of countries. Regarding management, patients’ accessibility to tertiary hospitals, to experts and to multidisciplinary teams was unequal between countries and groups of diseases. The availability of therapeutic options, such as botulinum toxin or more invasive treatments like deep brain stimulation, was limited in some countries. Conclusions The management of these conditions in EU countries is unequal. The survey provides evidence that a European care‐focused network that is able to address the unmet rare neurological disease care needs and inequalities is highly warranted.
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Affiliation(s)
- C Painous
- Neurology Service, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic Universitari, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - N J H van Os
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A Delamarre
- Institut des Maladies Neurodégénératives, UMR 5293, Université de Bordeaux, Bordeaux, France.,UMR 5293, CNRS, Institut des Maladies Neurodégénératives, Bordeaux, France
| | - I Michailoviene
- Faculty of Medicine, Institute of Biomedical Sciences, Vilnius, Vilnius University, Lithuania
| | - M J Marti
- Neurology Service, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic Universitari, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - B P van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - W G Meissner
- Institut des Maladies Neurodégénératives, UMR 5293, Université de Bordeaux, Bordeaux, France.,UMR 5293, CNRS, Institut des Maladies Neurodégénératives, Bordeaux, France.,Department of Medicine, University of Otago, Christchurch, New Zealand.,New Zealand Brain Research Institute, Christchurch, New Zealand
| | - A Utkus
- Faculty of Medicine, Institute of Biomedical Sciences, Vilnius, Vilnius University, Lithuania
| | - C Reinhard
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - H Graessner
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - M A Tijssen
- Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Expertise Center Movement Disorders Groningen, University Medical Center Groningen, Groningen, The Netherlands
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21
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Estimating the costs of genomic sequencing in cancer control. BMC Health Serv Res 2020; 20:492. [PMID: 32493298 PMCID: PMC7268398 DOI: 10.1186/s12913-020-05318-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 05/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the rapid uptake of genomic technologies within cancer care, few studies provide detailed information on the costs of sequencing across different applications. The objective of the study was to examine and categorise the complete costs involved in genomic sequencing for a range of applications within cancer settings. METHODS We performed a cost-analysis using gross and micro-costing approaches for genomic sequencing performed during 2017/2018 across different settings in Brisbane, Australia. Sequencing was undertaken for patients with lung, breast, oesophageal cancers, melanoma or mesothelioma. Aggregated resource data were captured for a total of 1433 patients and point estimates of per patient costs were generated. Deterministic sensitivity analyses addressed the uncertainty in the estimates. Estimated costs to the public health system for resources were categorised into seven distinct activities in the sequencing process: sampling, extraction, library preparation, sequencing, analysis, data storage and clinical reporting. Costs were also aggregated according to labour, consumables, testing, equipment and 'other' categories. RESULTS The per person costs were AU$347-429 (2018 US$240-297) for targeted panels, AU$871-$2788 (2018 US$604-1932) for exome sequencing, and AU$2895-4830 (2018 US$2006-3347) for whole genome sequencing. Cost proportions were highest for library preparation/sequencing materials (average 76.8% of total costs), sample extraction (8.1%), data analysis (9.2%) and data storage (2.6%). Capital costs for the sequencers were an additional AU$34-197 (2018 US$24-67) per person. CONCLUSIONS Total costs were most sensitive to consumables and sequencing activities driven by commercial prices. Per person sequencing costs for cancer are high when tumour/blood pairs require testing. Using the natural steps involved in sequencing and categorising resources accordingly, future evaluations of costs or cost-effectiveness of clinical genomics across cancer projects could be more standardised and facilitate easier comparison of cost drivers.
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22
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Luksic D, Sukhu R, Koval C, Cho MT, Espinal A, Rufino K, Loarte TV, Chung WK, Wynn J. A qualitative study of Latinx parents' experiences of clinical exome sequencing. J Genet Couns 2020; 29:574-586. [PMID: 32298033 DOI: 10.1002/jgc4.1276] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 01/29/2023]
Abstract
Clinical exome sequencing (CES) is an established method for genetic diagnosis and is used widely in clinical practice. Studies of the parental experience of CES, which inform guidelines for best practices for genetic counseling, have been predominately comprised of White, non-Latinx participants. The aim of this study was to explore the parental experiences of CES in a Latinx community and to understand how their experiences are influenced by culture and language. We conducted semi-structured interviews in English and Spanish with 38 Latinx parents of children who had CES. Some of the themes that emerged were common to those previously identified, including a sense of obligation to pursue testing and a mixed emotional response to their child's results. Parents who had lower education level and/or received care from a provider who did not share their language had more confusion about their child's CES results and greater dissatisfaction with care compared with parents who had higher education level and/or received care from a provider who spoke their language. We also found evidence of hampered shared decision making and/or disempowered patient decision making regarding CES testing. Our data suggest unique needs for Latinx families having CES, particularly those who are non-English speaking when an interpreter is used. Our data support the value in continuing to take steps to improve culturally competent care by improving interpretation services and recruiting and training a genetic workforce that is ethnically, linguistically, and culturally diverse.
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Affiliation(s)
- Daniel Luksic
- Graduate School of Genetic Counseling, Sarah Lawrence College, Bronxville, NY, USA
| | - Radha Sukhu
- Graduate School of Genetic Counseling, Sarah Lawrence College, Bronxville, NY, USA
| | - Carrie Koval
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Megan T Cho
- Graduate School of Genetic Counseling, Sarah Lawrence College, Bronxville, NY, USA
| | - Aileen Espinal
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Katiana Rufino
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Tania Vasquez Loarte
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
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23
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Blesson A, Cohen JS. Genetic Counseling in Neurodevelopmental Disorders. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036533. [PMID: 31501260 DOI: 10.1101/cshperspect.a036533] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neurodevelopmental disorders (NDDs), including global developmental delay (GDD), intellectual disability (ID), and autism spectrum disorder (ASD), represent a continuum of developmental brain dysfunction. Although the etiology of NDD is heterogeneous, genetic variation represents the largest contribution, strongly supporting the recommendation for genetic evaluation in individuals with GDD/ID and ASD. Technological advances now allow for a specific genetic diagnosis to be identified in a substantial portion of affected individuals. This information has important ramifications for treatment, prognosis, and recurrence risk, as well as psychological and social benefits for the family. Genetic counseling is a vital service to enable patients and their families to understand and adapt to the genetic contribution to NDDs. As the demand for genetic evaluation for NDDs increases, genetic counselors will have a predominant role in the ongoing evaluation of NDDs, especially as identification of genetic etiologies has the potential to lead to targeted treatments for NDDs in the future.
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Affiliation(s)
- Alyssa Blesson
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, Maryland 21211, USA
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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24
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Malinowski J, Miller DT, Demmer L, Gannon J, Pereira EM, Schroeder MC, Scheuner MT, Tsai ACH, Hickey SE, Shen J. Systematic evidence-based review: outcomes from exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability. Genet Med 2020; 22:986-1004. [PMID: 32203227 PMCID: PMC7222126 DOI: 10.1038/s41436-020-0771-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/31/2022] Open
Abstract
Purpose Exome and genome sequencing (ES/GS) are performed frequently in patients with congenital anomalies, developmental delay, or intellectual disability (CA/DD/ID), but the impact of results from ES/GS on clinical management and patient outcomes is not well characterized. A systematic evidence review (SER) can support future evidence-based guideline development for use of ES/GS in this patient population. Methods We undertook an SER to identify primary literature from January 2007 to March 2019 describing health, clinical, reproductive, and psychosocial outcomes resulting from ES/GS in patients with CA/DD/ID. A narrative synthesis of results was performed. Results We retrieved 2654 publications for full-text review from 7178 articles. Only 167 articles met our inclusion criteria, and these were primarily case reports or small case series of fewer than 20 patients. The most frequently reported outcomes from ES/GS were changes to clinical management or reproductive decision-making. Two studies reported on the reduction of mortality or morbidity or impact on quality of life following ES/GS. Conclusion There is evidence that ES/GS for patients with CA/DD/ID informs clinical and reproductive decision-making, which could lead to improved outcomes for patients and their family members. Further research is needed to generate evidence regarding health outcomes to inform robust guidelines regarding ES/GS in the care of patients with CA/DD/ID.
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Affiliation(s)
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Laurie Demmer
- Atrium Health's Levine Children's Hospital, Charlotte, NC, USA
| | - Jennifer Gannon
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri, Kansas City, MO, USA
| | - Elaine Maria Pereira
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Molly C Schroeder
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maren T Scheuner
- Division of Medical Genetics, Department of Pediatrics and Division of Hematology-Oncology, Department of Medicine, University of California, San Francisco, CA, USA.,San Francisco VA Healthcare System, San Francisco, CA, USA
| | - Anne Chun-Hui Tsai
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Scott E Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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25
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Burdick KJ, Cogan JD, Rives LC, Robertson AK, Koziura ME, Brokamp E, Duncan L, Hannig V, Pfotenhauer J, Vanzo R, Paul MS, Bican A, Morgan T, Duis J, Newman JH, Hamid R, Phillips JA. Limitations of exome sequencing in detecting rare and undiagnosed diseases. Am J Med Genet A 2020; 182:1400-1406. [PMID: 32190976 DOI: 10.1002/ajmg.a.61558] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/28/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
Abstract
While exome sequencing (ES) is commonly the final diagnostic step in clinical genetics, it may miss diagnoses. To clarify the limitations of ES, we investigated the diagnostic yield of genetic tests beyond ES in our Undiagnosed Diseases Network (UDN) participants. We reviewed the yield of additional genetic testing including genome sequencing (GS), copy number variant (CNV), noncoding variant (NCV), repeat expansion (RE), or methylation testing in UDN cases with nondiagnostic ES results. Overall, 36/54 (67%) of total diagnoses were based on clinical findings and coding variants found by ES and 3/54 (6%) were based on clinical findings only. The remaining 15/54 (28%) required testing beyond ES. Of these, 7/15 (47%) had NCV, 6/15 (40%) CNV, and 2/15 (13%) had a RE or a DNA methylation disorder. Thus 18/54 (33%) of diagnoses were not solved exclusively by ES. Several methods were needed to detect and/or confirm the functional effects of the variants missed by ES, and in some cases by GS. These results indicate that tests to detect elusive variants should be considered after nondiagnostic preliminary steps. Further studies are needed to determine the cost-effectiveness of tests beyond ES that provide diagnoses and insights to possible treatment.
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Affiliation(s)
- Kendall J Burdick
- University of Massachusetts of Medical School, Worcester, Massachusetts, USA
| | - Joy D Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lynette C Rives
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Amy K Robertson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mary E Koziura
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laura Duncan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Vickie Hannig
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jean Pfotenhauer
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rena Vanzo
- Lineagen Inc., Salt Lake City, Utah, USA
| | | | - Anna Bican
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Thomas Morgan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jessica Duis
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John H Newman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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26
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Froukh T, Nafie O, Al Hait SAS, Laugwitz L, Sommerfeld J, Sturm M, Baraghiti A, Issa T, Al-Nazer A, Koch PA, Hanselmann J, Kootz B, Bauer P, Al-Ameri W, Abou Jamra R, Alfrook AJ, Hamadallah M, Sofan L, Riess A, Haack TB, Riess O, Buchert R. Genetic basis of neurodevelopmental disorders in 103 Jordanian families. Clin Genet 2020; 97:621-627. [PMID: 32056211 DOI: 10.1111/cge.13720] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/15/2020] [Accepted: 02/05/2020] [Indexed: 10/25/2022]
Abstract
We recruited 103 families from Jordan with neurodevelopmental disorders (NDD) and patterns of inheritance mostly suggestive of autosomal recessive inheritance. In each family, we investigated at least one affected individual using exome sequencing and an in-house diagnostic variant interpretation pipeline including a search for copy number variation. This approach led us to identify the likely molecular defect in established disease genes in 37 families. We could identify 25 pathogenic nonsense and 11 missense variants as well as 3 pathogenic copy number variants and 1 repeat expansion. Notably, 11 of the disease-causal variants occurred de novo. In addition, we prioritized a homozygous frameshift variant in PUS3 in two sisters with intellectual disability. To our knowledge, PUS3 has been postulated only recently as a candidate disease gene for intellectual disability in a single family with three affected siblings. Our findings provide additional evidence to establish loss of PUS3 function as a cause of intellectual disability.
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Affiliation(s)
- Tawfiq Froukh
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Omar Nafie
- Faculty of Medicine, Mutah University, Alkarak, Jordan
| | | | - Lucia Laugwitz
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Julia Sommerfeld
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Aya Baraghiti
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Tala Issa
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Anis Al-Nazer
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Philipp A Koch
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Johannes Hanselmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Beate Kootz
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | | | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany
| | | | | | - Linda Sofan
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Angelika Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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27
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Fahr P, Buchanan J, Wordsworth S. A Review of Health Economic Studies Comparing Traditional and Massively Parallel Sequencing Diagnostic Pathways for Suspected Genetic Disorders. PHARMACOECONOMICS 2020; 38:143-158. [PMID: 31741314 DOI: 10.1007/s40273-019-00856-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Genetic disorders are clinically diverse and genetically heterogeneous, and are traditionally diagnosed based on an iterative phenotype-guided genetic assessment. However, such diagnostic approaches are long (diagnostic odysseys are common), misdiagnoses occur frequently, and diagnostic rates are low. Massively parallel sequencing (MPS) technologies may improve diagnostic rates and reduce the time to diagnosis for patients with suspected genetic disorders; however, MPS technologies are expensive and the health economic evidence base to support their use is limited. Several studies have compared the costs of traditional and MPS diagnostic pathways for patients with suspected genetic disorders, however costing methods and diagnostic scenarios are heterogeneous across studies. We conducted a literature review to identify and summarise information on these costing methods and diagnostic scenarios. Relevant studies were identified in MEDLINE, EMBASE, EconLit, University of York Centre for Reviews and Dissemination and the Cochrane Library, from 2010 to 2018. Twenty-four articles were included in the review. We observed considerable heterogeneity across studies with respect to the selection of items of resource use used to derive total diagnostic pathway cost estimates. We also observed structural differences in the diagnostic scenarios used to compare the traditional and MPS diagnostic pathways. There is a need for guidelines on the costing of diagnostic pathways to encourage the use of consistent methods. More micro-costing studies that evaluate diagnostic service delivery are also required. Greater homogeneity in costing approaches would facilitate more reliable comparisons between studies and improve the transferability of cost estimates across countries.
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Affiliation(s)
- Patrick Fahr
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK.
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
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28
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Scala M, Bianchi A, Bisulli F, Coppola A, Elia M, Trivisano M, Pruna D, Pippucci T, Canafoglia L, Lattanzi S, Franceschetti S, Nobile C, Gambardella A, Michelucci R, Zara F, Striano P. Advances in genetic testing and optimization of clinical management in children and adults with epilepsy. Expert Rev Neurother 2020; 20:251-269. [PMID: 31941393 DOI: 10.1080/14737175.2020.1713101] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Epileptic disorders are a heterogeneous group of medical conditions with epilepsy as the common denominator. Genetic causes, electro-clinical features, and management significantly vary according to the specific condition.Areas covered: Relevant diagnostic advances have been achieved thanks to the advent of Next Generation Sequencing (NGS)-based molecular techniques. These revolutionary tools allow to sequence all coding (whole exome sequencing, WES) and non-coding (whole genome sequencing, WGS) regions of human genome, with a potentially huge impact on patient care and scientific research.Expert opinion: The application of these tests in children and adults with epilepsy has led to the identification of new causative genes, widening the knowledge on the pathophysiology of epilepsy and resulting in therapeutic implications. This review will explore the most recent advancements in genetic testing and provide up-to-date approaches for the choice of the correct test in patients with epilepsy.
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Affiliation(s)
- Marcello Scala
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Amedeo Bianchi
- Division of Neurology, Hospital San Donato Arezzo, Arezzo, Italy
| | - Francesca Bisulli
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bologna, Italy; Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Antonietta Coppola
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy
| | - Maurizio Elia
- Unit of Neurology and Clinical Neurophysiopathology, IRCCS Oasi Research Institute, Troina, Italy
| | - Marina Trivisano
- Neurology Unit, Department of Neuroscience, IRCCS Bambino Gesù Children's Hospital, Rome, Italy.,Clinic of Nervous System Diseases, University of Foggia, Foggia, Italy
| | - Dario Pruna
- Epilepsy Unit, A. Cao Hospital, Cagliari, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, Polyclinic Sant' Orsola-Malpighi University Hospital, Bologna, Italy
| | | | - Simona Lattanzi
- Neurological Clinic, Department of Experimental and Clinical Medicine, Marche Polytechnic University, Ancona, Italy
| | | | - Carlo Nobile
- CNR-Neuroscience Institute and Department of Biomedical Sciences (C.N.), University of Padua, Padua, Italy
| | - Antonio Gambardella
- Dipartimento Di Scienze Mediche E Chirurgiche, Università Della Magna Graecia, Catanzaro, Istituto Di Scienze Neurologiche CNR Mangone, Cosenza, Italy
| | - Roberto Michelucci
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Ospedale Bellaria, Bologna, Italy
| | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
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29
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Manor J, Lalani SR. Overgrowth Syndromes-Evaluation, Diagnosis, and Management. Front Pediatr 2020; 8:574857. [PMID: 33194904 PMCID: PMC7661798 DOI: 10.3389/fped.2020.574857] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
Abnormally excessive growth results from perturbation of a complex interplay of genetic, epigenetic, and hormonal factors that orchestrate human growth. Overgrowth syndromes generally present with inherent health concerns and, in some instances, an increased risk of tumor predisposition that necessitate prompt diagnosis and appropriate referral. In this review, we introduce some of the more common overgrowth syndromes, along with their molecular mechanisms, diagnostics, and medical complications for improved recognition and management of patients affected with these disorders.
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Affiliation(s)
- Joshua Manor
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Seema R Lalani
- Department of Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
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30
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Glöcklhofer CR, Steinfurt J, Franke G, Hoppmann A, Glantschnig T, Perez-Feliz S, Alter S, Fischer J, Brunner M, Rainer PP, Köttgen A, Bode C, Odening KE. A novel LMNA nonsense mutation causes two distinct phenotypes of cardiomyopathy with high risk of sudden cardiac death in a large five-generation family. Europace 2019; 20:2003-2013. [PMID: 29947763 DOI: 10.1093/europace/euy127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/09/2018] [Indexed: 12/19/2022] Open
Abstract
Aims Characterization of the cardiac phenotype associated with the novel LMNA nonsense mutation c.544C>T, p.Q182*, which we have identified in a large five-generation family. Methods and results A family tree was constructed. Clinical data [arrhythmia, syncope, sudden cardiac death (SCD), New York Heart Association (NYHA) class] were collected from living and deceased family members. DNA of 23 living family members was analysed for mutations in LMNA. Additionally, dilated cardiomyopathy multi-gene-panel testing and whole exome sequencing were performed in some family members to identify potential phenotype-modifiers. In this five-generation family (n = 65), 17 SCDs occurred at 49.3 ± 10.0 years. Furthermore, we identified eight additional mutation-carriers, seven symptomatic (44 ± 13 years), and one asymptomatic (44 years). First signs of disease [sinus bradycardia with atrioventricular (AV)-block I°] occurred at 36.5 ± 8.1 years. Paroxysmal atrial fibrillation (AF) (onset at 41.8 ± 5.7 years) rapidly progressed to permanent AF (46.2 ± 9.8 years). Subsequently, AV-conduction worsened, syncope, pacemaker-dependence, and non-sustained ventricular tachycardia (43.3 ± 8.2 years) followed. Ventricular arrhythmia caused SCD in patients without implantable cardioverter-defibrillator (ICD). Patients protected by ICD developed rapidly progressive heart failure (45.2 ± 10.6 years). A different phenotype was seen in a sub-family in three patients with early onset of rapidly decompensating heart failure and only minor prior arrhythmia-related symptoms. One patient received high-urgency heart transplantation (HTX) at 32 years, while two died prior to HTX. One of them developed lethal peripartum-associated heart failure. Possible disease-modifiers were identified in this 'heart failure sub-family'. Conclusion The novel LMNA nonsense mutation c.544C>T causes a severe arrhythmogenic phenotype manifesting with high incidence of SCD in most patients; and in one sub-family, a distinct phenotype with fast progressing heart failure, indicating the need for early consideration of ICD-implantation and listing for heart-transplantation.
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Affiliation(s)
- Christina R Glöcklhofer
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Johannes Steinfurt
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gerlind Franke
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anselm Hoppmann
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Genetic Epidemiology, Medical Center University of Freiburg, Freiburg, Germany.,Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Stefanie Perez-Feliz
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Svenja Alter
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Human Genetics, Medical Center University of Freiburg, Freiburg, Germany
| | - Judith Fischer
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Human Genetics, Medical Center University of Freiburg, Freiburg, Germany
| | - Michael Brunner
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter P Rainer
- Division of Cardiology, Medical University of Graz, Graz, Austria
| | - Anna Köttgen
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Genetic Epidemiology, Medical Center University of Freiburg, Freiburg, Germany
| | - Christoph Bode
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katja E Odening
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
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31
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Abstract
Genomic testing has become routine in the diagnosis and management of pediatric patients with epilepsy. In a single test, hundreds to thousands of genes are examined for DNA changes that may not only explain the etiology of the patient's condition but may also inform management and seizure control. Clinical genomic testing has been in clinical practice for less than a decade, and because of this short period of time, the appropriate clinical use and interpretation of genomic testing is still evolving. Compared to the previous era of single-gene testing in epilepsy, which yielded a diagnosis in <5% of cases, many clinical genomic studies of epilepsy have demonstrated a clinically significant diagnosis in 30% or more of patients tested. This review will examine key studies of the past decade and indicate the clinical scenarios in which genomic testing should be considered standard of care.
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Affiliation(s)
- Drew M Thodeson
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, Texas 75235, USA
| | - Jason Y Park
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas 75235, USA.,Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75235, USA
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32
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Ma Y, Pei Y, Yin C, Jiang Y, Wang J, Li X, Li L, Kagan KO, Wu Q. Subchromosomal anomalies in small for gestational-age fetuses and newborns. Arch Gynecol Obstet 2019; 300:633-639. [PMID: 31273521 DOI: 10.1007/s00404-019-05235-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/27/2019] [Indexed: 11/29/2022]
Abstract
PURPOSE To analyze copy number variants (CNVs) in subjects with small for gestational age (SGA) in China. METHODS A total of 85 cases with estimated fetal weight (EFW) or birth weight below the 10th percentile for gestational age were recruited, including SGA associated with structural anomalies (Group A, n = 20) and isolated SGA (Group B, n = 65). In all cases, cytogenetic karyotyping and infection screening were normal. We examined DNA from fetuses (amniocentesis or cordocentesis) and newborns (cord blood) to detect CNVs using a single nucleotide polymorphism (SNP, n = 75) array or low-pass whole-genome sequencing (WGS, n = 10). RESULTS Of 85 total cases, 3 (4%) carried pathogenic chromosomal abnormalities, including 2 cases with pathological CNVs and 1 case with upd(22)pat. In Group A, the mean gestational age at the time of diagnosis was 26.8 (SD 4.1) weeks and mean EFW/birth weight was 907.2 (SD 567.8) g. In Group B, the mean gestational age at the time of diagnosis was 34.1 (SD 5.8) weeks. Mean EFW/birth weight was 1879.2 (SD 714.5) g. The pathologic detection rate was 10% (2/20) in Group A and 2% (1/65) in Group B. It was inclined that the lower the EFW percentile, the more frequent the occurrence of CNVs. CONCLUSIONS Pathological subchromosomal anomalies were detected by CMA or low-pass WGS in 10% and 2% of SGA subjects with and without malformation, respectively. SGA fetuses with structural anomalies presented with higher pathological subchromosomal anomalies. The molecular genetic analysis is not recommended for isolated SGA pregnancies without other abnormal findings.
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Affiliation(s)
- Ying Ma
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, China
| | - Yan Pei
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, China
| | - Chenghong Yin
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, China
| | - Yuxin Jiang
- Department of Ultrasound, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jingjing Wang
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, 251 Yaojia Yuan Road, Chaoyang District, Beijing, 100026, China
| | - Xiaofei Li
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, 251 Yaojia Yuan Road, Chaoyang District, Beijing, 100026, China
| | - Lin Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, China
| | - Karl Oliver Kagan
- Department of Women'S Health, University of Tuebingen, Tübingen, Germany
| | - Qingqing Wu
- Department of Ultrasound, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, 251 Yaojia Yuan Road, Chaoyang District, Beijing, 100026, China.
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33
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Srivastava S, Love-Nichols JA, Dies KA, Ledbetter DH, Martin CL, Chung WK, Firth HV, Frazier T, Hansen RL, Prock L, Brunner H, Hoang N, Scherer SW, Sahin M, Miller DT. Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Genet Med 2019; 21:2413-2421. [PMID: 31182824 PMCID: PMC6831729 DOI: 10.1038/s41436-019-0554-6] [Citation(s) in RCA: 338] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
Purpose For neurodevelopmental disorders (NDDs), etiological evaluation can
be a diagnostic odyssey involving numerous genetic tests, underscoring the need
to develop a streamlined algorithm maximizing molecular diagnostic yield for
this clinical indication. Our objective was to compare the yield of exome
sequencing (ES) with that of chromosomal microarray (CMA), the current
first-tier test for NDDs. Methods We performed a PubMed scoping review and meta-analysis investigating
the diagnostic yield of ES for NDDs as the basis of a consensus development
conference. We defined NDD as global developmental delay, intellectual
disability, and/or autism spectrum disorder. The consensus development
conference included input from genetics professionals, pediatric neurologists,
and developmental behavioral pediatricians. Results After applying strict inclusion/exclusion criteria, we identified 30
articles with data on molecular diagnostic yield in individuals with isolated
NDD, or NDD plus associated conditions (such as Rett-like features). Yield of ES
was 36% overall, 31% for isolated NDD, and 53% for the NDD plus associated
conditions. ES yield for NDDs is markedly greater than previous studies of CMA
(15–20%). Conclusion Our review demonstrates that ES consistently outperforms CMA for
evaluation of unexplained NDDs. We propose a diagnostic algorithm placing ES at
the beginning of the evaluation of unexplained NDDs.
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Affiliation(s)
- Siddharth Srivastava
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jamie A Love-Nichols
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kira A Dies
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David H Ledbetter
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA.,SFARI, Simons Foundation, New York, NY, USA
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Robin L Hansen
- MIND Institute, Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - Lisa Prock
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Developmental Medicine Center, Boston Children's Hospital, Boston, MA, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.,The Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ny Hoang
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre and Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mustafa Sahin
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
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Macnamara EF, Schoch K, Glanton E, Fieg E, Brokamp E, Signer R, LeBlanc K, McConkie-Rosell A, Palmer CGS. Cases from the Undiagnosed Diseases Network: The continued value of counseling skills in a new genomic era. J Genet Couns 2019; 28:194-201. [PMID: 30680851 PMCID: PMC6456366 DOI: 10.1002/jgc4.1091] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 01/15/2023]
Abstract
The "diagnostic odyssey" is well known and described in genetic counseling literature. Studies addressing the psychological, emotional, and financial costs of not having a diagnosis have shown how it permeates the lives of patients and families. The Undiagnosed Diseases Network aims to end this odyssey by providing diagnoses to individuals with undiagnosed conditions through multidisciplinary evaluations, whole exome and genome sequencing, and basic science research. It also provides an opportunity to learn from patients and families and to better understand their journeys and the impact of receiving a diagnosis. Seven cases are presented that outline challenges that come from working with chronically undiagnosed and newly diagnosed patients in a time when sequencing for clinical diagnosis is rapidly increasing. They illuminate the emotional journey of patients and families searching for a diagnosis and the mental health problems, financial distress, and chaos that can accompany not having answers. They also illustrate the surprising reactions patients and families can have to receiving a diagnosis, including anger, grief, and disappointment. While the lessons learned from these families are not novel, new strategies are presented for handling these challenges in undiagnosed and ultra-rare populations, groups that will increase with the rise of clinical sequencing.
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Affiliation(s)
- Ellen F Macnamara
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland
| | - Kelly Schoch
- Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina
| | - Emily Glanton
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Fieg
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Elly Brokamp
- Division of Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Rebecca Signer
- Department of Human Genetics, University of California, Los Angeles, California
| | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina
| | - Christina G S Palmer
- Department of Human Genetics, University of California, Los Angeles, California
- Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles, California
- Institute for Society and Genetics, University of California, Los Angeles, California
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Yadava SM, Ashkinadze E. Whole exome sequencing for prenatal diagnosis in cases with fetal anomalies: Criteria to improve diagnostic yield. J Genet Couns 2018; 28:251-255. [PMID: 30629328 DOI: 10.1002/jgc4.1045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/30/2018] [Accepted: 10/06/2018] [Indexed: 01/31/2023]
Abstract
Whole exome sequencing (WES) for prenatal diagnosis has a reported diagnostic yield of 6.2%-57%. Our aim was to identify patients with a high likelihood of genetic diagnosis using WES in cases with fetal ultrasound anomalies. This is a series of five selected cases for prenatal WES at our institution. Pregnant couples were initially identified due to fetal ultrasound anomalies. Candidates for WES for fetal diagnosis had a normal fetal karyotype and negative microarray with at least one of the following: parental consanguinity, large regions of homozygosity on fetal microarray, or high likelihood of single gene disorder based on ultrasound findings. All trios underwent sequencing of parental and fetal samples. WES was diagnostic in four of the five cases (80%). We identified two recessive conditions and two de novo mutations. Four couples consented to secondary findings and in one case, the father was found to have an MSH2 mutation associated with Lynch syndrome. The use of specific selection criteria for WES increased diagnostic yield to 80%. This is higher than previously reported. Wide application of our criteria can help identify those who may benefit most from this testing in prenatal diagnosis.
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Affiliation(s)
- Stacy M Yadava
- Department of Obstetrics, Gynecology and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Elena Ashkinadze
- Department of Obstetrics, Gynecology and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
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36
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Exome sequencing in adult neurology practice: Challenges and rewards in a mixed resource setting. Clin Neurol Neurosurg 2018; 174:48-56. [DOI: 10.1016/j.clineuro.2018.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 12/17/2022]
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Michalska E, Koppolu A, Dobrzańska A, Płoski R, Gruszfeld D. A case of severe trichothiodystrophy 3 in a neonate due to mutation in the GTF2H5 gene: Clinical report. Eur J Med Genet 2018; 62:103557. [PMID: 30359777 DOI: 10.1016/j.ejmg.2018.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/12/2018] [Accepted: 10/20/2018] [Indexed: 01/08/2023]
Abstract
Trichothiodystrophy (TTD) is a group of predominantly autosomal recessive disorders characterized by sulfur-deficient brittle hair. Clinical features of TTD consist of variable neuroectodermal symptoms including ichthyosis, nail abnormalities, mental retardation, short stature, decreased fertility and proneness to infections. Approximately half of the reported patients with TTD have clinical and cellular photosensitivity associated with mutations in three subunits (ERCC3, ERCC2, GTF2H5) of the basal transcription factor TFHII, which is involved in transcription and nucleotide excision repair. We report on a case of a male neonate with a novel GTF2H5 gene mutation, detected by whole exome sequencing. The GTF2H5 gene's role is to provide stability to the entire TFHII complex. The reported patient was born at 33 weeks' gestation from a pregnancy complicated by intrauterine growth restriction and premature rupture of membranes. His main clinical problems included severe congenital ichthyosis and proneness to infections with episodes of multiorgan failure. The infant's history displays the most severe clinical manifestations among patients with GTF2H5 gene mutations that have so far been reported.
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Affiliation(s)
- Eliza Michalska
- Department of Neonatal Intensive Care, The Children's Memorial Health Institute, Poland.
| | - Agnieszka Koppolu
- Department of Medical Genetics, Warsaw Medical University, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Anna Dobrzańska
- Department of Neonatal Intensive Care, The Children's Memorial Health Institute, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Poland
| | - Dariusz Gruszfeld
- Department of Neonatal Intensive Care, The Children's Memorial Health Institute, Poland
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Santoro JD. 50 Years Ago in The Journal of Pediatrics: Abnormally Small Head Size and Intellect in Children. J Pediatr 2018; 201:159. [PMID: 30244726 DOI: 10.1016/j.jpeds.2018.03.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Jonathan D Santoro
- Neurology Lucile Packard Children's Hospital at Stanford Palo Alto, California
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Abstract
OBJECTIVES Pitt-Hopkins syndrome (PTHS) is a rare genetic disorder caused by insufficient expression of the TCF4 gene. Most cases are characterized by severe intellectual disability, absent speech, motor delays, and autism spectrum disorder. Many have abnormal brain imaging, dysmorphic facial features, and medical comorbidities: myopia, constipation, epilepsy, and apneic spells. The present case study expands existing understanding of this disorder by presenting a unique phenotype with higher cognitive abilities and fewer medical comorbidities. METHODS The present case study reports on a 13-year-old, Caucasian male with a recent diagnosis of PTHS following genetic testing (i.e., whole exome sequencing). He was referred for a neuropsychological evaluation to document his neurocognitive functioning to assist with intervention planning. RESULTS Evaluation of intellectual, attention/executive, memory, visual-motor/fine-motor, academic, adaptive, and emotional/behavioral functioning revealed global impairment across all areas of functioning. However, he demonstrated abilities beyond what has been detailed in the literature, including use of full sentences, capacity to learn and solve novel problems, basic academic functioning, and independent ambulation. CONCLUSIONS Children with PTHS may demonstrate a spectrum of abilities beyond what has been documented in the literature thus far. Failure to recognize this spectrum can result in late identification of an accurate diagnosis. (JINS, 2018, 24, 995-1002).
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40
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Douglas MP, Parker SL, Trosman JR, Slavotinek AM, Phillips KA. Private payer coverage policies for exome sequencing (ES) in pediatric patients: trends over time and analysis of evidence cited. Genet Med 2018; 21:152-160. [PMID: 29997388 PMCID: PMC6329652 DOI: 10.1038/s41436-018-0043-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/05/2018] [Indexed: 11/16/2022] Open
Abstract
Purpose Whole Exome Sequencing (WES) is being adopted for neurodevelopmental
disorders in pediatric patients. However, little is known about current
coverage policies or the evidence cited supporting these policies. Our study
is the first in-depth review of private payer WES coverage policies for
pediatric patients with neurodevelopmental disorders. Methods We reviewed private payer coverage policies and examined evidence
cited in the policies of the 15 largest payers in 2017, and trends in
coverage policies and evidence cited (2015 – 2017) for the five
largest payers. Results There were four relevant policies (N=5 payers) in 2015 and 13
policies (N=15 payers) in 2017. In 2015, no payer covered WES, but
by 2017, three payers from the original registry payers did. In 2017, eight
of the 15 payers covered WES. We found variations in the number and types of
evidence cited. Positive coverage policies tended to include a larger number
and range of citations. Conclusion We conclude that more systematic assessment of evidence cited in
coverage policies can provide a greater understanding of coverage policies
and how evidence is used. Such assessments could facilitate the ability of
researchers to provide the needed evidence, and the ability of clinicians to
provide the most appropriate testing for patients.
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Affiliation(s)
- Michael P Douglas
- University of California at San Francisco, Department of Clinical Pharmacy; Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), 3333 California St, Room 420, Box 0613, San Francisco, California, USA.
| | | | - Julia R Trosman
- Center for Business Models in Healthcare, San Francisco, California, USA
| | - Anne M Slavotinek
- University of California, San Francisco, Department of Pediatrics, San Francisco, California, USA
| | - Kathryn A Phillips
- University of California at San Francisco, Department of Clinical Pharmacy; Center for Translational and Policy Research on Personalized Medicine (TRANSPERS); UCSF Philip R. Lee Institute for Health Policy; and UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
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Smith HS, Swint JM, Lalani SR, Yamal JM, de Oliveira Otto MC, Castellanos S, Taylor A, Lee BH, Russell HV. Clinical Application of Genome and Exome Sequencing as a Diagnostic Tool for Pediatric Patients: a Scoping Review of the Literature. Genet Med 2018; 21:3-16. [PMID: 29760485 DOI: 10.1038/s41436-018-0024-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/20/2018] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Availability of clinical genomic sequencing (CGS) has generated questions about the value of genome and exome sequencing as a diagnostic tool. Analysis of reported CGS application can inform uptake and direct further research. This scoping literature review aims to synthesize evidence on the clinical and economic impact of CGS. METHODS PubMed, Embase, and Cochrane were searched for peer-reviewed articles published between 2009 and 2017 on diagnostic CGS for infant and pediatric patients. Articles were classified according to sample size and whether economic evaluation was a primary research objective. Data on patient characteristics, clinical setting, and outcomes were extracted and narratively synthesized. RESULTS Of 171 included articles, 131 were case reports, 40 were aggregate analyses, and 4 had a primary economic evaluation aim. Diagnostic yield was the only consistently reported outcome. Median diagnostic yield in aggregate analyses was 33.2% but varied by broad clinical categories and test type. CONCLUSION Reported CGS use has rapidly increased and spans diverse clinical settings and patient phenotypes. Economic evaluations support the cost-saving potential of diagnostic CGS. Multidisciplinary implementation research, including more robust outcome measurement and economic evaluation, is needed to demonstrate clinical utility and cost-effectiveness of CGS.
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Affiliation(s)
- Hadley Stevens Smith
- Baylor College of Medicine, The University of Texas School of Public Health, Houston, Texas, USA
| | - J Michael Swint
- The University of Texas School of Public Health, The Center for Clinical Research and Evidence-Based Medicine, The University of Texas McGovern Medical School, Houston, Texas, USA
| | - Seema R Lalani
- Baylor College of Medicine, Baylor Genetics Laboratory, Houston, Texas, USA
| | - Jose-Miguel Yamal
- The University of Texas School of Public Health, Houston, Texas, USA
| | | | | | - Amy Taylor
- Texas Medical Center Library, Houston, Texas, USA
| | | | - Heidi V Russell
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
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Mattick JS, Dinger M, Schonrock N, Cowley M. Whole genome sequencing provides better diagnostic yield and future value than whole exome sequencing. Med J Aust 2018; 209:197-199. [DOI: 10.5694/mja17.01176] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/08/2018] [Indexed: 12/21/2022]
Affiliation(s)
- John S Mattick
- Garvan Institute of Medical Research, Sydney, NSW
- St Vincentˈs Clinical School, UNSW Sydney, Sydney, NSW
| | - Marcel Dinger
- Kinghorn Centre of Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW
| | - Nicole Schonrock
- Kinghorn Centre of Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW
| | - Mark Cowley
- Kinghorn Centre of Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW
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43
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Goodspeed K, Newsom C, Morris MA, Powell C, Evans P, Golla S. Pitt-Hopkins Syndrome: A Review of Current Literature, Clinical Approach, and 23-Patient Case Series. J Child Neurol 2018; 33:233-244. [PMID: 29318938 PMCID: PMC5922265 DOI: 10.1177/0883073817750490] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pitt-Hopkins syndrome (PTHS) is a rare, genetic disorder caused by a molecular variant of TCF4 which is involved in embryologic neuronal differentiation. PTHS is characterized by syndromic facies, psychomotor delay, and intellectual disability. Other associated features include early-onset myopia, seizures, constipation, and hyperventilation-apneic spells. Many also meet criteria for autism spectrum disorder. Here the authors present a series of 23 PTHS patients with molecularly confirmed TCF4 variants and describe 3 unique individuals. The first carries a small deletion but does not exhibit the typical facial features nor the typical pattern of developmental delay. The second exhibits typical facial features, but has attained more advanced motor and verbal skills than other reported cases to date. The third displays typical features of PTHS, however inherited a large chromosomal duplication involving TCF4 from his unaffected father with somatic mosaicism. To the authors' knowledge, this is the first chromosomal duplication case reported to date.
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Affiliation(s)
| | - Cassandra Newsom
- University of Texas Southwestern Medical School
- Children’s Health Dallas
| | | | | | - Patricia Evans
- University of Texas Southwestern Medical School
- Children’s Health Dallas
| | - Sailaja Golla
- University of Texas Southwestern Medical School
- Children’s Health Dallas
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44
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Dragojlovic N, Elliott AM, Adam S, van Karnebeek C, Lehman A, Mwenifumbo JC, Nelson TN, du Souich C, Friedman JM, Lynd LD. The cost and diagnostic yield of exome sequencing for children with suspected genetic disorders: a benchmarking study. Genet Med 2018; 20:1013-1021. [PMID: 29300375 DOI: 10.1038/gim.2017.226] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/03/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE This study aimed to generate benchmark estimates for the cost, diagnostic yield, and cost per positive diagnosis of diagnostic exome sequencing (ES) in heterogeneous pediatric patient populations and to illustrate how the design of an ES service can influence its cost and yield. METHODS A literature review and Monte Carlo simulations were used to generate benchmark estimates for singleton and trio ES. A cost model for the Clinical Assessment of the Utility of Sequencing and Evaluation as a Service (CAUSES) study, which is testing a proposed delivery model for diagnostic ES in British Columbia, is used to illustrate the potential effects of changing the service design. RESULTS The benchmark diagnostic yield was 34.3% (95% confidence interval (CI): 23.2-46.5) for trio ES and 26.5% (95% CI: 12.9-42.9) for singleton ES. The benchmark cost of delivery was C$6,437 (95% CI: $5,305-$7,704) in 2016 Canadian dollars (US$4,859; 4,391€) for trio ES and C$2,576 (95% CI: $1,993-$3,270) (US$1,944; 1,757€) for singleton ES. Scenario models for CAUSES suggest that alternative service designs could reduce costs but might lead to a higher cost per diagnosis due to lower yields. CONCLUSION Broad conclusions about the cost-effectiveness of ES should be drawn with caution when relying on studies that use cost or yield assumptions that lie at the extremes of the benchmark ranges.
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Affiliation(s)
- Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Shelin Adam
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada.,Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Anna Lehman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Jill C Mwenifumbo
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tanya N Nelson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Christèle du Souich
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada. .,Centre for Health Evaluation and Outcomes Sciences, Providence Health Research Institute, Vancouver, British Columbia, Canada.
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46
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Macchiaiolo M, Barresi S, Cecconi F, Zanni G, Niceta M, Bellacchio E, Lazzarino G, Amorini AM, Bertini ES, Rizza S, Contardi B, Tartaglia M, Bartuli A. A mild form of adenylosuccinate lyase deficiency in absence of typical brain MRI features diagnosed by whole exome sequencing. Ital J Pediatr 2017; 43:65. [PMID: 28768552 PMCID: PMC5541734 DOI: 10.1186/s13052-017-0383-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/28/2017] [Indexed: 08/24/2023] Open
Abstract
Background Adenylosuccinate lyase (ADSL) deficiency is a defect of purine metabolism affecting purinosome assembly and reducing metabolite fluxes through purine de novo synthesis and purine nucleotide recycling pathways. The disorder shows a wide spectrum of symptoms from slowly to rapidly progressing forms. The most severe form is characterized by neonatal encephalopathy, absence of spontaneous movement, respiratory failure, intractable seizures, and early death within the first weeks of life. More commonly, ADSL presents purely neurologic clinical picture characterized by severe psychomotor retardation, microcephaly, early onset of seizures, and autistic features (type I) or a more slowly progressing form with later onset, and major features including slight to moderate psychomotor retardation, and transient contact disturbances (type II). Diagnostic markers are the presence of succinylaminoimidazole carboxamide riboside (SAICAr) and succinyladenosine (SAdo) in extracellular fluids. ADSL is a rare disorder, although its prevalence remains unknown. Of note, the wide range of essentially nonspecific manifestations and lack of awareness of the condition often prevent diagnosis. Case presentation We present here the case of particularly mild, late onset ADSL that has been unsuccessfully investigated until whole exome sequencing (WES) was performed. Conclusions Besides emphasizing the valuable diagnostic value of WES, this report provides new data further documenting the relatively wide clinical manifestation of ADSL. Electronic supplementary material The online version of this article (doi:10.1186/s13052-017-0383-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Macchiaiolo
- Genetics and Rare Diseases, Research Division, Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00164, Rome, Italy.
| | - Sabina Barresi
- Genetics and Rare Diseases, Research Division, Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00164, Rome, Italy
| | - Francesco Cecconi
- Unit of Cell Stress and Survival Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Ginevra Zanni
- Genetics and Rare Diseases, Research Division, Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00164, Rome, Italy
| | - Marcello Niceta
- Genetics and Rare Diseases, Research Division, Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00164, Rome, Italy
| | - Emanuele Bellacchio
- Genetics and Rare Diseases, Research Division, Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00164, Rome, Italy
| | - Giacomo Lazzarino
- Institute of Biochemistry and Clinical Biochemistry, Catholic University of Rome, Rome, Italy
| | - Angela Maria Amorini
- Institute of Biochemistry and Clinical Biochemistry, Catholic University of Rome, Rome, Italy
| | - Enrico Silvio Bertini
- Genetics and Rare Diseases, Research Division, Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00164, Rome, Italy
| | - Salvatore Rizza
- Unit of Cell Stress and Survival Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Benedetta Contardi
- Pharmacist Mother of a Patient affected by Adenylosuccinate lyase deficiency, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases, Research Division, Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00164, Rome, Italy
| | - Andrea Bartuli
- Genetics and Rare Diseases, Research Division, Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00164, Rome, Italy
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Evers C, Staufner C, Granzow M, Paramasivam N, Hinderhofer K, Kaufmann L, Fischer C, Thiel C, Opladen T, Kotzaeridou U, Wiemann S, Schlesner M, Eils R, Kölker S, Bartram CR, Hoffmann GF, Moog U. Impact of clinical exomes in neurodevelopmental and neurometabolic disorders. Mol Genet Metab 2017; 121:297-307. [PMID: 28688840 DOI: 10.1016/j.ymgme.2017.06.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/29/2017] [Accepted: 06/29/2017] [Indexed: 01/06/2023]
Abstract
Whole exome sequencing (WES) is well established in research and is now being introduced into clinically indicated diagnostics (so-called clinical exomes). We evaluated the diagnostic yield and clinical implications of WES in 72 patients from 60 families with undiagnosed neurodevelopmental disorders (NDD), neurometabolic disorders, and dystonias. Pathogenic or likely pathogenic variants leading to a molecular diagnosis could be identified in 21 of the 60 families (overall 35%, in 36% of patients with NDD, in 43% of patients with neurometabolic disorders, in 25% of patients with dystonias). In one family two coexisting autosomal recessive diseases caused by homozygous pathogenic variants in two different genes were diagnosed. In another family, a homozygous frameshift variant in STRADA was found to cause a severe NDD with early onset epilepsy, brain anomalies, hypotonia, heart defect, nephrocalcinosis, macrocephaly and distinctive facies so far designated as PMSE (polyhydramnios, megalencephaly, symptomatic epilepsy) syndrome. In 7 of the 21 families with a molecular diagnosis the pathogenic variants were only identified by clinical follow-up, manual reevaluation of the literature, a change of filter setting, and/or reconsideration of inheritance pattern. Most importantly, clinical implications included management changes in 8 cases and impact on family planning in 20 families with a molecular diagnosis. This study shows that reevaluation and follow-up can improve the diagnostic rate and that WES results have important implications on medical management and family planning. Furthermore, we could confirm STRADA as a gene associated with syndromic ID but find it questionable if the current designation as PMSE depicts the most important clinical features.
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Affiliation(s)
- Christina Evers
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany.
| | - Christian Staufner
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Martin Granzow
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Nagarajan Paramasivam
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Katrin Hinderhofer
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christine Fischer
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christian Thiel
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Thomas Opladen
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Urania Kotzaeridou
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Stefan Wiemann
- Genomics & Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefan Kölker
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Claus R Bartram
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Georg F Hoffmann
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Ute Moog
- Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
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van der Ven AT, Shril S, Ityel H, Vivante A, Chen J, Hwang DY, Laricchia KM, Lek M, Tasic V, Hildebrandt F. Whole-Exome Sequencing Reveals FAT4 Mutations in a Clinically Unrecognizable Patient with Syndromic CAKUT: A Case Report. Mol Syndromol 2017; 8:272-277. [PMID: 28878612 DOI: 10.1159/000477750] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2017] [Indexed: 12/24/2022] Open
Abstract
We present the case of a patient of Macedonian origin with unilateral renal agenesis and ureterovesical junction obstruction in combination with further abnormalities including midface hypoplasia, scoliosis as well as camptodactyly of one toe. Whole-exome sequencing analysis revealed compound heterozygous variants in the FAT4 gene. Recessive variants in FAT4 are a known cause of van Maldergem syndrome (VMS) in which congenital anomalies of the kidney and urinary tract are a less characteristic but common feature. The initial presentation of our patient was not clinically recognizable. However, in view of the molecular findings, the most likely diagnosis is a mild manifestation of VMS. Only very few publications have reported patients with VMS and mutations in FAT4 to date. With this case, we hope to provide further insight into the phenotypic variability of this syndrome.
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Affiliation(s)
- Amelie T van der Ven
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hadas Ityel
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jing Chen
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daw-Yang Hwang
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Kassardjian CD, Amato AA, Boon AJ, Childers MK, Klein CJ. The utility of genetic testing in neuromuscular disease: A consensus statement from the AANEM on the clinical utility of genetic testing in diagnosis of neuromuscular disease. Muscle Nerve 2017; 54:1007-1009. [PMID: 27554703 DOI: 10.1002/mus.25387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2016] [Indexed: 01/16/2023]
Abstract
INTRODUCTION The aim of this consensus statement is to provide a recommendation from AANEM experts on the clinical utility of genetic testing. It is not meant to recommend or endorse any specific genetic testing methodology or algorithm. METHODS The AANEM Professional Practice Committee reached a consensus based on expert opinion on the utility of genetic testing in neuromuscular diseases and made recommendations on factors that physicians and patients should consider when deciding whether to proceed with such testing. RESULTS Despite the costs of genetic testing, these tests can be both valuable and beneficial in the diagnosis and treatment of neuromuscular diseases in many situations. CONCLUSIONS The AANEM believes that performing genetic testing to arrive at a specific molecular diagnosis is a critical step in providing high-quality care to neuromuscular patients. The cost of testing should not be a deterrent, as there are important clinical, safety, psychosocial, and research benefits. Muscle Nerve 54: 1007-1009, 2016.
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Affiliation(s)
- Charles D Kassardjian
- Policy Department, American Association of Neuromuscular & Electrodiagnostic Medicine, Rochester, Minnesota, USA
| | - Anthony A Amato
- Policy Department, American Association of Neuromuscular & Electrodiagnostic Medicine, Rochester, Minnesota, USA
| | - Andrea J Boon
- Policy Department, American Association of Neuromuscular & Electrodiagnostic Medicine, Rochester, Minnesota, USA
| | - Martin K Childers
- Policy Department, American Association of Neuromuscular & Electrodiagnostic Medicine, Rochester, Minnesota, USA
| | - Christopher J Klein
- Policy Department, American Association of Neuromuscular & Electrodiagnostic Medicine, Rochester, Minnesota, USA
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- Policy Department, American Association of Neuromuscular & Electrodiagnostic Medicine, Rochester, Minnesota, USA
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A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology. Genet Med 2017; 19:1055-1063. [PMID: 28333917 PMCID: PMC5589982 DOI: 10.1038/gim.2017.1] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/30/2016] [Indexed: 12/12/2022] Open
Abstract
Purpose: Implementation of novel genetic diagnostic tests is generally driven by technological advances because they promise shorter turnaround times and/or higher diagnostic yields. Other aspects, including impact on clinical management or cost-effectiveness, are often not assessed in detail prior to implementation. Methods: We studied the clinical utility of whole-exome sequencing (WES) in complex pediatric neurology in terms of diagnostic yield and costs. We analyzed 150 patients (and their parents) presenting with complex neurological disorders of suspected genetic origin. In a parallel study, all patients received both the standard diagnostic workup (e.g., cerebral imaging, muscle biopsies or lumbar punctures, and sequential gene-by-gene–based testing) and WES simultaneously. Results: Our unique study design allowed direct comparison of diagnostic yield of both trajectories and provided insight into the economic implications of implementing WES in this diagnostic trajectory. We showed that WES identified significantly more conclusive diagnoses (29.3%) than the standard care pathway (7.3%) without incurring higher costs. Exploratory analysis of WES as a first-tier diagnostic test indicates that WES may even be cost-saving, depending on the extent of other tests being omitted. Conclusion: Our data support such a use of WES in pediatric neurology for disorders of presumed genetic origin. Genet Med advance online publication 23 March 2017
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