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Kritioti E, Theodosiou A, Parpaite T, Alexandrou A, Nicolaou N, Papaevripidou I, Séjourné N, Coste B, Christophidou-Anastasiadou V, Tanteles GA, Sismani C. Unravelling the genetic causes of multiple malformation syndromes: A whole exome sequencing study of the Cypriot population. PLoS One 2021; 16:e0253562. [PMID: 34324503 PMCID: PMC8320927 DOI: 10.1371/journal.pone.0253562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/08/2021] [Indexed: 11/19/2022] Open
Abstract
Multiple malformation syndromes (MMS) belong to a group of genetic disorders characterised by neurodevelopmental anomalies and congenital malformations. Here we explore for the first time the genetic aetiology of MMS using whole-exome sequencing (WES) in undiagnosed patients from the Greek-Cypriot population after prior extensive diagnostics workup including karyotype and array-CGH. A total of 100 individuals (37 affected), from 32 families were recruited and family-based WES was applied to detect causative single-nucleotide variants (SNVs) and indels. A genetic diagnosis was reported for 16 MMS patients (43.2%), with 10/17 (58.8%) of the findings being novel. All autosomal dominant findings occurred de novo. Functional studies were also performed to elucidate the molecular mechanism relevant to the abnormal phenotypes, in cases where the clinical significance of the findings was unclear. The 17 variants identified in our cohort were located in 14 genes (PCNT, UBE3A, KAT6A, SPR, POMGNT1, PIEZO2, PXDN, KDM6A, PHIP, HECW2, TFAP2A, CNOT3, AGTPBP1 and GAMT). This study has highlighted the efficacy of WES through the high detection rate (43.2%) achieved for a challenging category of undiagnosed patients with MMS compared to other conventional diagnostic testing methods (10-20% for array-CGH and ~3% for G-banding karyotype analysis). As a result, family-based WES could potentially be considered as a first-tier cost effective diagnostic test for patients with MMS that facilitates better patient management, prognosis and offer accurate recurrence risks to the families.
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Affiliation(s)
- Evie Kritioti
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Athina Theodosiou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | - Angelos Alexandrou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nayia Nicolaou
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Ioannis Papaevripidou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nina Séjourné
- Aix Marseille Université, CNRS, LNC-UMR 7291, Marseille, France
| | - Bertrand Coste
- Aix Marseille Université, CNRS, LNC-UMR 7291, Marseille, France
| | | | - George A. Tanteles
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carolina Sismani
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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Abstract
Novel gene-disease discoveries, rapid advancements in technology, and improved bioinformatics tools all have the potential to yield additional molecular diagnoses through the reanalysis of exome sequencing data. Collaborations between clinical laboratories, ordering physicians, and researchers are also driving factors that can contribute to these new insights. Automation in ongoing natural history collection, evolving phenotype updates, advancements in processing next-generation sequencing data, and up-to-date variant-gene-disease databases are increasingly needed for systematic exome reanalysis. Here, we review some of the advantages and challenges for clinician-initiated and laboratory-initiated exome reanalysis, and we propose a model for the future that could potentially maximize the clinical utility of exome reanalysis by integrating information from electronic medical records and knowledge databases into routine clinical workflows.
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Exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:2029-2037. [PMID: 34211152 DOI: 10.1038/s41436-021-01242-6] [Citation(s) in RCA: 229] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE To develop an evidence-based clinical practice guideline for the use of exome and genome sequencing (ES/GS) in the care of pediatric patients with one or more congenital anomalies (CA) with onset prior to age 1 year or developmental delay (DD) or intellectual disability (ID) with onset prior to age 18 years. METHODS The Pediatric Exome/Genome Sequencing Evidence-Based Guideline Work Group (n = 10) used the Grading of Recommendations Assessment, Development and Evaluation (GRADE) evidence to decision (EtD) framework based on the recent American College of Medical Genetics and Genomics (ACMG) systematic review, and an Ontario Health Technology Assessment to develop and present evidence summaries and health-care recommendations. The document underwent extensive internal and external peer review, and public comment, before approval by the ACMG Board of Directors. RESULTS The literature supports the clinical utility and desirable effects of ES/GS on active and long-term clinical management of patients with CA/DD/ID, and on family-focused and reproductive outcomes with relatively few harms. Compared with standard genetic testing, ES/GS has a higher diagnostic yield and may be more cost-effective when ordered early in the diagnostic evaluation. CONCLUSION We strongly recommend that ES/GS be considered as a first- or second-tier test for patients with CA/DD/ID.
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Seaby EG, Ennis S. Challenges in the diagnosis and discovery of rare genetic disorders using contemporary sequencing technologies. Brief Funct Genomics 2021; 19:243-258. [PMID: 32393978 DOI: 10.1093/bfgp/elaa009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Next generation sequencing (NGS) has revolutionised rare disease diagnostics. Concomitant with advancing technologies has been a rise in the number of new gene disorders discovered and diagnoses made for patients and their families. However, despite the trend towards whole exome and whole genome sequencing, diagnostic rates remain suboptimal. On average, only ~30% of patients receive a molecular diagnosis. National sequencing projects launched in the last 5 years are integrating clinical diagnostic testing with research avenues to widen the spectrum of known genetic disorders. Consequently, efforts to diagnose genetic disorders in a clinical setting are now often shared with efforts to prioritise candidate variants for the detection of new disease genes. Herein we discuss some of the biggest obstacles precluding molecular diagnosis and discovery of new gene disorders. We consider bioinformatic and analytical challenges faced when interpreting next generation sequencing data and showcase some of the newest tools available to mitigate these issues. We consider how incomplete penetrance, non-coding variation and structural variants are likely to impact diagnostic rates, and we further discuss methods for uplifting novel gene discovery by adopting a gene-to-patient-based approach.
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55
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Fabiani M, Cogo F, Poli M, Capalbo A. Technical factors to consider when developing an Expanded Carrier Screening platform. Curr Opin Obstet Gynecol 2021; 33:178-183. [PMID: 33741771 DOI: 10.1097/gco.0000000000000706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Expanded Carrier Screening (ECS) is a genetic test able to detect carriers for a large number of autosomal recessive and X-linked diseases. Its clinical utilization is increasing but some technical aspects for its implementation are still controversial. RECENT FINDINGS In the current literature, several aspects of ECS panel implementation have been addressed. One of the most relevant topics involves which genes/pathologies should be included in an optimized ECS panel and which variants should be reported. SUMMARY Here, we review the best practice criteria to refine and improve clinical utility and validity of an ECS panel. The criteria for optimal ECS panel implementation include the severity of pathologies, the prevalence of diseases in general population and a definitive or strong gene/disease association. Moreover, we discuss the main complications associated with the reporting of Variant of Uncertain Significance and the need for periodic reassessment.
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Affiliation(s)
| | | | | | - Antonio Capalbo
- Igenomix Italia, Marostica, Vicenza, Italy.,Igenomix Foundation, Valencia, Spain
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56
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Kojic M, Gawda T, Gaik M, Begg A, Salerno-Kochan A, Kurniawan ND, Jones A, Drożdżyk K, Kościelniak A, Chramiec-Głąbik A, Hediyeh-Zadeh S, Kasherman M, Shim WJ, Sinniah E, Genovesi LA, Abrahamsen RK, Fenger CD, Madsen CG, Cohen JS, Fatemi A, Stark Z, Lunke S, Lee J, Hansen JK, Boxill MF, Keren B, Marey I, Saenz MS, Brown K, Alexander SA, Mureev S, Batzilla A, Davis MJ, Piper M, Bodén M, Burne THJ, Palpant NJ, Møller RS, Glatt S, Wainwright BJ. Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype. Nat Commun 2021; 12:2678. [PMID: 33976153 PMCID: PMC8113450 DOI: 10.1038/s41467-021-22888-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are the most common neurodevelopmental disorders and are characterized by substantial impairment in intellectual and adaptive functioning, with their genetic and molecular basis remaining largely unknown. Here, we identify biallelic variants in the gene encoding one of the Elongator complex subunits, ELP2, in patients with ID and ASD. Modelling the variants in mice recapitulates the patient features, with brain imaging and tractography analysis revealing microcephaly, loss of white matter tract integrity and an aberrant functional connectome. We show that the Elp2 mutations negatively impact the activity of the complex and its function in translation via tRNA modification. Further, we elucidate that the mutations perturb protein homeostasis leading to impaired neurogenesis, myelin loss and neurodegeneration. Collectively, our data demonstrate an unexpected role for tRNA modification in the pathogenesis of monogenic ID and ASD and define Elp2 as a key regulator of brain development.
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Affiliation(s)
- Marija Kojic
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Tomasz Gawda
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Monika Gaik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alexander Begg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anna Salerno-Kochan
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Nyoman D Kurniawan
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Katarzyna Drożdżyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Maria Kasherman
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Laura A Genovesi
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Rannvá K Abrahamsen
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Christina D Fenger
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Camilla G Madsen
- Centre for Functional and Diagnostic Imaging and Research, Hvidovre Hospital, Hvidovre, Denmark
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ali Fatemi
- Department of Neurology and Developmental Medicine, Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zornitza Stark
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Australian Genomics Health Alliance, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Australian Genomics Health Alliance, Parkville, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Joy Lee
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Department of Metabolic Medicine, Royal Children's Hospital, Parkville, VIC, Australia
| | - Jonas K Hansen
- Department of Paediatrics, Regional Hospital Viborg, Viborg, Denmark
| | - Martin F Boxill
- Department of Paediatrics, Regional Hospital Viborg, Viborg, Denmark
| | - Boris Keren
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Isabelle Marey
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Margarita S Saenz
- The University of Colorado Anschutz, Children's Hospital Colorado, Aurora, CO, USA
| | - Kathleen Brown
- The University of Colorado Anschutz, Children's Hospital Colorado, Aurora, CO, USA
| | - Suzanne A Alexander
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, Australia
| | - Sergey Mureev
- CSIRO-QUT Synthetic Biology Alliance, Centre for Tropical Crops and Bio-commodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Alina Batzilla
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- The Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas H J Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Department for Regional Health Research, The University of Southern Denmark, Odense, Denmark
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Brandon J Wainwright
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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57
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Sundercombe SL, Berbic M, Evans CA, Cliffe C, Elakis G, Temple SEL, Selvanathan A, Ewans L, Quayum N, Nixon CY, Dias KR, Lang S, Richards A, Goh S, Wilson M, Mowat D, Sachdev R, Sandaradura S, Walsh M, Farrar MA, Walsh R, Fletcher J, Kirk EP, Teunisse GM, Schofield D, Buckley MF, Zhu Y, Roscioli T. Clinically Responsive Genomic Analysis Pipelines: Elements to Improve Detection Rate and Efficiency. J Mol Diagn 2021; 23:894-905. [PMID: 33962052 DOI: 10.1016/j.jmoldx.2021.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/27/2021] [Accepted: 04/21/2021] [Indexed: 11/25/2022] Open
Abstract
Massively parallel sequencing has markedly improved mendelian diagnostic rates. This study assessed the effects of custom alterations to a diagnostic genomic bioinformatic pipeline in response to clinical need and derived practice recommendations relative to diagnostic rates and efficiency. The Genomic Annotation and Interpretation Application (GAIA) bioinformatics pipeline was designed to detect panel, exome, and genome sample integrity and prioritize gene variants in mendelian disorders. Reanalysis of selected negative cases was performed after improvements to the pipeline. GAIA improvements and their effect on sensitivity are described, including addition of a PubMed search for gene-disease associations not in the Online Mendelian Inheritance of Man database, inclusion of a process for calling low-quality variants (known as QPatch), and gene symbol nomenclature consistency checking. The new pipeline increased the diagnostic rate and reduced staff costs, resulting in a saving of US$844.34 per additional diagnosis. Recommendations for genomic analysis pipeline requirements are summarized. Clinically responsive bioinformatics pipeline improvements increase diagnostic sensitivity and increase cost-effectiveness.
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Affiliation(s)
| | - Marina Berbic
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, University of New South Wales Sydney, Kensington, New South Wales, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Corrina Cliffe
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - George Elakis
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Suzanna E L Temple
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Arthavan Selvanathan
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Discipline of Child and Adolescent Health, The University of Sydney, New South Wales, Australia
| | - Lisa Ewans
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia; Central Clinical School, Sydney Medical School, The University of Sydney, New South Wales, Australia
| | - Nila Quayum
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Cheng-Yee Nixon
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Kerith-Rae Dias
- Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales Sydney, Kensington, New South Wales, Australia
| | - Sarah Lang
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Anna Richards
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Shuxiang Goh
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, Westmead, New South Wales, Australia
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Sarah Sandaradura
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, Westmead, New South Wales, Australia
| | - Maie Walsh
- Genetic Medicine Department, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michelle A Farrar
- School of Women's and Children's Health, University of New South Wales Sydney, Kensington, New South Wales, Australia; Neurology Department, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Rebecca Walsh
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Janice Fletcher
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Edwin P Kirk
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, University of New South Wales Sydney, Kensington, New South Wales, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia
| | - Guus M Teunisse
- Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia
| | - Deborah Schofield
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Michael Francis Buckley
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Ying Zhu
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Genetics of Learning Disability Service, Hunter Genetics, Waratah Newcastle, New South Wales, Australia
| | - Tony Roscioli
- NSW Health Pathology Randwick Genomics, Prince of Wales Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia (NeuRA), Randwick, New South Wales, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Randwick, New South Wales, Australia.
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58
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Abe‐Hatano C, Iida A, Kosugi S, Momozawa Y, Terao C, Ishikawa K, Okubo M, Hachiya Y, Nishida H, Nakamura K, Miyata R, Murakami C, Takahashi K, Hoshino K, Sakamoto H, Ohta S, Kubota M, Takeshita E, Ishiyama A, Nakagawa E, Sasaki M, Kato M, Matsumoto N, Kamatani Y, Kubo M, Takahashi Y, Natsume J, Inoue K, Goto Y. Whole genome sequencing of 45 Japanese patients with intellectual disability. Am J Med Genet A 2021; 185:1468-1480. [PMID: 33624935 PMCID: PMC8247954 DOI: 10.1002/ajmg.a.62138] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/23/2020] [Accepted: 02/06/2021] [Indexed: 02/06/2023]
Abstract
Intellectual disability (ID) is characterized by significant limitations in both intellectual functioning and adaptive behaviors, originating before the age of 18 years. However, the genetic etiologies of ID are still incompletely elucidated due to the wide range of clinical and genetic heterogeneity. Whole genome sequencing (WGS) has been applied as a single-step clinical diagnostic tool for ID because it detects genetic variations with a wide range of resolution from single nucleotide variants (SNVs) to structural variants (SVs). To explore the causative genes for ID, we employed WGS in 45 patients from 44 unrelated Japanese families and performed a stepwise screening approach focusing on the coding variants in the genes. Here, we report 12 pathogenic and likely pathogenic variants: seven heterozygous variants of ADNP, SATB2, ANKRD11, PTEN, TCF4, SPAST, and KCNA2, three hemizygous variants of SMS, SLC6A8, and IQSEC2, and one homozygous variant in AGTPBP1. Of these, four were considered novel. Furthermore, a novel 76 kb deletion containing exons 1 and 2 in DYRK1A was identified. We confirmed the clinical and genetic heterogeneity and high frequency of de novo causative variants (8/12, 66.7%). This is the first report of WGS analysis in Japanese patients with ID. Our results would provide insight into the correlation between novel variants and expanded phenotypes of the disease.
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Affiliation(s)
- Chihiro Abe‐Hatano
- Department of Mental Retardation and Birth Defect ResearchNational Institute of Neuroscience, National Center of Neurology and PsychiatryTokyoJapan
- Department of PediatricsNagoya University Graduate School of MedicineAichiJapan
| | - Aritoshi Iida
- Medical Genome CenterNational Center of Neurology and PsychiatryTokyoJapan
| | - Shunichi Kosugi
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical SciencesKanagawaJapan
| | - Yukihide Momozawa
- Laboratory for Genotyping DevelopmentRIKEN Center for Integrative Medical SciencesKanagawaJapan
| | - Chikashi Terao
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical SciencesKanagawaJapan
- Clinical Research CenterShizuoka General HospitalShizuokaJapan
- The Department of Applied GeneticsThe School of Pharmaceutical Sciences, University of ShizuokaShizuokaJapan
| | - Keiko Ishikawa
- Medical Genome CenterNational Center of Neurology and PsychiatryTokyoJapan
| | - Mariko Okubo
- Department of Child NeurologyNational Center Hospital, National Center of Neurology and PsychiatryTokyoJapan
| | - Yasuo Hachiya
- Department of NeuropediatricsTokyo Metropolitan Neurological HospitalTokyoJapan
| | - Hiroya Nishida
- Department of NeuropediatricsTokyo Metropolitan Neurological HospitalTokyoJapan
| | - Kazuyuki Nakamura
- Department of PediatricsYamagata University Faculty of MedicineYamagataJapan
| | - Rie Miyata
- Department of PediatricsTokyo‐Kita Medical CenterTokyoJapan
| | - Chie Murakami
- Department of PediatricsKitakyusyu Children's Rehabilitation CenterFukuokaJapan
| | - Kan Takahashi
- Department of PediatricsOme Municipal General HospitalTokyoJapan
| | - Kyoko Hoshino
- Department of PediatricsMinami Wakayama Medical CenterWakayamaJapan
| | - Haruko Sakamoto
- Department of NeonatologyJapanese Red Cross Osaka HospitalOsakaJapan
| | - Sayaka Ohta
- Division of NeurologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Masaya Kubota
- Division of NeurologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Eri Takeshita
- Department of Child NeurologyNational Center Hospital, National Center of Neurology and PsychiatryTokyoJapan
| | - Akihiko Ishiyama
- Department of Child NeurologyNational Center Hospital, National Center of Neurology and PsychiatryTokyoJapan
| | - Eiji Nakagawa
- Department of Child NeurologyNational Center Hospital, National Center of Neurology and PsychiatryTokyoJapan
| | - Masayuki Sasaki
- Department of Child NeurologyNational Center Hospital, National Center of Neurology and PsychiatryTokyoJapan
| | - Mitsuhiro Kato
- Department of PediatricsYamagata University Faculty of MedicineYamagataJapan
- Department of PediatricsShowa University School of MedicineTokyoJapan
| | - Naomichi Matsumoto
- Department of Human GeneticsYokohama City University Graduate School of MedicineKanagawaJapan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical SciencesKanagawaJapan
- Department of Computational Biology and Medical SciencesGraduate School of Frontier Sciences, The University of TokyoTokyoJapan
| | - Michiaki Kubo
- Laboratory for Genotyping DevelopmentRIKEN Center for Integrative Medical SciencesKanagawaJapan
| | - Yoshiyuki Takahashi
- Department of PediatricsNagoya University Graduate School of MedicineAichiJapan
| | - Jun Natsume
- Department of PediatricsNagoya University Graduate School of MedicineAichiJapan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect ResearchNational Institute of Neuroscience, National Center of Neurology and PsychiatryTokyoJapan
| | - Yu‐Ichi Goto
- Department of Mental Retardation and Birth Defect ResearchNational Institute of Neuroscience, National Center of Neurology and PsychiatryTokyoJapan
- Medical Genome CenterNational Center of Neurology and PsychiatryTokyoJapan
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59
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Thomas Q, Vitobello A, Tran Mau-Them F, Duffourd Y, Fromont A, Giroud M, Daubail B, Jacquin-Piques A, Hervieu-Begue M, Moreau T, Osseby GV, Garret P, Nambot S, Delanne J, Bruel AL, Sorlin A, Callier P, Denomme-Pichon AS, Faivre L, Béjot Y, Philippe C, Thauvin-Robinet C, Moutton S. High efficiency and clinical relevance of exome sequencing in the daily practice of neurogenetics. J Med Genet 2021; 59:445-452. [PMID: 34085946 DOI: 10.1136/jmedgenet-2020-107369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 02/08/2021] [Accepted: 02/19/2021] [Indexed: 01/13/2023]
Abstract
OBJECTIVE To assess the efficiency and relevance of clinical exome sequencing (cES) as a first-tier or second-tier test for the diagnosis of progressive neurological disorders in the daily practice of Neurology and Genetic Departments. METHODS Sixty-seven probands with various progressive neurological disorders (cerebellar ataxias, neuromuscular disorders, spastic paraplegias, movement disorders and individuals with complex phenotypes labelled 'other') were recruited over a 4-year period regardless of their age, gender, familial history and clinical framework. Individuals could have had prior genetic tests as long as it was not cES. cES was performed in a proband-only (60/67) or trio (7/67) strategy depending on available samples and was analysed with an in-house pipeline including software for CNV and mitochondrial-DNA variant detection. RESULTS In 29/67 individuals, cES identified clearly pathogenic variants leading to a 43% positive yield. When performed as a first-tier test, cES identified pathogenic variants for 53% of individuals (10/19). Difficult cases were solved including double diagnoses within a kindred or identification of a neurodegeneration with brain iron accumulation in a patient with encephalopathy of suspected mitochondrial origin. CONCLUSION This study shows that cES is a powerful tool for the daily practice of neurogenetics offering an efficient (43%) and appropriate approach for clinically and genetically complex and heterogeneous disorders.
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Affiliation(s)
- Quentin Thomas
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France .,Genetics Center, FHU-TRANSLAD, Dijon University Hospital, Dijon, Burgundy, France.,Neurology Department, Dijon University Hospital, Dijon, Burgundy, France
| | - Antonio Vitobello
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.,Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
| | - Frederic Tran Mau-Them
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.,Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
| | - Yannis Duffourd
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.,Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
| | - Agnès Fromont
- Neurology Department, Dijon University Hospital, Dijon, Burgundy, France
| | - Maurice Giroud
- Neurology Department, Dijon University Hospital, Dijon, Burgundy, France.,Dijon Stroke Registry, EA7460, Pathophysiology and Epidemiology of Cerebro-Cardiovascular Diseases (PEC2), University of Burgundy and Franche-Comté, Dijon, Burgundy, France
| | - Benoit Daubail
- Department of Adult Neurophysiology, Dijon University Hospital, Dijon, Burgundy, France
| | - Agnès Jacquin-Piques
- Department of Adult Neurophysiology, Dijon University Hospital, Dijon, Burgundy, France
| | | | - Thibault Moreau
- Neurology Department, Dijon University Hospital, Dijon, Burgundy, France
| | - Guy-Victor Osseby
- Neurology Department, Dijon University Hospital, Dijon, Burgundy, France
| | - Philippine Garret
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.,Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
| | - Sophie Nambot
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.,Genetics Center, FHU-TRANSLAD, Dijon University Hospital, Dijon, Burgundy, France
| | - Julian Delanne
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.,Genetics Center, FHU-TRANSLAD, Dijon University Hospital, Dijon, Burgundy, France
| | - Ange-Line Bruel
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.,Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
| | - Arthur Sorlin
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.,Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
| | - Patrick Callier
- Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
| | - Anne-Sophie Denomme-Pichon
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.,Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
| | - Laurence Faivre
- Genetics Center, FHU-TRANSLAD, Dijon University Hospital, Dijon, Burgundy, France
| | - Yannick Béjot
- Neurology Department, Dijon University Hospital, Dijon, Burgundy, France.,Dijon Stroke Registry, EA7460, Pathophysiology and Epidemiology of Cerebro-Cardiovascular Diseases (PEC2), University of Burgundy and Franche-Comté, Dijon, Burgundy, France
| | - Christophe Philippe
- Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
| | - Christel Thauvin-Robinet
- Genetics Center, FHU-TRANSLAD, Dijon University Hospital, Dijon, Burgundy, France.,Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
| | - Sébastien Moutton
- Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France.,Genetics Center, FHU-TRANSLAD, Dijon University Hospital, Dijon, Burgundy, France
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60
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Jiang YL, Song C, Wang Y, Zhao J, Yang F, Gao Q, Leng X, Man Y, Jiang W. Clinical Utility of Exome Sequencing and Reinterpreting Genetic Test Results in Children and Adults With Epilepsy. Front Genet 2020; 11:591434. [PMID: 33391346 PMCID: PMC7775549 DOI: 10.3389/fgene.2020.591434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022] Open
Abstract
The clinical utility of genetic testing for epilepsy has been enhanced with the advancement of next-generation sequencing (NGS) technology along with the rapid updating of publicly available databases. The aim of this study was to evaluate the diagnostic yield of NGS and assess the value of reinterpreting genetic test results in children and adults with epilepsy. We performed genetic testing on 200 patients, including 82 children and 118 adults. The results were classified into three categories: positive, inconclusive, or negative. The reinterpretation of inconclusive results was conducted in April 2020. Overall, we identified disease-causing variants in 12% of the patients in the original analysis, and 14.5% at reinterpretation. The diagnostic yield for adults with epilepsy was similar to that for children (11 vs. 19.5%, p = 0.145). After reinterpretation, 9 of the 86 patients who initially had inconclusive results obtained a clinically significant change in diagnosis. Among these nine revised cases, five obtained positive diagnoses, representing a diagnosis rate of 5.8% (5/86). Manual searches for additional evidence of pathogenicity for candidate variants and updated patient clinical information were the main reasons for diagnostic reclassification. This study emphasizes the diagnostic potential of combining NGS and reinterpretation of inconclusive genetic test reports in children and adults with epilepsy.
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Affiliation(s)
- Yong-Li Jiang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Changgeng Song
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yuanyuan Wang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jingjing Zhao
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Fang Yang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Qiong Gao
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiuxiu Leng
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yulin Man
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Wen Jiang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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61
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Quaio CRDC, Moreira CM, Novo‐Filho GM, Sacramento‐Bobotis PR, Groenner Penna M, Perazzio SF, Dutra AP, Silva RA, Santos MNP, Arruda VYN, Freitas VG, Pereira VC, Pintao MC, Fornari ARDS, Buzolin AL, Oku AY, Burger M, Ramalho RF, Marco Antonio DS, Ferreira EN, Pereira OJE, Cantagalli VD, Trindade ACG, Sousa RRF, Reys Furuzawa C, Verzini F, Matalhana SD, Romano N, Paixão D, Olivati C, Spolador GM, Maciel GAR, Rocha VZ, Miguelez J, Carvalho MHB, Souza AWS, Andrade LEC, Chauffaille MDL, Perazzio ADSB, Catelani ALPM, Mitne‐Neto M, Kim CA, Baratela WADR. Diagnostic power and clinical impact of exome sequencing in a cohort of 500 patients with rare diseases. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:955-964. [DOI: 10.1002/ajmg.c.31860] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Caio Robledo D'Angioli Costa Quaio
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
- Instituto da Crianca (Children's Hospital) Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo Sao Paulo SP Brazil
| | | | | | | | | | - Sandro Felix Perazzio
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
- Rheumatology Division, Department of Medicine, Escola Paulista de Medicina Universidade Federal de Sao Paulo São Paulo SP Brazil
| | | | - Rafael Alves Silva
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
- Escola Paulista de Medicina, Laboratório de Hepatologia Molecular Aplicada (LHeMA) Universidade Federal de São Paulo São Paulo SP Brazil
| | | | | | - Vanessa Galdeno Freitas
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
- Instituto de Matemática e Estatística da Universidade de São Paulo e Instituto de Ensino e Pesquisa do Hospital Sírio Libanês São Paulo SP Brazil
| | | | | | | | | | - Andre Yuji Oku
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
| | - Matheus Burger
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
| | | | | | | | | | | | | | | | | | | | | | - Naiade Romano
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
| | - Daniele Paixão
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
| | | | | | - Gustavo Arantes Rosa Maciel
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
- Discipline of Gynecology Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo São Paulo SP Brazil
| | - Viviane Zorzanelli Rocha
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
- Heart Institute (InCor) Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo São Paulo SP Brazil
| | | | - Mario Henrique Burlacchini Carvalho
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
- Disciplina de Obstetrícia, Departamento de Obstetrícia e Ginecologia Faculdade de Medicina FMUSP, Universidade de Sao Paulo São Paulo SP Brazil
| | - Alexandre Wagner Silva Souza
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
- Rheumatology Division, Department of Medicine, Escola Paulista de Medicina Universidade Federal de Sao Paulo São Paulo SP Brazil
| | - Luis Eduardo Coelho Andrade
- Fleury Medicina e Saúde Grupo Fleury São Paulo SP Brazil
- Rheumatology Division, Department of Medicine, Escola Paulista de Medicina Universidade Federal de Sao Paulo São Paulo SP Brazil
| | | | | | | | | | - Chong Ae Kim
- Instituto da Crianca (Children's Hospital) Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo Sao Paulo SP Brazil
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Guell X, Anteraper SA, Ghosh SS, Gabrieli JDE, Schmahmann JD. Neurodevelopmental and Psychiatric Symptoms in Patients with a Cyst Compressing the Cerebellum: an Ongoing Enigma. THE CEREBELLUM 2020; 19:16-29. [PMID: 31321675 DOI: 10.1007/s12311-019-01050-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A patient diagnosed with developmental delay, intellectual disability, and autistic and obsessive-compulsive symptoms was found to have a posterior fossa arachnoid cyst (PFAC) compressing the cerebellum. The patient was referred to our Ataxia Unit for consideration of surgical drainage of the cyst to improve his clinical constellation. This scenario led to an in-depth analysis including a literature review, functional resting-state MRI analysis of our patient compared to a group of controls, and genetic testing. While it is reasonable to consider that there may be a causal relationship between PFAC and neurodevelopmental or psychiatric symptoms in some patients, there is also a nontrivial prevalence of PFAC in the asymptomatic population and a significant possibility that many PFAC are incidental findings in the context of primary cognitive or psychiatric symptoms. Our functional MRI analysis is the first to examine brain function, and to report cerebellar dysfunction, in a patient presenting with cognitive/psychiatric symptoms found to have a structural abnormality compressing the cerebellum. These neuroimaging findings are inherently limited due to their correlational nature but provide unprecedented evidence suggesting that cerebellar compression may be associated with cerebellar dysfunction. Exome gene sequencing revealed additional etiological possibilities, highlighting the complexity of this field of cerebellar clinical and scientific practice. Our findings and discussion may guide future investigations addressing an important knowledge gap-namely, is there a link between cerebellar compression (including arachnoid cysts and possibly other forms of cerebellar compression such as Chiari malformation), cerebellar dysfunction (including fMRI abnormalities reported here), and neuropsychiatric symptoms?
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Affiliation(s)
- Xavier Guell
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Cambridge, MA, USA. .,Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Sheeba A Anteraper
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Alan and Lorraine Bressler Clinical and Research Program for Autism Spectrum Disorder, Massachusetts General Hospital, Boston, MA, USA.,PEN Laboratory, Northeastern University, Boston, MA, USA
| | - Satrajit S Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Otolaryngology, Harvard Medical School, Boston, MA, USA
| | - John D E Gabrieli
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeremy D Schmahmann
- Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Ataxia Unit, Cognitive Behavioral Neurology Unit, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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63
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JARID2 haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. Genet Med 2020; 23:374-383. [PMID: 33077894 DOI: 10.1038/s41436-020-00992-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/23/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE JARID2, located on chromosome 6p22.3, is a regulator of histone methyltransferase complexes that is expressed in human neurons. So far, 13 individuals sharing clinical features including intellectual disability (ID) were reported with de novo heterozygous deletions in 6p22-p24 encompassing the full length JARID2 gene (OMIM 601594). However, all published individuals to date have a deletion of at least one other adjoining gene, making it difficult to determine if JARID2 is the critical gene responsible for the shared features. We aim to confirm JARID2 as a human disease gene and further elucidate the associated clinical phenotype. METHODS Chromosome microarray analysis, exome sequencing, and an online matching platform (GeneMatcher) were used to identify individuals with single-nucleotide variants or deletions involving JARID2. RESULTS We report 16 individuals in 15 families with a deletion or single-nucleotide variant in JARID2. Several of these variants are likely to result in haploinsufficiency due to nonsense-mediated messenger RNA (mRNA) decay. All individuals have developmental delay and/or ID and share some overlapping clinical characteristics such as facial features with those who have larger deletions involving JARID2. CONCLUSION We report that JARID2 haploinsufficiency leads to a clinically distinct neurodevelopmental syndrome, thus establishing gene-disease validity for the purpose of diagnostic reporting.
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64
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Li D, Shen KM, Zackai EH, Bhoj EJ. Clinical variability of TUBB-associated disorders: Diagnosis through reanalysis. Am J Med Genet A 2020; 182:3035-3039. [PMID: 33016642 DOI: 10.1002/ajmg.a.61897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 11/06/2022]
Abstract
A range of clinical findings have been associated with heterozygous mutations in the Beta Tubulin (TUBB) gene, including microcephaly, structural brain abnormalities, intellectual disability, and skin creases. We report a 5-year-old male who presented for evaluation of cleft palate, cardiac defects, growth retardation, hemivertebrae causing scoliosis, and preauricular skin tags. Previous clinical exome sequencing of this patient was nondiagnostic, but reanalysis in the research setting identified a de novo missense c. 925C>G p.(Arg309Gly) mutation in TUBB. This mutation was not found in population allele frequency databases, and was classified to be likely pathogenic. This patient shares some phenotypic characteristics with previous reported patients of TUBB mutations of the two TUBB-related phenotypes: "Cortical dysplasia, complex, with other brain malformations 6" [MIM 615771] and "Circumferential Skin Creases Kunze type (CSC-KT)" [MIM 156610], but has no excess skin creases or structural brain anomalies. We also report previously undescribed features, including transposition of the great arteries and vertebral fusion, thus representing phenotype expansion of TUBB-associated disorders.
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Affiliation(s)
- Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kaitlyn M Shen
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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65
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Tan NB, Stapleton R, Stark Z, Delatycki MB, Yeung A, Hunter MF, Amor DJ, Brown NJ, Stutterd CA, McGillivray G, Yap P, Regan M, Chong B, Fanjul Fernandez M, Marum J, Phelan D, Pais LS, White SM, Lunke S, Tan TY. Evaluating systematic reanalysis of clinical genomic data in rare disease from single center experience and literature review. Mol Genet Genomic Med 2020; 8:e1508. [PMID: 32969205 PMCID: PMC7667328 DOI: 10.1002/mgg3.1508] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/15/2020] [Accepted: 08/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Our primary aim was to evaluate the systematic reanalysis of singleton exome sequencing (ES) data for unsolved cases referred for any indication. A secondary objective was to undertake a literature review of studies examining the reanalysis of genomic data from unsolved cases. Methods We examined data from 58 unsolved cases referred between June 2016 and March 2017. First reanalysis at 4–13 months after the initial report considered genes newly associated with disease since the original analysis; second reanalysis at 9–18 months considered all disease‐associated genes. At 25–34 months we reviewed all cases and the strategies which solved them. Results Reanalysis of existing ES data alone at two timepoints did not yield new diagnoses. Over the same timeframe, 10 new diagnoses were obtained (17%) from additional strategies, such as microarray detection of copy number variation, repeat sequencing to improve coverage, and trio sequencing. Twenty‐seven peer‐reviewed articles were identified on the literature review, with a median new diagnosis rate via reanalysis of 15% and median reanalysis timeframe of 22 months. Conclusion Our findings suggest that an interval of greater than 18 months from the original report may be optimal for reanalysis. We also recommend a multi‐faceted strategy for cases remaining unsolved after singleton ES.
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Affiliation(s)
- Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Rachel Stapleton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - David J Amor
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - Chloe A Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Patrick Yap
- Genetic Health Service NZ, Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew Regan
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Miriam Fanjul Fernandez
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Justine Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
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A three-year follow-up study evaluating clinical utility of exome sequencing and diagnostic potential of reanalysis. NPJ Genom Med 2020; 5:37. [PMID: 32963807 PMCID: PMC7484757 DOI: 10.1038/s41525-020-00144-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/14/2020] [Indexed: 01/05/2023] Open
Abstract
Exome sequencing (ES) has become one of the important diagnostic tools in clinical genetics with a reported diagnostic rate of 25–58%. Many studies have illustrated the diagnostic and immediate clinical impact of ES. However, up to 75% of individuals remain undiagnosed and there is scarce evidence supporting clinical utility beyond a follow-up period of >1 year. This is a 3-year follow-up analysis to our previous publication by Mak et al. (NPJ Genom. Med. 3:19, 2018), to evaluate the long-term clinical utility of ES and the diagnostic potential of exome reanalysis. The diagnostic yield of the initial study was 41% (43/104). Exome reanalysis in 46 undiagnosed individuals has achieved 12 new diagnoses. The additional yield compared with the initial analysis was at least 12% (increased from 41% to at least 53%). After a median follow-up period of 3.4 years, change in clinical management was observed in 72.2% of the individuals (26/36), leading to positive change in clinical outcome in four individuals (11%). There was a minimum healthcare cost saving of HKD$152,078 (USD$19,497; €17,282) annually for these four individuals. There were a total of six pregnancies from five families within the period. Prenatal diagnosis was performed in four pregnancies; one fetus was affected and resulted in termination. None of the parents underwent preimplantation genetic diagnosis. This 3-year follow-up study demonstrated the long-term clinical utility of ES at individual, familial and health system level, and the promising diagnostic potential of subsequent reanalysis. This highlights the benefits of implementing ES and regular reanalysis in the clinical setting.
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Abstract
Canalization refers to the evolution of populations such that the number of individuals who deviate from the optimum trait, or experience disease, is minimized. In the presence of rapid cultural, environmental, or genetic change, the reverse process of decanalization may contribute to observed increases in disease prevalence. This review starts by defining relevant concepts, drawing distinctions between the canalization of populations and robustness of individuals. It then considers evidence pertaining to three continuous traits and six domains of disease. In each case, existing genetic evidence for genotype-by-environment interactions is insufficient to support a strong inference of decanalization, but we argue that the advent of genome-wide polygenic risk assessment now makes an empirical evaluation of the role of canalization in preventing disease possible. Finally, the contributions of both rare and common variants to congenital abnormality and adult onset disease are considered in light of a new kerplunk model of genetic effects.
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Affiliation(s)
- Greg Gibson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| | - Kristine A Lacek
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
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James KN, Clark MM, Camp B, Kint C, Schols P, Batalov S, Briggs B, Veeraraghavan N, Chowdhury S, Kingsmore SF. Partially automated whole-genome sequencing reanalysis of previously undiagnosed pediatric patients can efficiently yield new diagnoses. NPJ Genom Med 2020; 5:33. [PMID: 32821428 PMCID: PMC7419288 DOI: 10.1038/s41525-020-00140-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/14/2020] [Indexed: 01/16/2023] Open
Abstract
To investigate the diagnostic and clinical utility of a partially automated reanalysis pipeline, forty-eight cases of seriously ill children with suspected genetic disease who did not receive a diagnosis upon initial manual analysis of whole-genome sequencing (WGS) were reanalyzed at least 1 year later. Clinical natural language processing (CNLP) of medical records provided automated, updated patient phenotypes, and an automated analysis system delivered limited lists of possible diagnostic variants for each case. CNLP identified a median of 79 new clinical features per patient at least 1 year later. Compared to a standard manual reanalysis pipeline, the partially automated pipeline reduced the number of variants to be analyzed by 90% (range: 74%-96%). In 2 cases, diagnoses were made upon reinterpretation, representing an incremental diagnostic yield of 4.2% (2/48, 95% CI: 0.5–14.3%). Four additional cases were flagged with a possible diagnosis to be considered during subsequent reanalysis. Separately, copy number analysis led to diagnoses in two cases. Ongoing discovery of new disease genes and refined variant classification necessitate periodic reanalysis of negative WGS cases. The clinical features of patients sequenced as infants evolve rapidly with age. Partially automated reanalysis, including automated re-phenotyping through CNLP, has the potential to identify molecular diagnoses with reduced expert labor intensity.
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Affiliation(s)
- Kiely N James
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | - Michelle M Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | - Brandon Camp
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | | | | | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | - Benjamin Briggs
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
| | | | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA USA
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69
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Lefebvre M, Bruel AL, Tisserant E, Bourgon N, Duffourd Y, Collardeau-Frachon S, Attie-Bitach T, Kuentz P, Assoum M, Schaefer E, El Chehadeh S, Antal MC, Kremer V, Girard-Lemaitre F, Mandel JL, Lehalle D, Nambot S, Jean-Marçais N, Houcinat N, Moutton S, Marle N, Lambert L, Jonveaux P, Foliguet B, Mazutti JP, Gaillard D, Alanio E, Poirisier C, Lebre AS, Aubert-Lenoir M, Arbez-Gindre F, Odent S, Quélin C, Loget P, Fradin M, Willems M, Bigi N, Perez MJ, Blesson S, Francannet C, Beaufrere AM, Patrier-Sallebert S, Guerrot AM, Goldenberg A, Brehin AC, Lespinasse J, Touraine R, Capri Y, Saint-Frison MH, Laurent N, Philippe C, Tran Mau-Them F, Thevenon J, Faivre L, Thauvin-Robinet C, Vitobello A. Genotype-first in a cohort of 95 fetuses with multiple congenital abnormalities: when exome sequencing reveals unexpected fetal phenotype-genotype correlations. J Med Genet 2020; 58:400-413. [PMID: 32732226 DOI: 10.1136/jmedgenet-2020-106867] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/04/2020] [Accepted: 05/21/2020] [Indexed: 11/03/2022]
Abstract
PURPOSE Molecular diagnosis based on singleton exome sequencing (sES) is particularly challenging in fetuses with multiple congenital abnormalities (MCA). Indeed, some studies reveal a diagnostic yield of about 20%, far lower than in live birth individuals showing developmental abnormalities (30%), suggesting that standard analyses, based on the correlation between clinical hallmarks described in postnatal syndromic presentations and genotype, may underestimate the impact of the genetic variants identified in fetal analyses. METHODS We performed sES in 95 fetuses with MCA. Blind to phenotype, we applied a genotype-first approach consisting of combined analyses based on variants annotation and bioinformatics predictions followed by reverse phenotyping. Initially applied to OMIM-morbid genes, analyses were then extended to all genes. We complemented our approach by using reverse phenotyping, variant segregation analysis, bibliographic search and data sharing in order to establish the clinical significance of the prioritised variants. RESULTS sES rapidly identified causal variant in 24/95 fetuses (25%), variants of unknown significance in OMIM genes in 8/95 fetuses (8%) and six novel candidate genes in 6/95 fetuses (6%). CONCLUSIONS This method, based on a genotype-first approach followed by reverse phenotyping, shed light on unexpected fetal phenotype-genotype correlations, emphasising the relevance of prenatal studies to reveal extreme clinical presentations associated with well-known Mendelian disorders.
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Affiliation(s)
- Mathilde Lefebvre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Laboratoire d'Anatomo-Pathologie, Plateforme de Biologie Hospitalo-Universitaire, CHU de Dijon Bourgogne, Dijon, France
| | - Ange-Line Bruel
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Emilie Tisserant
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Nicolas Bourgon
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Yannis Duffourd
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | | | - Tania Attie-Bitach
- Laboratoire d'Embryologie et de Génétique des Malformations Congénitales, Hopital Necker, APHP, Paris Cedex 15, France
| | - Paul Kuentz
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Mirna Assoum
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Elise Schaefer
- Service de Génétique Médicale, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Salima El Chehadeh
- Service de Génétique Médicale, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Maria Cristina Antal
- Service de Fœtopathologie, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Valérie Kremer
- Laboratoire de Cytogénétique constitutionnelle et prénatale, CHU de Strasbourg, Strasbourg, France
| | - Françoise Girard-Lemaitre
- Département Médecine translationnelle et neurogénétique, Institut de génétique et de biologie moléculaire et cellulaire, Strasbourg, France
| | - Jean-Louis Mandel
- Département Médecine translationnelle et neurogénétique, Institut de génétique et de biologie moléculaire et cellulaire, Strasbourg, France
| | - Daphne Lehalle
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Nolwenn Jean-Marçais
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Nada Houcinat
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sébastien Moutton
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire de Génétique chromosomique et moléculaire, CHU de Dijon Bourgogne, Dijon, France
| | - Laetita Lambert
- UF de Génétique médicale, Maternité régionale, CHU de Nancy, Nancy, France
| | | | - Bernard Foliguet
- Laboratoire de Biologie de la Reproduction et du Développement Maternité de Nancy, CHU de Nancy, Nancy, France
| | - Jean-Pierre Mazutti
- Laboratoire de Biologie de la Reproduction et du Développement Maternité de Nancy, CHU de Nancy, Nancy, France
| | | | | | | | - Anne-Sophie Lebre
- Service de Génétique et Biologie de la Reproduction, CHU de Reims, Reims, France
| | | | | | - Sylvie Odent
- Service de Génétique Clinique, Hôpital Sud, CLAD Ouest, CNRS UMR6290 Génétique et Pathologies du Développement, Université de Rennes, Rennes, France
| | - Chloé Quélin
- Service de Génétique Clinique, Hôpital Sud, CLAD Ouest, CNRS UMR6290 Génétique et Pathologies du Développement, Université de Rennes, Rennes, France.,Service de Fœtopathologie, CHU de Rennes, Rennes, France
| | - Philippe Loget
- Service de Fœtopathologie, CHU de Rennes, Rennes, France
| | - Melanie Fradin
- Service de Génétique Clinique, Hôpital Sud, CLAD Ouest, CNRS UMR6290 Génétique et Pathologies du Développement, Université de Rennes, Rennes, France
| | - Marjolaine Willems
- Equipe Maladies Génétiques de l'Enfant et de l'Adulte, CHU de Montpellier, Montpellier, France
| | - Nicole Bigi
- Service de Fœtopathologie, CHU de Montpellier, Montpellier, France
| | - Marie-José Perez
- Service de Fœtopathologie, CHU de Montpellier, Montpellier, France
| | | | - Christine Francannet
- Service de Génétique médicale, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | | | | | | | | | | | | | - Renaud Touraine
- Service de Genetique Clinique, C.H.U. De Saint Etienne-Hopital Nord, Saint Etienne Cedex 2, France
| | - Yline Capri
- Service de génétique clinique, Hôpital Robert Debré - APHP, Paris, France
| | | | - Nicole Laurent
- Laboratoire d'Anatomo-Pathologie, Plateforme de Biologie Hospitalo-Universitaire, CHU de Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Frederic Tran Mau-Them
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Julien Thevenon
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Département de Génétique et Procréation, CHU Grenoble Alpes, Université Grenoble Alpes, Grenoble, France
| | - Laurence Faivre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France .,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France .,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
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70
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Mansour-Hendili L, Aissat A, Badaoui B, Sakka M, Gameiro C, Ortonne V, Wagner-Ballon O, Pissard S, Picard V, Ghazal K, Bahuau M, Guitton C, Mansour Z, Duplan M, Petit A, Costedoat-Chalumeau N, Michel M, Bartolucci P, Moutereau S, Funalot B, Galactéros F. Exome sequencing for diagnosis of congenital hemolytic anemia. Orphanet J Rare Dis 2020; 15:180. [PMID: 32641076 PMCID: PMC7341591 DOI: 10.1186/s13023-020-01425-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/27/2020] [Indexed: 02/07/2023] Open
Abstract
Background Congenital hemolytic anemia constitutes a heterogeneous group of rare genetic disorders of red blood cells. Diagnosis is based on clinical data, family history and phenotypic testing, genetic analyses being usually performed as a late step. In this study, we explored 40 patients with congenital hemolytic anemia by whole exome sequencing: 20 patients with hereditary spherocytosis and 20 patients with unexplained hemolysis. Results A probable genetic cause of disease was identified in 82.5% of the patients (33/40): 100% of those with suspected hereditary spherocytosis (20/20) and 65% of those with unexplained hemolysis (13/20). We found that several patients carried genetic variations in more than one gene (3/20 in the hereditary spherocytosis group, 6/13 fully elucidated patients in the unexplained hemolysis group), giving a more accurate picture of the genetic complexity of congenital hemolytic anemia. In addition, whole exome sequencing allowed us to identify genetic variants in non-congenital hemolytic anemia genes that explained part of the phenotype in 3 patients. Conclusion The rapid development of next generation sequencing has rendered the genetic study of these diseases much easier and cheaper. Whole exome sequencing in congenital hemolytic anemia could provide a more precise and quicker diagnosis, improve patients’ healthcare and probably has to be democratized notably for complex cases.
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Affiliation(s)
- Lamisse Mansour-Hendili
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France. .,Univ Paris Est Creteil, INSERM, IMRB, F-94010, Creteil, France.
| | - Abdelrazak Aissat
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France.,Univ Paris Est Creteil, INSERM, IMRB, F-94010, Creteil, France
| | - Bouchra Badaoui
- Département d'hématologie et d'immunologie, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France
| | - Mehdi Sakka
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France.,Univ Paris Est Creteil, INSERM, IMRB, F-94010, Creteil, France
| | - Christine Gameiro
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France
| | - Valérie Ortonne
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France
| | - Orianne Wagner-Ballon
- Univ Paris Est Creteil, INSERM, IMRB, F-94010, Creteil, France.,Département d'hématologie et d'immunologie, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France
| | - Serge Pissard
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France.,Univ Paris Est Creteil, INSERM, IMRB, F-94010, Creteil, France
| | - Véronique Picard
- Département d'hématologie, AP-HP, Hôpital Bicêtre, F-94270, Le Kremlin-Bicêtre, France
| | - Khaldoun Ghazal
- Département de Biochimie, AP-HP, Hôpital Bicêtre, F-94270, Le Kremlin-Bicêtre, France
| | - Michel Bahuau
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France
| | - Corinne Guitton
- Département d'hématologie pédiatrique, AP-HP, Hôpital Bicêtre, F-94270, Le Kremlin-Bicêtre, France
| | - Ziad Mansour
- Clinique ADASSA, Maternité, F-67000, Strasbourg, France
| | - Mylène Duplan
- Département d'onco-hématologie pédiatrique, CHU d'Angers, 4 Rue Larrey, 49100, Angers, France
| | - Arnaud Petit
- Département d'onco-hématologie pédiatrique, AP-HP, Hôpital Armand Trousseau, F-75012, Paris, France
| | | | - Marc Michel
- Univ Paris Est Creteil, INSERM, IMRB, F-94010, Creteil, France.,Département de médecine interne, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France
| | - Pablo Bartolucci
- Univ Paris Est Creteil, INSERM, IMRB, F-94010, Creteil, France.,Département de médecine interne, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France.,Unité des maladies génétiques du globule rouge (UMGGR), AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France
| | - Stéphane Moutereau
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France.,Univ Paris Est Creteil, INSERM, IMRB, F-94010, Creteil, France
| | - Benoît Funalot
- Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France.,Univ Paris Est Creteil, INSERM, IMRB, F-94010, Creteil, France
| | - Frédéric Galactéros
- Univ Paris Est Creteil, INSERM, IMRB, F-94010, Creteil, France.,Département de médecine interne, AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France.,Unité des maladies génétiques du globule rouge (UMGGR), AP-HP, Hôpitaux Universitaires Henri Mondor, F-94010, Creteil, France
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71
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Won D, Kim SH, Kim B, Lee ST, Kang HC, Choi JR. Reanalysis of Genomic Sequencing Results in a Clinical Laboratory: Advantages and Limitations. Front Neurol 2020; 11:612. [PMID: 32695065 PMCID: PMC7338758 DOI: 10.3389/fneur.2020.00612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/25/2020] [Indexed: 11/13/2022] Open
Abstract
Genetic diagnosis of patients with neurodevelopmental disorders is imperative and a standard clinical practice. Considering the continuous accumulation of data on disease-causing variants, reanalysis of previously established sequencing data is important. Periodic reanalysis of variants with uncertain significance has become mandatory in clinical laboratories. Therefore, to confirm the utility of the reanalysis of targeted gene panel data in clinical laboratories, we re-evaluated the data of two groups of patients who had undergone targeted gene panel testing for neurodevelopmental disorders (n = 116) and epileptic encephalopathy (n = 384). This reanalysis was based on a reannotation process reflecting updated databases. Six (5.2%) and seven (1.8%) new pathogenic or likely pathogenic variants were identified in these two groups, respectively, attributable to the updated guidelines and de novo reports from unrelated patients. Although relatively low, considerable increase in the diagnostic yield was confirmed. We suggest that reanalysis of genetic variants, mainly using changes in databases and updated interpretations, should be implemented as a routine practice in clinical laboratories.
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Affiliation(s)
- Dongju Won
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Se Hee Kim
- Division of Pediatric Neurology, Department of Pediatrics, Epilepsy Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Borahm Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Hoon-Chul Kang
- Division of Pediatric Neurology, Department of Pediatrics, Epilepsy Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
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72
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Miller CR, Lee K, Pfau RB, Reshmi SC, Corsmeier DJ, Hashimoto S, Dave-Wala A, Jayaraman V, Koboldt D, Matthews T, Mouhlas D, Stein M, McKinney A, Grossman T, Kelly BJ, White P, Magrini V, Wilson RK, Mardis ER, Cottrell CE. Disease-associated mosaic variation in clinical exome sequencing: a two-year pediatric tertiary care experience. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005231. [PMID: 32371413 PMCID: PMC7304353 DOI: 10.1101/mcs.a005231] [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: 02/15/2020] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Exome sequencing (ES) has become an important tool in pediatric genomic medicine, improving identification of disease-associated variation due to assay breadth. Depth is also afforded by ES, enabling detection of lower-frequency mosaic variation compared to Sanger sequencing in the studied tissue, thus enhancing diagnostic yield. Within a pediatric tertiary-care hospital, we report two years of clinical ES data from probands evaluated for genetic disease to assess diagnostic yield, characteristics of causal variants, and prevalence of mosaicism among disease-causing variants. Exome-derived, phenotype-driven variant data from 357 probands was analyzed concurrent with parental ES data, when available. Blood was the source of nucleic acid. Sequence read alignments were manually reviewed for all assessed variants. Sanger sequencing was used for suspected de novo or mosaic variation. Clinical provider notes were reviewed to determine concordance between laboratory-reported data and the ordering provider's interpretation of variant-associated disease causality. Laboratory-derived diagnostic yield and provider-substantiated diagnoses had 91.4% concordance. The cohort returned 117 provider-substantiated diagnoses among 115 probands for a diagnostic yield of 32.2%. De novo variants represented 64.9% of disease-associated variation within trio analyses. Among the 115 probands, five harbored disease-associated somatic mosaic variation. Two additional probands were observed to inherit a disease-associated variant from an unaffected mosaic parent. Among inheritance patterns, de novo variation was the most frequent disease etiology. Somatic mosaicism is increasingly recognized as a significant contributor to genetic disease, particularly with increased sequence depth attainable from ES. This report highlights the potential and importance of detecting mosaicism in ES.
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Affiliation(s)
- Cecelia R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology
| | - Ruthann B Pfau
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shalini C Reshmi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Donald J Corsmeier
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Sayaka Hashimoto
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Ashita Dave-Wala
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Daniel Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Theodora Matthews
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Danielle Mouhlas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Maggie Stein
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Aimee McKinney
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Tom Grossman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
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73
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Rexach J, Lee H, Martinez-Agosto JA, Németh AH, Fogel BL. Clinical application of next-generation sequencing to the practice of neurology. Lancet Neurol 2020; 18:492-503. [PMID: 30981321 DOI: 10.1016/s1474-4422(19)30033-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 01/05/2023]
Abstract
Next-generation sequencing technologies allow for rapid and inexpensive large-scale genomic analysis, creating unprecedented opportunities to integrate genomic data into the clinical diagnosis and management of neurological disorders. However, the scale and complexity of these data make them difficult to interpret and require the use of sophisticated bioinformatics applied to extensive datasets, including whole exome and genome sequences. Detailed analysis of genetic data has shown that accurate phenotype information is essential for correct interpretation of genetic variants and might necessitate re-evaluation of the patient in some cases. A multidisciplinary approach that incorporates bioinformatics, clinical evaluation, and human genetics can help to address these challenges. However, despite numerous studies that show the efficacy of next-generation sequencing in establishing molecular diagnoses, pathogenic mutations are generally identified in fewer than half of all patients with genetic neurological disorders, exposing considerable gaps in the understanding of the human genome and providing opportunities to focus research on improving the usefulness of genomics in clinical practice. Looking forward, the emergence of precision health in neurological care will increasingly apply genomic data analysis to pharmacogenetics, preventive medicine, and patient-targeted therapies.
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Affiliation(s)
- Jessica Rexach
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Brent L Fogel
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Clinical Neurogenomics Research Center, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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74
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Bertacchi M, Romano AL, Loubat A, Tran Mau-Them F, Willems M, Faivre L, Khau van Kien P, Perrin L, Devillard F, Sorlin A, Kuentz P, Philippe C, Garde A, Neri F, Di Giaimo R, Oliviero S, Cappello S, D'Incerti L, Frassoni C, Studer M. NR2F1 regulates regional progenitor dynamics in the mouse neocortex and cortical gyrification in BBSOAS patients. EMBO J 2020; 39:e104163. [PMID: 32484994 PMCID: PMC7327499 DOI: 10.15252/embj.2019104163] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/01/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
The relationships between impaired cortical development and consequent malformations in neurodevelopmental disorders, as well as the genes implicated in these processes, are not fully elucidated to date. In this study, we report six novel cases of patients affected by BBSOAS (Boonstra‐Bosch‐Schaff optic atrophy syndrome), a newly emerging rare neurodevelopmental disorder, caused by loss‐of‐function mutations of the transcriptional regulator NR2F1. Young patients with NR2F1 haploinsufficiency display mild to moderate intellectual disability and show reproducible polymicrogyria‐like brain malformations in the parietal and occipital cortex. Using a recently established BBSOAS mouse model, we found that Nr2f1 regionally controls long‐term self‐renewal of neural progenitor cells via modulation of cell cycle genes and key cortical development master genes, such as Pax6. In the human fetal cortex, distinct NR2F1 expression levels encompass gyri and sulci and correlate with local degrees of neurogenic activity. In addition, reduced NR2F1 levels in cerebral organoids affect neurogenesis and PAX6 expression. We propose NR2F1 as an area‐specific regulator of mouse and human brain morphology and a novel causative gene of abnormal gyrification.
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Affiliation(s)
- Michele Bertacchi
- Université Côte d'Azur, CNRS, Inserm, iBV, Paris, France.,Clinical and Experimental Epileptology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | | | - Agnès Loubat
- Université Côte d'Azur, CNRS, Inserm, iBV, Paris, France
| | - Frederic Tran Mau-Them
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Marjolaine Willems
- Hôpital Arnaud de Villeneuve, Service de Génétique Médicale, CHU de Montpellier, Montpellier, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence maladies rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Philippe Khau van Kien
- Hôpital Carémeau, UF de Génétique Médicale et Cytogénétique, Centre de Compétences Anomalies du Développement et Syndromes Malformatifs, CHU de Nîmes, Nîmes, France
| | - Laurence Perrin
- Unité Fonctionnelle de Génétique Clinique, Hôpital Robert Debré, Paris, France
| | - Françoise Devillard
- Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France
| | - Arthur Sorlin
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence maladies rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de référence maladies rares « Déficiences intellectuelles de causes rares », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Paul Kuentz
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Génétique Biologique, PCBio, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Christophe Philippe
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Aurore Garde
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence maladies rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Francesco Neri
- Epigenetics Unit, Italian Institute for Genomic Medicine, University of Torino, Torino, Italy.,Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Rossella Di Giaimo
- Department of Biology, University of Naples Federico II, Napoli, Italy.,Max Planck Institute of Psychiatry, München, Germany
| | - Salvatore Oliviero
- Epigenetics Unit, Italian Institute for Genomic Medicine, University of Torino, Torino, Italy
| | | | - Ludovico D'Incerti
- Neuroradiology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Carolina Frassoni
- Clinical and Experimental Epileptology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Michèle Studer
- Université Côte d'Azur, CNRS, Inserm, iBV, Paris, France
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75
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Bruel A, Vitobello A, Tran Mau‐Them F, Nambot S, Sorlin A, Denommé‐Pichon A, Delanne J, Moutton S, Callier P, Duffourd Y, Philippe C, Faivre L, Thauvin‐Robinet C. Next‐generation
sequencing approaches and challenges in the diagnosis of developmental anomalies and intellectual disability. Clin Genet 2020; 98:433-444. [DOI: 10.1111/cge.13764] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Ange‐Line Bruel
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Déficiences Intellectuelles de causes rares, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Antonio Vitobello
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Frédéric Tran Mau‐Them
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Sophie Nambot
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Arthur Sorlin
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Maladies dermatologiques en mosaïque Service de dermatologie, CHU Dijon Bourgogne Dijon France
| | - Anne‐Sophie Denommé‐Pichon
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Julian Delanne
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Sébastien Moutton
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Patrick Callier
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Yannis Duffourd
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Christophe Philippe
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Laurence Faivre
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
| | - Christel Thauvin‐Robinet
- Inserm UMR1231 GAD Université Bourgogne‐Franche Comté Dijon France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Déficiences Intellectuelles de causes rares, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
- Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs, Centre de Génétique, FHU‐TRANSLAD, CHU Dijon Bourgogne Dijon France
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76
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Stenton SL, Prokisch H. Genetics of mitochondrial diseases: Identifying mutations to help diagnosis. EBioMedicine 2020; 56:102784. [PMID: 32454403 PMCID: PMC7248429 DOI: 10.1016/j.ebiom.2020.102784] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial diseases are amongst the most genetically and phenotypically diverse groups of inherited diseases. The vast phenotypic overlap with other disease entities together with the absence of reliable biomarkers act as driving forces for the integration of unbiased methodologies early in the diagnostic algorithm, such as whole exome sequencing (WES) and whole genome sequencing (WGS). Such approaches are used in variant discovery and in combination with high-throughput functional assays such as transcriptomics in simultaneous variant discovery and validation. By capturing all genes, they not only increase the diagnostic rate in heterogenous mitochondrial disease patients, but accelerate novel disease gene discovery, and are valuable in side-stepping the risk of overlooking unexpected or even treatable genetic disease diagnoses.
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Affiliation(s)
- Sarah L Stenton
- Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Trogerstraße 32, 81675 München, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Holger Prokisch
- Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Trogerstraße 32, 81675 München, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany.
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77
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Clark MM, Hildreth A, Batalov S, Ding Y, Chowdhury S, Watkins K, Ellsworth K, Camp B, Kint CI, Yacoubian C, Farnaes L, Bainbridge MN, Beebe C, Braun JJA, Bray M, Carroll J, Cakici JA, Caylor SA, Clarke C, Creed MP, Friedman J, Frith A, Gain R, Gaughran M, George S, Gilmer S, Gleeson J, Gore J, Grunenwald H, Hovey RL, Janes ML, Lin K, McDonagh PD, McBride K, Mulrooney P, Nahas S, Oh D, Oriol A, Puckett L, Rady Z, Reese MG, Ryu J, Salz L, Sanford E, Stewart L, Sweeney N, Tokita M, Van Der Kraan L, White S, Wigby K, Williams B, Wong T, Wright MS, Yamada C, Schols P, Reynders J, Hall K, Dimmock D, Veeraraghavan N, Defay T, Kingsmore SF. Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation. Sci Transl Med 2020; 11:11/489/eaat6177. [PMID: 31019026 DOI: 10.1126/scitranslmed.aat6177] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 10/24/2018] [Accepted: 04/01/2019] [Indexed: 12/19/2022]
Abstract
By informing timely targeted treatments, rapid whole-genome sequencing can improve the outcomes of seriously ill children with genetic diseases, particularly infants in neonatal and pediatric intensive care units (ICUs). The need for highly qualified professionals to decipher results, however, precludes widespread implementation. We describe a platform for population-scale, provisional diagnosis of genetic diseases with automated phenotyping and interpretation. Genome sequencing was expedited by bead-based genome library preparation directly from blood samples and sequencing of paired 100-nt reads in 15.5 hours. Clinical natural language processing (CNLP) automatically extracted children's deep phenomes from electronic health records with 80% precision and 93% recall. In 101 children with 105 genetic diseases, a mean of 4.3 CNLP-extracted phenotypic features matched the expected phenotypic features of those diseases, compared with a match of 0.9 phenotypic features used in manual interpretation. We automated provisional diagnosis by combining the ranking of the similarity of a patient's CNLP phenome with respect to the expected phenotypic features of all genetic diseases, together with the ranking of the pathogenicity of all of the patient's genomic variants. Automated, retrospective diagnoses concurred well with expert manual interpretation (97% recall and 99% precision in 95 children with 97 genetic diseases). Prospectively, our platform correctly diagnosed three of seven seriously ill ICU infants (100% precision and recall) with a mean time saving of 22:19 hours. In each case, the diagnosis affected treatment. Genome sequencing with automated phenotyping and interpretation in a median of 20:10 hours may increase adoption in ICUs and, thereby, timely implementation of precise treatments.
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Affiliation(s)
- Michelle M Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Amber Hildreth
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA.,Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kelly Watkins
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Brandon Camp
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | | | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Matthew N Bainbridge
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Codified Genomics, LLC, Houston, TX 77033, USA
| | - Curtis Beebe
- Rady Children's Hospital, San Diego, CA 92123, USA
| | - Joshua J A Braun
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Margaret Bray
- Alexion Pharmaceuticals Inc., New Haven, CT 06510, USA
| | - Jeanne Carroll
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Julie A Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sara A Caylor
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Christina Clarke
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Mitchell P Creed
- University of Kansas School of Medicine, Kansas City, MO 66160, USA
| | - Jennifer Friedman
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Neurosciences, University of California San Diego, San Diego, CA 92093, USA
| | | | | | - Mary Gaughran
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | | | - Joseph Gleeson
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Neurosciences, University of California San Diego, San Diego, CA 92093, USA
| | | | | | - Raymond L Hovey
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Marie L Janes
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kejia Lin
- Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Kyle McBride
- Rady Children's Hospital, San Diego, CA 92123, USA
| | - Patrick Mulrooney
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Daeheon Oh
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Albert Oriol
- Rady Children's Hospital, San Diego, CA 92123, USA
| | - Laura Puckett
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Zia Rady
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Julie Ryu
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Lisa Salz
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Erica Sanford
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Nathaly Sweeney
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Mari Tokita
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Luca Van Der Kraan
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sarah White
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kristen Wigby
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Terence Wong
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Meredith S Wright
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Catherine Yamada
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - John Reynders
- Alexion Pharmaceuticals Inc., New Haven, CT 06510, USA
| | | | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Thomas Defay
- Alexion Pharmaceuticals Inc., New Haven, CT 06510, USA
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78
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Issa MY, Chechlacz Z, Stanley V, George RD, McEvoy-Venneri J, Belandres D, Elbendary HM, Gaber KR, Nabil A, Abdel-Hamid MS, Zaki MS, Gleeson JG. Molecular diagnosis in recessive pediatric neurogenetic disease can help reduce disease recurrence in families. BMC Med Genomics 2020; 13:68. [PMID: 32404165 PMCID: PMC7218834 DOI: 10.1186/s12920-020-0714-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Background The causes for thousands of individually rare recessive diseases have been discovered since the adoption of next generation sequencing (NGS). Following the molecular diagnosis in older children in a family, parents could use this information to opt for fetal genotyping in subsequent pregnancies, which could inform decisions about elective termination of pregnancy. The use of NGS diagnostic sequencing in families has not been demonstrated to yield benefit in subsequent pregnancies to reduce recurrence. Here we evaluated whether genetic diagnosis in older children in families supports reduction in recurrence of recessive neurogenetic disease. Methods Retrospective study involving families with a child with a recessive pediatric brain disease (rPBD) that underwent NGS-based molecular diagnosis. Prenatal molecular testing was offered to couples in which a molecular diagnosis was made, to help couples seeking to prevent recurrence. With this information, families made decisions about elective termination. Pregnancies that were carried to term were assessed for the health of child and mother, and compared with historic recurrence risk of recessive disease. Results Between 2010 and 2016, 1172 families presented with a child a likely rPBD, 526 families received a molecular diagnosis, 91 families returned to the clinic with 101 subsequent pregnancies, and 84 opted for fetal genotyping. Sixty tested negative for recurrence for the biallelic mutation in the fetus, and all, except for one spontaneous abortion, carried to term, and were unaffected at follow-up. Of 24 that genotyped positive for the biallelic mutation, 16 were electively terminated, and 8 were carried to term and showed features of disease similar to that of the older affected sibling(s). Among the 101 pregnancies, disease recurrence in living offspring deviated from the expected 25% to the observed 12% ([95% CI 0·04 to 0·20], p = 0·011). Conclusions Molecular diagnosis in an older child, coupled with prenatal fetal genotyping in subsequent pregnancies and genetic counselling, allows families to make informed decisions to reduce recessive neurogenetic disease recurrence.
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Affiliation(s)
- Mahmoud Y Issa
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Zinayida Chechlacz
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Valentina Stanley
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Renee D George
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jennifer McEvoy-Venneri
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Denice Belandres
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Hasnaa M Elbendary
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Khaled R Gaber
- Prenatal Diagnosis and Fetal Medicine Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Ahmed Nabil
- Prenatal Diagnosis and Fetal Medicine Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, 12311, Egypt.
| | - Joseph G Gleeson
- Departments of Neurosciences and Pediatrics, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA.
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79
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Second-tier trio exome sequencing after negative solo clinical exome sequencing: an efficient strategy to increase diagnostic yield and decipher molecular bases in undiagnosed developmental disorders. Hum Genet 2020; 139:1381-1390. [PMID: 32399599 DOI: 10.1007/s00439-020-02178-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023]
Abstract
Developmental disorders (DD), characterized by malformations/dysmorphism and/or intellectual disability, affecting around 3% of worldwide population, are mostly linked to genetic anomalies. Despite clinical exome sequencing (cES) centered on genes involved in human genetic disorders, the majority of patients affected by DD remain undiagnosed after solo-cES. Trio-based strategy is expected to facilitate variant selection thanks to rapid parental segregation. We performed a second step trio-ES (not only focusing on genes involved in human disorders) analysis in 70 patients with negative results after solo-cES. All candidate variants were shared with a MatchMaking exchange system to identify additional patients carrying variants in the same genes and with similar phenotype. In 18/70 patients (26%), we confirmed causal implication of nine OMIM-morbid genes and identified nine new strong candidate genes (eight de novo and one compound heterozygous variants). These nine new candidate genes were validated through the identification of patients with similar phenotype and genotype thanks to data sharing. Moreover, 11 genes harbored variants of unknown significance in 10/70 patients (14%). In DD, a second step trio-based ES analysis appears an efficient strategy in diagnostic and translational research to identify highly candidate genes and improve diagnostic yield.
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80
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Angural A, Spolia A, Mahajan A, Verma V, Sharma A, Kumar P, Dhar MK, Pandita KK, Rai E, Sharma S. Review: Understanding Rare Genetic Diseases in Low Resource Regions Like Jammu and Kashmir - India. Front Genet 2020; 11:415. [PMID: 32425985 PMCID: PMC7203485 DOI: 10.3389/fgene.2020.00415] [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: 08/03/2019] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Rare diseases (RDs) are the clinical conditions affecting a few percentage of individuals in a general population compared to other diseases. Limited clinical information and a lack of reliable epidemiological data make their timely diagnosis and therapeutic management difficult. Emerging Next-Generation DNA Sequencing technologies have enhanced our horizons on patho-physiological understanding of many of the RDs and ushered us into an era of diagnostic and therapeutic research related to this ignored health challenge. Unfortunately, relevant research is meager in developing countries which lack a reliable estimate of the exact burden of most of the RDs. India is to be considered as the "Pandora's Box of genetic disorders." Owing to its huge population heterogeneity and high inbreeding or endogamy rates, a higher burden of rare recessive genetic diseases is expected and supported by the literature findings that endogamy is highly detrimental to health as it enhances the degree of homozygosity of recessive alleles in the general population. The population of a low resource region Jammu and Kashmir (J&K) - India, is highly inbred. Some of its population groups variably practice consanguinity. In context with the region's typical geographical topography, highly inbred population structure and unique but heterogeneous gene pool, a huge burden of known and uncharacterized genetic disorders is expected. Unfortunately, many suspected cases of genetic disorders remain undiagnosed or misdiagnosed due to lack of appropriate clinical as well as diagnostic resources in the region, causing patients to face a huge psycho-socio-economic crisis and many a time suffer life-long with their ailment. In this review, the major challenges associated with RDs are highlighted in general and an account on the methods that can be adopted for conducting fruitful molecular genetic studies in genetically vulnerable and low resource regions is also provided, with an example of a region like J&K - India.
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Affiliation(s)
- Arshia Angural
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Akshi Spolia
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ankit Mahajan
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Vijeshwar Verma
- Bioinformatics Infrastructure Facility, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ankush Sharma
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
| | - Parvinder Kumar
- Institute of Human Genetics, University of Jammu, Jammu, India
| | | | - Kamal Kishore Pandita
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
- Independent Researcher, Health Clinic, Jammu, India
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
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81
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Campaner R, Cerri M. Manipulative evidence and medical interventions: some qualifications. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2020; 42:15. [PMID: 32347395 DOI: 10.1007/s40656-020-00309-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
The notion of causal evidence in medicine has been the subject of wide philosophical debate in recent years. The notion of evidence has been discussed mostly in connection with Evidence Based Medicine and, more in general, with the assessment of causal nexus in medical, and especially research contexts. "Manipulative evidence" is one of the notions of causal evidence that has stimulated much debate. It has been defined in slightly different ways, attributed different relevance, and recently placed at the core of Gillies' "action-related theory of causality", a view specifically meant to address causation in medicine. While in general sympathetic to Gillies' account, and totally convinced of the relevance of manipulative evidence and different sorts of interventions in the biomedical sciences, we believe that some further qualifications are needed to allow the notion of manipulative evidence to better express features of medical practice. In particular, we provide some qualification of the role of "interventional evidence" proposed by Gillies, suggesting a distinction between "interventional evidence" and "evidence for interventions". A case study from research on rare diseases is analyzed in depth and a multifaceted notion of manipulative evidence put forward that allows better understanding of what manipulations in medical contexts amount to and what their targets are.
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Affiliation(s)
- Raffaella Campaner
- Department of Philosophy and Communication Studies, University of Bologna, Via Zamboni 38, 40126, Bologna, Italy.
| | - Matteo Cerri
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Via Ugo Foscolo 7, 40123, Bologna, Italy
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82
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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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83
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Bouillet B, Crevisy E, Baillot-Rudoni S, Gallegarine D, Jouan T, Duffourd Y, Petit JM, Vergès B, Callier P. Whole-exome sequencing identifies the first French MODY 6 family with a new mutation in the NEUROD1 gene. DIABETES & METABOLISM 2020; 46:400-402. [PMID: 32184107 DOI: 10.1016/j.diabet.2020.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/05/2020] [Accepted: 03/04/2020] [Indexed: 11/30/2022]
Abstract
AIM The aim of the present study was to identify the affected gene in a French family with maturity-onset diabetes of the young (MODY) using whole-exome sequencing (WES). METHODS WES was performed in one patient with MODY, and candidate variants were confirmed in members of the immediate family by Sanger sequencing. RESULTS In the proband, a new heterozygous missense mutation (c.340A>C) was identified in the NEUROD1 gene by WES analysis and confirmed by Sanger sequencing. Additional Sanger sequencing of the proband's sister and mother revealed the same heterozygous mutation. The proband and his sister displayed typical clinical characteristics of MODY, while their mother had the same typical MODY features except for later onset. When clinical and biological profiles were established for all three patients, the severity of diabetes-related complications varied substantially from one family member to another. CONCLUSION A novel missense mutation found in NEUROD1 was associated with MODY 6 features in a single French family.
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Affiliation(s)
- B Bouillet
- Department of Endocrinology, Diabetes and Metabolic Disorders, Dijon University Hospital, hôpital François Mitterrand, BP 77908, 21079 Dijon, France; Inserm Unit, LNC-UMR 1231, University of Burgundy, Dijon, France.
| | - E Crevisy
- Department of Endocrinology, Diabetes and Metabolic Disorders, Dijon University Hospital, hôpital François Mitterrand, BP 77908, 21079 Dijon, France
| | - S Baillot-Rudoni
- Department of Endocrinology, Diabetes and Metabolic Disorders, Dijon University Hospital, hôpital François Mitterrand, BP 77908, 21079 Dijon, France
| | - D Gallegarine
- Genetics Department, Dijon University Hospital, Dijon, France
| | - T Jouan
- Genetics Department, Dijon University Hospital, Dijon, France
| | - Y Duffourd
- Genetics Department, Dijon University Hospital, Dijon, France
| | - J M Petit
- Department of Endocrinology, Diabetes and Metabolic Disorders, Dijon University Hospital, hôpital François Mitterrand, BP 77908, 21079 Dijon, France; Inserm Unit, LNC-UMR 1231, University of Burgundy, Dijon, France
| | - B Vergès
- Department of Endocrinology, Diabetes and Metabolic Disorders, Dijon University Hospital, hôpital François Mitterrand, BP 77908, 21079 Dijon, France; Inserm Unit, LNC-UMR 1231, University of Burgundy, Dijon, France
| | - P Callier
- Genetics Department, Dijon University Hospital, Dijon, France
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84
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Garret P, Ebstein F, Delplancq G, Dozieres-Puyravel B, Boughalem A, Auvin S, Duffourd Y, Klafack S, Zieba BA, Mahmoudi S, Singh KK, Duplomb L, Thauvin-Robinet C, Costa JM, Krüger E, Trost D, Verloes A, Faivre L, Vitobello A. Report of the first patient with a homozygous OTUD7A variant responsible for epileptic encephalopathy and related proteasome dysfunction. Clin Genet 2020; 97:567-575. [PMID: 31997314 DOI: 10.1111/cge.13709] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/29/2022]
Abstract
Heterozygous microdeletions of chromosome 15q13.3 (MIM: 612001) show incomplete penetrance and are associated with a highly variable phenotype that may include intellectual disability, epilepsy, facial dysmorphism and digit anomalies. Rare patients carrying homozygous deletions show more severe phenotypes including epileptic encephalopathy, hypotonia and poor growth. For years, CHRNA7 (MIM: 118511), was considered the candidate gene that could account for this syndrome. However, recent studies in mouse models have shown that OTUD7A/CEZANNE2 (MIM: 612024), which encodes for an ovarian tumor (OTU) deubiquitinase, should be considered the critical gene responsible for brain dysfunction. In this study, a patient presenting with severe global developmental delay, language impairment and epileptic encephalopathy was referred to our genetics center. Trio exome sequencing (tES) analysis identified a homozygous OTUD7A missense variant (NM_130901.2:c.697C>T), predicted to alter an ultraconserved amino acid, p.(Leu233Phe), lying within the OTU catalytic domain. Its subsequent segregation analysis revealed that the parents, presenting with learning disability, and brother were heterozygous carriers. Biochemical assays demonstrated that proteasome complex formation and function were significantly reduced in patient-derived fibroblasts and in OTUD7A knockout HAP1 cell line. We provide evidence that biallelic pathogenic OTUD7A variation is linked to early-onset epileptic encephalopathy and proteasome dysfunction.
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Affiliation(s)
- Philippine Garret
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Laboratoire CERBA, Saint-Ouen l'Aumône, France
| | - Frédéric Ebstein
- Universitätsmedizin Greifswald, Institut für Medizinische Biochemie und Molekularbiologie, Greifswald, Germany
| | - Geoffroy Delplancq
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | | | - Stéphane Auvin
- AP-HP, Hôpital Robert Debré, Service de Neurologie pédiatrique, Paris, France.,UMR1141 INSERM, Université Paris Diderot, Paris, France
| | - Yannis Duffourd
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sandro Klafack
- Universitätsmedizin Greifswald, Institut für Medizinische Biochemie und Molekularbiologie, Greifswald, Germany
| | - Barbara A Zieba
- Universitätsmedizin Greifswald, Institut für Medizinische Biochemie und Molekularbiologie, Greifswald, Germany
| | - Sana Mahmoudi
- Service de Pédiatrie, Centre Hospitalier René-Dubos, Pontoise, France
| | - Karun K Singh
- Department of Biochemistry and Biomedical Sciences, Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Canada
| | - Laurence Duplomb
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Maladies Rares "déficience intellectuelle", centre de génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | - Elke Krüger
- Universitätsmedizin Greifswald, Institut für Medizinische Biochemie und Molekularbiologie, Greifswald, Germany
| | | | - Alain Verloes
- UMR1141 INSERM, Université Paris Diderot, Paris, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", centre de génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
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85
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Barbitoff YA, Polev DE, Glotov AS, Serebryakova EA, Shcherbakova IV, Kiselev AM, Kostareva AA, Glotov OS, Predeus AV. Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage. Sci Rep 2020; 10:2057. [PMID: 32029882 PMCID: PMC7005158 DOI: 10.1038/s41598-020-59026-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/22/2020] [Indexed: 12/30/2022] Open
Abstract
Advantages and diagnostic effectiveness of the two most widely used resequencing approaches, whole exome (WES) and whole genome (WGS) sequencing, are often debated. WES dominated large-scale resequencing projects because of lower cost and easier data storage and processing. Rapid development of 3rd generation sequencing methods and novel exome sequencing kits predicate the need for a robust statistical framework allowing informative and easy performance comparison of the emerging methods. In our study we developed a set of statistical tools to systematically assess coverage of coding regions provided by several modern WES platforms, as well as PCR-free WGS. We identified a substantial problem in most previously published comparisons which did not account for mappability limitations of short reads. Using regression analysis and simple machine learning, as well as several novel metrics of coverage evenness, we analyzed the contribution from the major determinants of CDS coverage. Contrary to a common view, most of the observed bias in modern WES stems from mappability limitations of short reads and exome probe design rather than sequence composition. We also identified the ~ 500 kb region of human exome that could not be effectively characterized using short read technology and should receive special attention during variant analysis. Using our novel metrics of sequencing coverage, we identified main determinants of WES and WGS performance. Overall, our study points out avenues for improvement of enrichment-based methods and development of novel approaches that would maximize variant discovery at optimal cost.
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Affiliation(s)
- Yury A Barbitoff
- Bioinformatics Institute, Saint Petersburg, Russia.,Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology, and Reproduction, Saint Petersburg, Russia.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,Cerbalab LTD, Saint Petersburg, Russia
| | | | - Andrey S Glotov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology, and Reproduction, Saint Petersburg, Russia.,Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia.,City Hospital №40, Saint Petersburg, Russia.,Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Elena A Serebryakova
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology, and Reproduction, Saint Petersburg, Russia
| | - Irina V Shcherbakova
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152, Planegg-Martinsried, Germany
| | - Artem M Kiselev
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Anna A Kostareva
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Oleg S Glotov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology, and Reproduction, Saint Petersburg, Russia.,City Hospital №40, Saint Petersburg, Russia
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86
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Rochtus A, Olson HE, Smith L, Keith LG, El Achkar C, Taylor A, Mahida S, Park M, Kelly M, Shain C, Rockowitz S, Sheidley BR, Poduri A. Genetic diagnoses in epilepsy: The impact of dynamic exome analysis in a pediatric cohort. Epilepsia 2020; 61:249-258. [PMID: 31957018 PMCID: PMC7404709 DOI: 10.1111/epi.16427] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVE We evaluated the yield of systematic analysis and/or reanalysis of whole exome sequencing (WES) data from a cohort of well-phenotyped pediatric patients with epilepsy and suspected but previously undetermined genetic etiology. METHODS We identified and phenotyped 125 participants with pediatric epilepsy. Etiology was unexplained at the time of enrollment despite clinical testing, which included chromosomal microarray (57 patients), epilepsy gene panel (n = 48), both (n = 28), or WES (n = 8). Clinical epilepsy diagnoses included developmental and epileptic encephalopathy (DEE), febrile infection-related epilepsy syndrome, Rasmussen encephalitis, and other focal and generalized epilepsies. We analyzed WES data and compared the yield in participants with and without prior clinical genetic testing. RESULTS Overall, we identified pathogenic or likely pathogenic variants in 40% (50/125) of our study participants. Nine patients with DEE had genetic variants in recently published genes that had not been recognized as epilepsy-related at the time of clinical testing (FGF12, GABBR1, GABBR2, ITPA, KAT6A, PTPN23, RHOBTB2, SATB2), and eight patients had genetic variants in candidate epilepsy genes (CAMTA1, FAT3, GABRA6, HUWE1, PTCHD1). Ninety participants had concomitant or subsequent clinical genetic testing, which was ultimately explanatory for 26% (23/90). Of the 67 participants whose molecular diagnoses were "unsolved" through clinical genetic testing, we identified pathogenic or likely pathogenic variants in 17 (25%). SIGNIFICANCE Our data argue for early consideration of WES with iterative reanalysis for patients with epilepsy, particularly those with DEE or epilepsy with intellectual disability. Rigorous analysis of WES data of well-phenotyped patients with epilepsy leads to a broader understanding of gene-specific phenotypic spectra as well as candidate disease gene identification. We illustrate the dynamic nature of genetic diagnosis over time, with analysis and in some cases reanalysis of exome data leading to the identification of disease-associated variants among participants with previously nondiagnostic results from a variety of clinical testing strategies.
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Affiliation(s)
- Anne Rochtus
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, University of Leuven, Leuven, Belgium
| | - Heather E. Olson
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Lacey Smith
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Louisa G. Keith
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Christelle El Achkar
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Alan Taylor
- Department of Genomics, Al Jalila Children’s Specialty Hospital, Dubai, UAE
| | - Sonal Mahida
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Meredith Park
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - McKenna Kelly
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Catherine Shain
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Shira Rockowitz
- Information Services Department, Boston Children’s Hospital, Boston, MA, USA
| | - Beth Rosen Sheidley
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
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87
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Delplancq G, Tarris G, Vitobello A, Nambot S, Sorlin A, Philippe C, Carmignac V, Duffourd Y, Denis C, Eicher JC, Chevarin M, Millat G, Khallouk B, Rousseau T, Falcon-Eicher S, Vasiljevic A, Harizay FT, Thauvin-Robinet C, Faivre L, Kuentz P. Cardiomyopathy due to PRDM16 mutation: First description of a fetal presentation, with possible modifier genes. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:129-135. [PMID: 31965688 DOI: 10.1002/ajmg.c.31766] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/09/2020] [Indexed: 12/15/2022]
Abstract
PRDM16 (positive regulatory domain 16) is localized in the critical region for cardiomyopathy in patients with deletions of chromosome 1p36, as defined by Gajecka et al., American Journal of Medical Genetics, 2010, 152A, 3074-3083, and encodes a zinc finger transcription factor. We present the first fetal case of left ventricular non-compaction (LVNC) with a PRDM16 variant. The third-trimester obstetric ultrasound revealed a hydropic fetus with hydramnios and expanded hypokinetic heart. After termination of pregnancy, foetopathology showed a eutrophic fetus with isolated cardiomegaly. Endocardial fibroelastosis was associated with non-compaction of the myocardium of the left ventricle. Exome sequencing (ES) identified a de novo unreported p.(Gln353*) heterozygous nonsense variant in PRDM16. ES also identified two rare variants of unknown significance, according to the American College of Medical Genetics and Genomics guidelines, in the titin gene (TTN): a de novo missense p.(Lys14773Asn) variant and a c.33043+5A>G variant inherited from the mother. Along with the PRDM16 de novo probably pathogenic variant, TTN VOUS variants could possibly contribute to the severity and early onset of the cardiac phenotype. Because of the genetic heterogeneity of cardiomyopathies, large panels or even ES could be considered as the main approaches for the molecular diagnosis, particularly in fetal presentations, where multiple hits seem to be common.
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Affiliation(s)
- Geoffroy Delplancq
- Laboratoire de Génétique chromosomique et moléculaire, UF Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | | | - Antonio Vitobello
- Laboratoire de Génétique chromosomique et moléculaire, UF Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Équipe GAD (Génétique des Anomalies du Développement), UMR INSERM 1231, Université de Bourgogne, Dijon, France
| | - Sophie Nambot
- Équipe GAD (Génétique des Anomalies du Développement), UMR INSERM 1231, Université de Bourgogne, Dijon, France.,Centre de Génétique et Centre de Référence Maladies Rares 'Anomalies du Développement' de l'Interrégion Est, Hôpital d'Enfants, CHU, Dijon, France
| | - Arthur Sorlin
- Laboratoire de Génétique chromosomique et moléculaire, UF Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Équipe GAD (Génétique des Anomalies du Développement), UMR INSERM 1231, Université de Bourgogne, Dijon, France
| | - Christophe Philippe
- Laboratoire de Génétique chromosomique et moléculaire, UF Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Équipe GAD (Génétique des Anomalies du Développement), UMR INSERM 1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), Centre Hospitalier Universitaire de Dijon et Université de Bourgogne-Franche Comté, Dijon, France
| | - Virginie Carmignac
- Équipe GAD (Génétique des Anomalies du Développement), UMR INSERM 1231, Université de Bourgogne, Dijon, France.,Centre de référence MAGEC (Maladies génétiques à expression cutanée), CHU Dijon, Dijon, France
| | - Yannis Duffourd
- Équipe GAD (Génétique des Anomalies du Développement), UMR INSERM 1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), Centre Hospitalier Universitaire de Dijon et Université de Bourgogne-Franche Comté, Dijon, France
| | - Charlotte Denis
- Département de Cardiologie Pédiatrique, CHU Dijon, Dijon, France
| | | | - Martin Chevarin
- Laboratoire de Génétique chromosomique et moléculaire, UF Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Équipe GAD (Génétique des Anomalies du Développement), UMR INSERM 1231, Université de Bourgogne, Dijon, France
| | - Gilles Millat
- Laboratoire Cardiogénétique, Centre de Biologie et Pathologie Est, CHU de Lyon HCL - GH Est, Lyon, France
| | - Bouchra Khallouk
- Département de Gynécologie Obstétrique, CHU Dijon, Dijon, France
| | - Thierry Rousseau
- Département de Gynécologie Obstétrique, CHU Dijon, Dijon, France
| | | | - Alexandre Vasiljevic
- Institut de Pathologie Multi-sites des HCL/Centre de Pathologie et Fœtopathologie Est, CHU Lyon, Lyon, France
| | | | - Christel Thauvin-Robinet
- Laboratoire de Génétique chromosomique et moléculaire, UF Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France.,Équipe GAD (Génétique des Anomalies du Développement), UMR INSERM 1231, Université de Bourgogne, Dijon, France.,Centre de Génétique et Centre de Référence Maladies Rares 'Anomalies du Développement' de l'Interrégion Est, Hôpital d'Enfants, CHU, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), Centre Hospitalier Universitaire de Dijon et Université de Bourgogne-Franche Comté, Dijon, France
| | - Laurence Faivre
- Équipe GAD (Génétique des Anomalies du Développement), UMR INSERM 1231, Université de Bourgogne, Dijon, France.,Centre de Génétique et Centre de Référence Maladies Rares 'Anomalies du Développement' de l'Interrégion Est, Hôpital d'Enfants, CHU, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), Centre Hospitalier Universitaire de Dijon et Université de Bourgogne-Franche Comté, Dijon, France
| | - Paul Kuentz
- Équipe GAD (Génétique des Anomalies du Développement), UMR INSERM 1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), Centre Hospitalier Universitaire de Dijon et Université de Bourgogne-Franche Comté, Dijon, France.,Génétique biologique, PCBio, Centre Hospitalier Universitaire de Besançon, Besançon, France
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88
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Guerrini R, Parrini E, Esposito A, Fassio A, Conti V. Lesional and non-lesional epilepsies: A blurring genetic boundary. Eur J Paediatr Neurol 2020; 24:24-29. [PMID: 31875834 DOI: 10.1016/j.ejpn.2019.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 01/02/2023]
Abstract
There has been a traditional conceptual partition between the so-called non-lesional genetic epilepsies and the genetically determined interposed epileptogenic structural abnormalities. In this review, we summarise how growing evidence acquired through neuroimaging and neurobiology modelling is demonstrating that a distinction between lesional and functional (or non-lesional) epileptogenesis is less obvious than previously thought, particularly for epileptogenic neurodevelopmental disorders, but also for most genetically determined epilepsies.
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Affiliation(s)
- Renzo Guerrini
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital Anna Meyer-University of Florence, 50139, Florence, Italy.
| | - Elena Parrini
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital Anna Meyer-University of Florence, 50139, Florence, Italy
| | - Alessandro Esposito
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, 16100, Genoa, Italy; Department of Experimental Medicine, University of Genoa, 16100, Genoa, Italy
| | - Anna Fassio
- Department of Experimental Medicine, University of Genoa, 16100, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, 16100, Genoa, Italy
| | - Valerio Conti
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital Anna Meyer-University of Florence, 50139, Florence, Italy
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89
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Salfati EL, Spencer EG, Topol SE, Muse ED, Rueda M, Lucas JR, Wagner GN, Campman S, Topol EJ, Torkamani A. Re-analysis of whole-exome sequencing data uncovers novel diagnostic variants and improves molecular diagnostic yields for sudden death and idiopathic diseases. Genome Med 2019; 11:83. [PMID: 31847883 PMCID: PMC6916453 DOI: 10.1186/s13073-019-0702-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/03/2019] [Indexed: 12/24/2022] Open
Abstract
Background Whole-exome sequencing (WES) has become an efficient diagnostic test for patients with likely monogenic conditions such as rare idiopathic diseases or sudden unexplained death. Yet, many cases remain undiagnosed. Here, we report the added diagnostic yield achieved for 101 WES cases re-analyzed 1 to 7 years after initial analysis. Methods Of the 101 WES cases, 51 were rare idiopathic disease cases and 50 were postmortem “molecular autopsy” cases of early sudden unexplained death. Variants considered for reporting were prioritized and classified into three groups: (1) diagnostic variants, pathogenic and likely pathogenic variants in genes known to cause the phenotype of interest; (2) possibly diagnostic variants, possibly pathogenic variants in genes known to cause the phenotype of interest or pathogenic variants in genes possibly causing the phenotype of interest; and (3) variants of uncertain diagnostic significance, potentially deleterious variants in genes possibly causing the phenotype of interest. Results Initial analysis revealed diagnostic variants in 13 rare disease cases (25.4%) and 5 sudden death cases (10%). Re-analysis resulted in the identification of additional diagnostic variants in 3 rare disease cases (5.9%) and 1 sudden unexplained death case (2%), which increased our molecular diagnostic yield to 31.4% and 12%, respectively. Conclusions The basis of new findings ranged from improvement in variant classification tools, updated genetic databases, and updated clinical phenotypes. Our findings highlight the potential for re-analysis to reveal diagnostic variants in cases that remain undiagnosed after initial WES.
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Affiliation(s)
- Elias L Salfati
- Scripps Research Translational Institute at Scripps Research, La Jolla, CA, USA
| | - Emily G Spencer
- Scripps Research Translational Institute at Scripps Research, La Jolla, CA, USA
| | - Sarah E Topol
- Scripps Research Translational Institute at Scripps Research, La Jolla, CA, USA
| | - Evan D Muse
- Scripps Research Translational Institute at Scripps Research, La Jolla, CA, USA.,Division of Cardiology, Scripps Clinic, La Jolla, CA, USA
| | - Manuel Rueda
- Scripps Research Translational Institute at Scripps Research, La Jolla, CA, USA
| | - Jonathan R Lucas
- Los Angeles County Department of Medical Examiner-Coroner, Los Angeles, CA, USA
| | - Glenn N Wagner
- San Diego County Medical Examiner's Office, San Diego, CA, USA
| | - Steven Campman
- San Diego County Medical Examiner's Office, San Diego, CA, USA
| | - Eric J Topol
- Scripps Research Translational Institute at Scripps Research, La Jolla, CA, USA.,Division of Cardiology, Scripps Clinic, La Jolla, CA, USA
| | - Ali Torkamani
- Scripps Research Translational Institute at Scripps Research, La Jolla, CA, USA.
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90
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Li J, Gao K, Cai S, Liu Y, Wang Y, Huang S, Zha J, Hu W, Yu S, Yang Z, Xie H, Yan H, Wang J, Wu Y, Jiang Y. Germline de novo variants in CSNK2B in Chinese patients with epilepsy. Sci Rep 2019; 9:17909. [PMID: 31784560 PMCID: PMC6884442 DOI: 10.1038/s41598-019-53484-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/16/2019] [Indexed: 01/16/2023] Open
Abstract
CSNK2B, which encodes the beta subunit of casein kinase II (CK2), plays an important role in neuron morphology and synaptic transmission. Variants in CSNK2B associated with epilepsy and/or intellectual disability (ID)/developmental delay (DD) have been reported in five cases only. Among the 816 probands suspected hereditary epilepsy whose initial report of trio-based whole exome sequencing (WES) were negative, 10 de novo pathogenic or likely pathogenic variants of CSNK2B in nine probands were identified after reanalysis of their raw Trio-WES data. Six of the nine epileptic patients had ID/DD. The age of seizure onset of these nine patients with CSNK2B variants ranged from 2–12 months. Eight patients had age of seizure onset of less than 6 months. The epilepsy of most probands (8/9) was generalized tonic-clonic seizure and clustered (6/9). Most patients had normal electroencephalogram (5/9) and brain magnetic resonance image (7/9) results. Most patients (7/9) had easy-to-control seizures. Levetiracetam was the most commonly used drug in seizure-free patients (5/7). The variants detected in five patients (5/9, 55.6%) were located in the zinc-binding domain. In summary, our research provided evidence that variants in CSNK2B are associated with epilepsy with or without ID/DD. CSNK2B-related epilepsy is relatively easy to be controlled. The zinc-binding domain appears to be the hotspot region for mutation.
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Affiliation(s)
- Jinliang Li
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Kai Gao
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Shuying Cai
- Department of Pediatric Neurology Rehabilitation, Maternal and Child Health Care of Xiamen, Xiamen, Fujian, 361003, China
| | - Yin Liu
- Department of Pediatric Neurology, Tangshan Maternal and Child Health Hospital, Tangshan, Hebei, 063000, China
| | - Yuzhen Wang
- Department of Pediatric Neurology, Tangshan Maternal and Child Health Hospital, Tangshan, Hebei, 063000, China
| | - Shaoping Huang
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, 710004, China
| | - Jian Zha
- Department of Pediatric Neurology, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, 330006, China
| | - Wenjing Hu
- Second Department of Neurology, Hunan Province Children's Hospital, Changsha, Hunan, 410007, China
| | - Shujie Yu
- Department of Pediatric Neurology, Harbin Children's Hospital, Harbin, Heilongjiang, 150010, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Han Xie
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Huifang Yan
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China.
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91
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Ngo KJ, Rexach JE, Lee H, Petty LE, Perlman S, Valera JM, Deignan JL, Mao Y, Aker M, Posey JE, Jhangiani SN, Coban-Akdemir ZH, Boerwinkle E, Muzny D, Nelson AB, Hassin-Baer S, Poke G, Neas K, Geschwind MD, Grody WW, Gibbs R, Geschwind DH, Lupski JR, Below JE, Nelson SF, Fogel BL. A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders. Hum Mutat 2019; 41:487-501. [PMID: 31692161 DOI: 10.1002/humu.23946] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/25/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022]
Abstract
Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.
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Affiliation(s)
- Kathie J Ngo
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jessica E Rexach
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Lauren E Petty
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Susan Perlman
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Juliana M Valera
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Yuanming Mao
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Mamdouh Aker
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Human Genetics Center, University of Texas Health Science Center, Houston, Texas
| | - Donna Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Alexandra B Nelson
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Sharon Hassin-Baer
- Department of Neurology, Chaim Sheba Medical Center, Movement Disorders Institute, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gemma Poke
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Katherine Neas
- Genetic Health Service NZ, Central Hub, Wellington Hospital, Wellington, New Zealand
| | - Michael D Geschwind
- Department of Neurology, UCSF Memory and Aging Center, University of California, San Francisco, California
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Richard Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Daniel H Geschwind
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Jennifer E Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stanley F Nelson
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Brent L Fogel
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Clinical Neurogenomics Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
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92
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Chromosomal Aberrations in Pediatric Patients with Developmental Delay/Intellectual Disability: A Single-Center Clinical Investigation. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9352581. [PMID: 31781653 PMCID: PMC6875000 DOI: 10.1155/2019/9352581] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/03/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022]
Abstract
Introduction Chromosomal microarray analysis (CMA) has currently been considered as the first-tier genetic test for patients with developmental delay/intellectual disability (DD/ID) in many countries. In this study, we performed an extensive assessment of the value of CMA for the diagnosis of children with ID/DD in China. Methods A total of 633 patients diagnosed with DD/ID in West China Second University Hospital, Sichuan University, were recruited from January 2014 to March 2019. The patients were classified into 4 subgroups: isolated DD/ID, DD/ID with multiple congenital anomalies (MCA), isolated autism spectrum disorders (ASDs), and DD/ID with epilepsy. CMA was performed on Affymetrix 750K platform. Results Among the 633 patients, 127 cases were identified as having pathogenic copy number variations (pCNVs) with an overall positive rate of 20.06%. Of the 127 cases with abnormal results, 76 cases had 35 types of microdeletion/microduplication syndromes (59.84%) including 5 cases caused by uniparental disomy (UPD), and 18 cases had unbalanced rearrangements (14.17%) including 10 cases inherited from parental balanced translocations or pericentric inversions. The diagnostic yields of pCNVs for the subgroups of isolated DD/ID, DD/ID with MCA, isolated ASD, and DD/ID with epilepsy were 18.07% (60/332), 34.90% (52/149), 3.70% (3/81), and 16.90% (12/71), respectively. The diagnostic yield of pCNVs in DD/ID patients with MCA was significantly higher than that of the other three subgroups, and the diagnostic yield of pCNVs in isolated ASD patients was significantly lower than that of the other three subgroups (p < 0.05). Conclusion Microdeletion/microduplication syndromes and unbalanced rearrangements are probably the main genetic etiological factors for DD/ID. DD/ID patients with MCA have a higher rate of chromosomal aberrations. Parents of DD/ID children with submicroscopic unbalance rearrangements are more likely to have chromosome balanced translocations or pericentric inversions, which might have been missed by karyotyping. CMA can significantly improve the diagnostic rate for patients with DD/ID, which is of great value for medical management and clinical guidance for genetic counseling.
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93
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Preconception carrier screening yield: effect of variants of unknown significance in partners of carriers with clinically significant variants. Genet Med 2019; 22:646-653. [DOI: 10.1038/s41436-019-0676-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/27/2019] [Indexed: 02/04/2023] Open
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94
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Yamamoto T, Imaizumi T, Yamamoto-Shimojima K, Lu Y, Yanagishita T, Shimada S, Chong PF, Kira R, Ueda R, Ishiyama A, Takeshita E, Momosaki K, Ozasa S, Akiyama T, Kobayashi K, Oomatsu H, Kitahara H, Yamaguchi T, Imai K, Kurahashi H, Okumura A, Oguni H, Seto T, Okamoto N. Genomic backgrounds of Japanese patients with undiagnosed neurodevelopmental disorders. Brain Dev 2019; 41:776-782. [PMID: 31171384 DOI: 10.1016/j.braindev.2019.05.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/08/2019] [Accepted: 05/21/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND Recently, many genes related to neurodevelopmental disorders have been identified by high-throughput genomic analysis; however, a comprehensive understanding of the mechanism underlying neurodevelopmental disorders remains to be established. To further understand these underlying mechanisms, we performed a comprehensive genomic analysis of patients with undiagnosed neurodevelopmental disorders. METHODS Genomic analysis using next-generation sequencing with a targeted panel was performed for a total of 133 Japanese patients (male/female, 81/52) with previously undiagnosed neurodevelopmental disorders, including developmental delay (DD), intellectual disability (ID), autism spectrum disorder (ASD), and epilepsy. Genomic copy numbers were also analyzed using the eXome Hidden Markov Model (XHMM). RESULTS Thirty-nine patients (29.3%) exhibited pathogenic or likely pathogenic findings with single-gene variants or chromosomal aberrations. Among them, 20 patients were presented here. Pathogenic or likely pathogenic variants were identified in 18 genes, including ACTG1, CACNA1A, CHD2, CDKL5, DNMT3A, EHMT1, GABRB3, GABRG2, GRIN2B, KCNQ3, KDM5C, MED13L, SCN2A, SHANK3, SMARCA2, STXBP1, SYNGAP1, and TBL1XR1. CONCLUSION A diagnostic yield of 29.3% in this study was nearly the same as that previously reported from other countries. Thus, we suggest that there is no difference in genomic backgrounds in Japanese patients with undiagnosed neurodevelopmental disabilities. Although most of the patients possessed de novo variants, one of the patients showed an X-linked inheritance pattern. As X-linked recessive disorders exhibit the possibility of recurrent occurrence in the family, comprehensive molecular diagnosis is important for genetic counseling.
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Affiliation(s)
- Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan.
| | - Taichi Imaizumi
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Department of Pediatrics, St. Mariannna University School of Medicine, Kawasaki, Japan
| | - Keiko Yamamoto-Shimojima
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan
| | - Yongping Lu
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Tomoe Yanagishita
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Shino Shimada
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Pin Fee Chong
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Ryutaro Kira
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Riyo Ueda
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Akihiko Ishiyama
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Ken Momosaki
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Shiro Ozasa
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomoyuki Akiyama
- Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Katsuhiro Kobayashi
- Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroo Oomatsu
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | - Hikaru Kitahara
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | - Tokito Yamaguchi
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | - Katsumi Imai
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | | | - Akihisa Okumura
- Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Hirokazu Oguni
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Seto
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
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95
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Bruel AL, Nambot S, Quéré V, Vitobello A, Thevenon J, Assoum M, Moutton S, Houcinat N, Lehalle D, Jean-Marçais N, Chevarin M, Jouan T, Poë C, Callier P, Tisserand E, Philippe C, Them FTM, Duffourd Y, Faivre L, Thauvin-Robinet C. Increased diagnostic and new genes identification outcome using research reanalysis of singleton exome sequencing. Eur J Hum Genet 2019; 27:1519-1531. [PMID: 31231135 PMCID: PMC6777617 DOI: 10.1038/s41431-019-0442-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/30/2019] [Accepted: 05/21/2019] [Indexed: 12/31/2022] Open
Abstract
In clinical exome sequencing (cES), the American College of Medical Genetics and Genomics recommends limiting variant interpretation to established human-disease genes. The diagnostic yield of cES in intellectual disability and/or multiple congenital anomalies (ID/MCA) is currently about 30%. Though the results may seem acceptable for rare diseases, they mean that 70% of affected individuals remain genetically undiagnosed. Further analysis extended to all mutated genes in a research environment is a valuable strategy for improving diagnostic yields. This study presents the results of systematic research reanalysis of negative cES in a cohort of 313 individuals with ID/MCA. We identified 17 new genes not related to human disease, implicated 22 non-OMIM disease-causing genes recently or previously rarely related to disease, and described 1 new phenotype associated with a known gene. Twenty-six candidate genes were identified and are waiting for future recurrence. Overall, we diagnose 15% of the individuals with initial negative cES, increasing the diagnostic yield from 30% to more than 40% (or 46% if strong candidate genes are considered). This study demonstrates the power of such extended research reanalysis to increase scientific knowledge of rare diseases. These novel findings can then be applied in the field of diagnostics.
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Affiliation(s)
- Ange-Line Bruel
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France.
| | - Sophie Nambot
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Virginie Quéré
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Antonio Vitobello
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Julien Thevenon
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Mirna Assoum
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Sébastien Moutton
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Nada Houcinat
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Daphné Lehalle
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Nolwenn Jean-Marçais
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Martin Chevarin
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Thibaud Jouan
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Charlotte Poë
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Patrick Callier
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Emilie Tisserand
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Christophe Philippe
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Frédéric Tran Mau Them
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Yannis Duffourd
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
| | - Christel Thauvin-Robinet
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Unité Fonctionnelle "Innovation diagnostique dans les maladies rares" laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
- Centre de Référence Maladies Rares "Anomalies du Développement et syndromes maformatifs", FHU-TRANSLAD, CHU Dijon Bourgogne, France
- Centre de Référence Maladies Rares "Déficiences Intellectuelles de causes rares", FHU-TRANSLAD, CHU Dijon Bourgogne, France
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96
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97
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Ouyang Q, Kavanaugh BC, Joesch-Cohen L, Dubois B, Wu Q, Schmidt M, Baytas O, Pastore SF, Harripaul R, Mishra S, Hussain A, Kim KH, Holler-Managan YF, Ayub M, Mir A, Vincent JB, Liu JS, Morrow EM. GPT2 mutations in autosomal recessive developmental disability: extending the clinical phenotype and population prevalence estimates. Hum Genet 2019; 138:1183-1200. [PMID: 31471722 PMCID: PMC6748651 DOI: 10.1007/s00439-019-02057-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/24/2019] [Indexed: 10/26/2022]
Abstract
The glutamate pyruvate transaminase 2 (GPT2) gene produces a nuclear-encoded mitochondrial enzyme that catalyzes the reversible transfer of an amino group from glutamate to pyruvate, generating alanine and alpha-ketoglutarate. Recessive mutations in GPT2 have been recently identified in a new syndrome involving intellectual and developmental disability (IDD), postnatal microcephaly, and spastic paraplegia. We have identified additional families with recessive GPT2 mutations and expanded the phenotype to include small stature. GPT2 loss-of-function mutations were identified in four families, nine patients total, including: a homozygous mutation in one child [c.775T>C (p.C259R)]; compound heterozygous mutations in two siblings [c.812A>C (p.N271T)/c.1432_1433delGT (p.V478Rfs*73)]; a novel homozygous, putative splicing mutation [c.1035C>T (p.G345=)]; and finally, a recurrent mutation, previously identified in a distinct family [c.1210C>T (p.R404*)]. All patients were diagnosed with IDD. A majority of patients had remarkably small stature throughout development, many < 1st percentile for height and weight. Given the potential biological function of GPT2 in cellular growth, this phenotype is strongly suggestive of a newly identified clinical susceptibility. Further, homozygous GPT2 mutations manifested in at least 2 of 176 families with IDD (approximately 1.1%) in a Pakistani cohort, thereby representing a relatively common cause of recessive IDD in this population, with recurrence of the p.R404* mutation in this population. Based on variants in the ExAC database, we estimated that approximately 1 in 248 individuals are carriers of moderately or severely deleterious variants in GPT2.
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Affiliation(s)
- Qing Ouyang
- Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University and Emma Pendleton Bradley Hospital, East Providence, RI, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Brian C Kavanaugh
- Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University and Emma Pendleton Bradley Hospital, East Providence, RI, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Lena Joesch-Cohen
- Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Bethany Dubois
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Qing Wu
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Michael Schmidt
- Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University and Emma Pendleton Bradley Hospital, East Providence, RI, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Ozan Baytas
- Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University and Emma Pendleton Bradley Hospital, East Providence, RI, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Stephen F Pastore
- Molecular Neuropsychiatry and Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Ricardo Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Sasmita Mishra
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Abrar Hussain
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Katherine H Kim
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yolanda F Holler-Managan
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Muhammad Ayub
- Department of Psychiatry, Queens University Kingston, Kingston, ON, Canada
| | - Asif Mir
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Judy S Liu
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA.,Department of Neurology, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Eric M Morrow
- Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University and Emma Pendleton Bradley Hospital, East Providence, RI, USA. .,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA. .,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA. .,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA. .,Laboratories for Molecular Medicine, Brown University, 70 Ship Street, Box G-E4, Providence, RI, 02912, USA.
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98
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Schmitz-Abe K, Li Q, Rosen SM, Nori N, Madden JA, Genetti CA, Wojcik MH, Ponnaluri S, Gubbels CS, Picker JD, O'Donnell-Luria AH, Yu TW, Bodamer O, Brownstein CA, Beggs AH, Agrawal PB. Unique bioinformatic approach and comprehensive reanalysis improve diagnostic yield of clinical exomes. Eur J Hum Genet 2019; 27:1398-1405. [PMID: 30979967 PMCID: PMC6777619 DOI: 10.1038/s41431-019-0401-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/11/2019] [Accepted: 03/26/2019] [Indexed: 01/30/2023] Open
Abstract
Clinical exome sequencing (CES) is increasingly being utilized; however, a large proportion of patients remain undiagnosed, creating a need for a systematic approach to increase the diagnostic yield. We have reanalyzed CES data for a clinically heterogeneous cohort of 102 probands with likely Mendelian conditions, including 74 negative cases and 28 cases with candidate variants, but reanalysis requested by clinicians. Reanalysis was performed by an interdisciplinary team using a validated custom-built pipeline, "Variant Explorer Pipeline" (VExP). This reanalysis approach and results were compared with existing literature. Reanalysis of candidate variants from CES in 28 cases revealed 1 interpretation that needed to be reclassified. A confirmed or potential genetic diagnosis was identified in 24 of 75 CES-negative/reclassified cases (32.0%), including variants in known disease-causing genes (n = 6) or candidate genes (n = 18). This yield was higher compared with similar studies demonstrating the utility of this approach. In summary, reanalysis of negative CES in a research setting enhances diagnostic yield by about a third. This study suggests the need for comprehensive, continued reanalysis of exome data when molecular diagnosis is elusive.
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Affiliation(s)
- Klaus Schmitz-Abe
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Qifei Li
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Samantha M Rosen
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Neeharika Nori
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Monica H Wojcik
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Sadhana Ponnaluri
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Cynthia S Gubbels
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jonathan D Picker
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne H O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Timothy W Yu
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Olaf Bodamer
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine and Neonatal Genomics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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99
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A head-to-head evaluation of the diagnostic efficacy and costs of trio versus singleton exome sequencing analysis. Eur J Hum Genet 2019; 27:1791-1799. [PMID: 31320747 DOI: 10.1038/s41431-019-0471-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 04/24/2019] [Accepted: 07/02/2019] [Indexed: 01/22/2023] Open
Abstract
Diagnostic exome sequencing (ES) can be performed on the proband only (singleton; sES) or with additional samples, often including both biological parents with the proband (trio; tES). In this study we sought to compare the efficiencies of exome sequencing (ES) by trio (tES) versus singleton (sES) approach, determine costs, and identify factors to consider when deciding on optimal implementation strategies for the diagnosis of monogenic disorders. We undertook ES in 30 trios and analysed each proband's sES and tES data in parallel. Two teams were randomly allocated to either sES or tES analysis for each case and blinded to each other's work. Each task was timed and cost analyses were based on time taken and diagnostic yield. We modelled three scenarios to determine the factors to consider in the implementation of tES. sES diagnosed 11/30 (36.7%) cases and tES identified one additional diagnosis (12/30 (40.0%)). tES obviated the need for Sanger segregation, reduced the number of variants for curation, and had lower cost-per-diagnosis when considering analysis alone. When sequencing costs were included, tES nearly doubled the cost of sES. Reflexing to tES in those who remain undiagnosed after sES was cost-saving over tES in all as first-line. This approach requires a large differential in diagnostic yield between sES and tES for maximal benefit given current sequencing costs. tES may be preferable when scaling up laboratory throughput due to efficiency gains and opportunity cost considerations. Our findings are relevant to clinicians, laboratories and health services considering tES over sES.
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100
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Li J, Gao K, Yan H, Xiangwei W, Liu N, Wang T, Xu H, Lin Z, Xie H, Wang J, Wu Y, Jiang Y. Reanalysis of whole exome sequencing data in patients with epilepsy and intellectual disability/mental retardation. Gene 2019; 700:168-175. [DOI: 10.1016/j.gene.2019.03.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/11/2019] [Accepted: 03/19/2019] [Indexed: 12/13/2022]
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