151
|
Rojahn S, Hambuch T, Adrian J, Gafni E, Gileta A, Hatchell H, Johnson B, Kallman B, Karfilis K, Kautzer C, Kennemer M, Kirk L, Kvitek D, Lettes J, Macrae F, Mendez F, Paul J, Pellegrino M, Preciado R, Risinger J, Schultz M, Spurka L, Swamy S, Truty R, Usem N, Velenich A, Aradhya S. Scalable detection of technically challenging variants through modified next-generation sequencing. Mol Genet Genomic Med 2022; 10:e2072. [PMID: 36251442 PMCID: PMC9747563 DOI: 10.1002/mgg3.2072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Some clinically important genetic variants are not easily evaluated with next-generation sequencing (NGS) methods due to technical challenges arising from high- similarity copies (e.g., PMS2, SMN1/SMN2, GBA1, HBA1/HBA2, CYP21A2), repetitive short sequences (e.g., ARX polyalanine repeats, FMR1 AGG interruptions in CGG repeats, CFTR poly-T/TG repeats), and other complexities (e.g., MSH2 Boland inversions). METHODS We customized our NGS processes to detect the technically challenging variants mentioned above with adaptations including target enrichment and bioinformatic masking of similar sequences. Adaptations were validated with samples of known genotypes. RESULTS Our adaptations provided high-sensitivity and high-specificity detection for most of the variants and provided a high-sensitivity primary assay to be followed with orthogonal disambiguation for the others. The sensitivity of the NGS adaptations was 100% for all of the technically challenging variants. Specificity was 100% for those in PMS2, GBA1, SMN1/SMN2, and HBA1/HBA2, and for the MSH2 Boland inversion; 97.8%-100% for CYP21A2 variants; and 85.7% for ARX polyalanine repeats. CONCLUSIONS NGS assays can detect technically challenging variants when chemistries and bioinformatics are jointly refined. The adaptations described support a scalable, cost-effective path to identifying all clinically relevant variants within a single sample.
Collapse
|
152
|
Skryabin NA, Zhigalina DI, Stepanov VA. The Role of Splicing in the Pathogenesis of Monogenic Diseases. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
153
|
Sörmann J, Schewe M, Proks P, Jouen-Tachoire T, Rao S, Riel EB, Agre KE, Begtrup A, Dean J, Descartes M, Fischer J, Gardham A, Lahner C, Mark PR, Muppidi S, Pichurin PN, Porrmann J, Schallner J, Smith K, Straub V, Vasudevan P, Willaert R, Carpenter EP, Rödström KEJ, Hahn MG, Müller T, Baukrowitz T, Hurles ME, Wright CF, Tucker SJ. Gain-of-function mutations in KCNK3 cause a developmental disorder with sleep apnea. Nat Genet 2022; 54:1534-1543. [PMID: 36195757 PMCID: PMC9534757 DOI: 10.1038/s41588-022-01185-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/09/2022] [Indexed: 11/07/2022]
Abstract
Sleep apnea is a common disorder that represents a global public health burden. KCNK3 encodes TASK-1, a K+ channel implicated in the control of breathing, but its link with sleep apnea remains poorly understood. Here we describe a new developmental disorder with associated sleep apnea (developmental delay with sleep apnea, or DDSA) caused by rare de novo gain-of-function mutations in KCNK3. The mutations cluster around the 'X-gate', a gating motif that controls channel opening, and produce overactive channels that no longer respond to inhibition by G-protein-coupled receptor pathways. However, despite their defective X-gating, these mutant channels can still be inhibited by a range of known TASK channel inhibitors. These results not only highlight an important new role for TASK-1 K+ channels and their link with sleep apnea but also identify possible therapeutic strategies.
Collapse
Affiliation(s)
- Janina Sörmann
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Marcus Schewe
- Institute of Physiology, Faculty of Medicine, Kiel University, Kiel, Germany
| | - Peter Proks
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Thibault Jouen-Tachoire
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
- Department of Pharmacology, University of Oxford, Oxford, UK
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Elena B Riel
- Institute of Physiology, Faculty of Medicine, Kiel University, Kiel, Germany
| | | | | | - John Dean
- Department of Medical Genetics, NHS Grampian, Aberdeen, UK
| | - Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jan Fischer
- Institute for Clinical Genetics, Universitätsklinikum, Technischen Universität Dresden, Dresden, Germany
| | - Alice Gardham
- North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, London, UK
| | | | - Paul R Mark
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | | | | | - Joseph Porrmann
- Institute for Clinical Genetics, Universitätsklinikum, Technischen Universität Dresden, Dresden, Germany
| | - Jens Schallner
- Department of Neuropediatrics, Universitätsklinikum, Technischen Universität Dresden, Dresden, Germany
| | - Kirstin Smith
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Volker Straub
- Institute of Translational and Clinical Research, Newcastle University, Newcastle upon Tyne, UK
| | - Pradeep Vasudevan
- University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK
| | | | - Elisabeth P Carpenter
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | | | - Michael G Hahn
- Bayer AG, Research & Development, Pharmaceuticals, Wuppertal, Germany
| | - Thomas Müller
- Bayer AG, Research & Development, Pharmaceuticals, Wuppertal, Germany
| | - Thomas Baukrowitz
- Institute of Physiology, Faculty of Medicine, Kiel University, Kiel, Germany
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, UK.
| |
Collapse
|
154
|
Zhang K, Yu L, Lin G, Li J. A multi-laboratory assessment of clinical exome sequencing for detection of hereditary disease variants: 4441 ClinVar variants for clinical genomic test development and validation. Clin Chim Acta 2022; 535:99-107. [PMID: 35985503 DOI: 10.1016/j.cca.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND AIMS Whole-exome sequencing (WES) technology has become an essential tool in the clinical diagnostic for rare genetic disorders, however, the issues that reduce testing precision, sensitivity, and concordance are not clear under routine testing conditions. The study is to systematically evaluate the comparability of clinical WES testing results in laboratories under routine conditions. METHODS We designed a multi-laboratory study across 24 participating laboratories in China. We assessed sequencing quality across capture methods and sequencing platforms, benchmarked the impact of coverage and callable regions on detecting single nucleotide variants (SNVs), small insertions and deletions (Indels) under the same computational approaches, and compared the sensitivity, precision and reproducibility on detecting mutations across laboratories. RESULTS High inter-laboratory variability on variants detection were found across participating laboratories. Sample DNA concentration and sequencing evenness are two major variables that lead to the coverage variation. The difference in bioinformatics tools and computational settings affect the sensitivity and precision of the final output. Besides, copy-number variants (CNVs) identification is less reproducible than SNVs and Indels in the WES testing. We also compiled a list of 4441 low coverage ClinVar variants of 1176 genes from this study, which can be used as a source for creating in silico and synthetic DNA reference materials for clinical genetic disorder detection. CONCLUSIONS The considerable inter-laboratory variability seen in both sequencing coverage evenness and variants detection highlights the urgent need to improve the precision, sensitivity and comparability of the results generated across different laboratories. The list of low coverage variants can have important implications for the development and validation of clinical genetic disorder tests by laboratories. This study also serves to best practice inform guidelines for detecting clinical genetic disorders by exome sequencing.
Collapse
Affiliation(s)
- Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
| | - Lijia Yu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
| |
Collapse
|
155
|
Brodie KD, Liao EN, Florentine MM, Chan DK. Impact of Genetic Testing on Hearing Interventions. Laryngoscope 2022. [PMID: 36165585 DOI: 10.1002/lary.30409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Clinical guidelines recommend genetic testing when evaluating congenital and late-onset sensorineural hearing loss (SNHL). Genetic diagnoses can provide parents additional information regarding anticipated hearing loss progression, comorbid conditions, and family planning. Additionally, obtaining a genetic diagnosis may increase parental acceptance of hearing loss and subsequent pursuit of intervention. This study evaluates the association between genetic diagnoses and hearing loss intervention. METHODS We included children ages 0-18 years with SNHL who were hearing aid or cochlear implant candidates but non-users and underwent hearing-loss gene panel testing prior to initiating intervention. Univariate analyses were performed to identify predictors of hearing aid fitting or cochlear implantation. Multivariate logistic regression evaluated the impact of demographic and clinical factors on subsequent intervention. RESULTS Of the 385 children with SNHL who underwent hearing loss gene panel testing, 111 were included. Median age was 7.5 years. 56% were underrepresented minorities, 71% were non-White, and 71% were publicly insured. Those found to have a genetic diagnosis were 4.6 times as likely to subsequently undergo intervention (p = 0.035). Additionally, bilateral hearing loss and earlier age of genetic testing were associated with increased likelihood of intervention. CONCLUSION Up to half of children with SNHL are suspected to have an underlying genetic etiology. Children diagnosed with a genetic diagnosis are significantly more likely to subsequently utilize hearing aids or cochlear implantation. This provides additional support for clinical guidelines recommending genetic testing not only due to the impact of prognostication but also on treatment decision-making. LEVEL OF EVIDENCE 4 Laryngoscope, 2022.
Collapse
Affiliation(s)
- Kara D Brodie
- Department of Otolaryngology-Head & Neck Surgery, University of California, San Francisco, San Francisco, California, U.S.A
| | - Elizabeth N Liao
- Department of Otolaryngology-Head & Neck Surgery, University of California, San Francisco, San Francisco, California, U.S.A
| | - Michelle M Florentine
- Department of Otolaryngology-Head & Neck Surgery, University of California, San Francisco, San Francisco, California, U.S.A
| | - Dylan K Chan
- Department of Otolaryngology-Head & Neck Surgery, University of California, San Francisco, San Francisco, California, U.S.A
| |
Collapse
|
156
|
Park S, Jang SS, Lee S, Kim M, Sim H, Jeon H, Hong SE, Lee J, Lee J, Jeon EY, Lee J, Lee CR, Kim SY, Kim MJ, Yoon JG, Lim BC, Kim WJ, Kim KJ, Ko JM, Cho A, Lee JS, Choi M, Chae JH. Systematic analysis of inheritance pattern determination in genes that cause rare neurodevelopmental diseases. Front Genet 2022; 13:990015. [PMID: 36212160 PMCID: PMC9533195 DOI: 10.3389/fgene.2022.990015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023] Open
Abstract
Despite recent advancements in our understanding of genetic etiology and its molecular and physiological consequences, it is not yet clear what genetic features determine the inheritance pattern of a disease. To address this issue, we conducted whole exome sequencing analysis to characterize genetic variants in 1,180 Korean patients with neurological symptoms. The diagnostic yield for definitive pathogenic variant findings was 50.8%, after including 33 cases (5.9%) additionally diagnosed by reanalysis. Of diagnosed patients, 33.4% carried inherited variants. At the genetic level, autosomal recessive-inherited genes were characterized by enrichments in metabolic process, muscle organization and metal ion homeostasis pathways. Transcriptome and interactome profiling analyses revealed less brain-centered expression and fewer protein-protein interactions for recessive genes. The majority of autosomal recessive genes were more tolerant of variation, and functional prediction scores of recessively-inherited variants tended to be lower than those of dominantly-inherited variants. Additionally, we were able to predict the rates of carriers for recessive variants. Our results showed that genes responsible for neurodevelopmental disorders harbor different molecular mechanisms and expression patterns according to their inheritance patterns. Also, calculated frequency rates for recessive variants could be utilized to pre-screen rare neurodevelopmental disorder carriers.
Collapse
Affiliation(s)
- Soojin Park
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Se Song Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Seungbok Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea,Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Minsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyungtai Sim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyeongseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Eun Hong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jean Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeongeun Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Eun Young Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeongha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Cho-Rong Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea,Rare Disease Center, Seoul National University Hospital, Seoul, South Korea
| | - Jihoon G. Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Woo Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Ki Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Anna Cho
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jin Sook Lee
- Department of Pediatrics, Seoul National University Hospital Child Cancer and Rare Disease Administration, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea,*Correspondence: Murim Choi, ; Jong-Hee Chae,
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea,Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea,*Correspondence: Murim Choi, ; Jong-Hee Chae,
| |
Collapse
|
157
|
Yu K, Dou J, Huang W, Wang F, Wu Y. Expanding the genetic spectrum of tooth agenesis using whole-exome sequencing. Clin Genet 2022; 102:503-516. [PMID: 36071541 DOI: 10.1111/cge.14225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Tooth agenesis is a high genetic heterogeneous disorder with more than eighty genes identified as associated molecular causes. The present study aimed to detect the possible pathogenic variants in a cohort of well-characterized probands with a clinical diagnosis of tooth agenesis. METHODS We performed whole-exome sequencing (WES) in 131 tooth agenesis patients with no previously identified molecular diagnosis. All the potential pathogenic variants were verified by Sanger sequencing in patients and their family members. Results Seventy-three patients were genetically diagnosed in 131 unrelated Chinese patients with tooth agenesis, providing a positive molecular diagnostic rate of 55.7%, including 53.8% (49/91) in the non-syndromic tooth agenesis (NSTA) group, and 60.0% (24/40) in syndromic tooth agenesis (STA) group. A total of 75 variants from 13 different genes were identified, including 33 novel variants, and WNT10A and EDA are the most common causative genes associated with non-syndromic and syndromic tooth agenesis, respectively. CONCLUSIONS This study further extends the variant spectrum and clinical profiles of tooth agenesis, which has a positive significance for clinical practice, genetic diagnosis, prenatal counseling and future treatment.
Collapse
Affiliation(s)
- Kang Yu
- Department of Second Dental Center, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Jiaqi Dou
- Department of Second Dental Center, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Wei Huang
- Department of Second Dental Center, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Feng Wang
- Department of Oral Implantology, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - Yiqun Wu
- Department of Second Dental Center, Ninth People's Hospital Affiliated with Shanghai Jiao Tong University, School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| |
Collapse
|
158
|
Fell CW, Hagelkruys A, Cicvaric A, Horrer M, Liu L, Li JSS, Stadlmann J, Polyansky AA, Mereiter S, Tejada MA, Kokotović T, Achuta VS, Scaramuzza A, Twyman KA, Morrow MM, Juusola J, Yan H, Wang J, Burmeister M, Choudhury B, Andersen TL, Wirnsberger G, Holmskov U, Perrimon N, Žagrović B, Monje FJ, Moeller JB, Penninger JM, Nagy V. FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder. EMBO Mol Med 2022; 14:e15829. [PMID: 35916241 PMCID: PMC9449597 DOI: 10.15252/emmm.202215829] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/21/2022] Open
Abstract
Whole-exome sequencing of two patients with idiopathic complex neurodevelopmental disorder (NDD) identified biallelic variants of unknown significance within FIBCD1, encoding an endocytic acetyl group-binding transmembrane receptor with no known function in the central nervous system. We found that FIBCD1 preferentially binds and endocytoses glycosaminoglycan (GAG) chondroitin sulphate-4S (CS-4S) and regulates GAG content of the brain extracellular matrix (ECM). In silico molecular simulation studies and GAG binding analyses of patient variants determined that such variants are loss-of-function by disrupting FIBCD1-CS-4S association. Gene knockdown in flies resulted in morphological disruption of the neuromuscular junction and motor-related behavioural deficits. In humans and mice, FIBCD1 is expressed in discrete brain regions, including the hippocampus. Fibcd1 KO mice exhibited normal hippocampal neuronal morphology but impaired hippocampal-dependent learning. Further, hippocampal synaptic remodelling in acute slices from Fibcd1 KO mice was deficient but restored upon enzymatically modulating the ECM. Together, we identified FIBCD1 as an endocytic receptor for GAGs in the brain ECM and a novel gene associated with an NDD, revealing a critical role in nervous system structure, function and plasticity.
Collapse
Affiliation(s)
- Christopher W Fell
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Astrid Hagelkruys
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Ana Cicvaric
- Department of Neurophysiology and Neuropharmacology, Centre for Physiology and PharmacologyMedical University of ViennaViennaAustria
- Department of Psychiatry and Behavioral Sciences, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Marion Horrer
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Lucy Liu
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Joshua Shing Shun Li
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Johannes Stadlmann
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Institute of BiochemistryUniversity of Natural Resource and Life SciencesViennaAustria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max Perutz LabsUniversity of ViennaViennaAustria
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
| | - Stefan Mereiter
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Miguel Angel Tejada
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Research Unit on Women's Health‐Institute of Health Research INCLIVAValenciaSpain
| | - Tomislav Kokotović
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Venkat Swaroop Achuta
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Angelica Scaramuzza
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | | | | | | | - Huifang Yan
- Department of PediatricsPeking University First HospitalBeijingChina
- Joint International Research Center of Translational and Clinical ResearchBeijingChina
| | - Jingmin Wang
- Department of PediatricsPeking University First HospitalBeijingChina
- Joint International Research Center of Translational and Clinical ResearchBeijingChina
| | - Margit Burmeister
- Michigan Neuroscience InstituteUniversity of MichiganAnn ArborMIUSA
- Departments of Computational Medicine & Bioinformatics, Psychiatry and Human GeneticsUniversity of MichiganAnn ArborMIUSA
| | - Biswa Choudhury
- Department of Cellular and Molecular MedicineUCSDLa JollaCAUSA
| | - Thomas Levin Andersen
- Clinical Cell Biology, Department of PathologyOdense University HospitalOdenseDenmark
- Pathology Research Unit, Department of Clinical Research and Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Gerald Wirnsberger
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Apeiron Biologics AG, Vienna BioCenter CampusViennaAustria
| | - Uffe Holmskov
- Cancer and Inflammation Research, Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Bojan Žagrović
- Department of Structural and Computational Biology, Max Perutz LabsUniversity of ViennaViennaAustria
| | - Francisco J Monje
- Department of Neurophysiology and Neuropharmacology, Centre for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Jesper Bonnet Moeller
- Cancer and Inflammation Research, Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
- Danish Institute for Advanced StudyUniversity of Southern DenmarkOdenseDenmark
| | - Josef M Penninger
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Department of Medical Genetics, Life Science InstituteUniversity of British ColumbiaVancouverBCCanada
| | - Vanja Nagy
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| |
Collapse
|
159
|
Rodríguez-Salgado LE, Silva-Aldana CT, Medina-Méndez E, Bareño-Silva J, Arcos-Burgos M, Silgado-Guzmán DF, Restrepo CM. Frequency of actionable Exomic secondary findings in 160 Colombian patients: Impact in the healthcare system. Gene 2022; 838:146699. [PMID: 35803546 DOI: 10.1016/j.gene.2022.146699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION By 2021, the American College of Medical Genetics and Genomics (ACMG) published the last version of their secondary findings (SF) reporting recommendations for cases in which a person receives a genetic test. OBJECTIVE To determine in a sample of the Colombian population the prevalence of SF for the 59 genes on the ACMG SF v2.0 list associated with 27 genetic diseases. MATERIALS AND METHODS An analytical cross-sectional study was developed by examining the sequences of 160 exomes. Based on the ACMG guidelines, a variant classification algorithm was designed to filter and select reportable SF. RESULTS Eleven pathogenic variants were identified in 13/160 (8.13%) patients in genes APOB, BRCA2, CACNA1S, COL3A1, LDLR, MYBPC3, PCSK9, PKP2, PMS2 and RYR2. No association was found between the sociodemographic variables and the SF to report (P > 0,05). CONCLUSION We reported the first approach of actionable pathogenic variants spectrum in the Colombian population. Given the frequency found in this study and the clinical impact of genomic variants on health, it is essential to actively search for SF having the opportunity to receive genetic counselling, prevention and clinical management.
Collapse
Affiliation(s)
| | | | | | - José Bareño-Silva
- School of Medicine, Mental Health Research Group, CES University, Medellin, Colombia
| | - Mauricio Arcos-Burgos
- Research Group on Psychiatric Disorders (GIPSI), Department of Psychiatry, Institute of Medical Research, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | - Carlos M Restrepo
- Center for Research in Genetics and Genomics (CIGGUR), GeniURos Research Group, School of Medicine and Health Sciences, University of Rosario, Bogotá, Colombia.
| |
Collapse
|
160
|
Integrating rapid exome sequencing into NICU clinical care after a pilot research study. NPJ Genom Med 2022; 7:51. [PMID: 36064943 PMCID: PMC9441819 DOI: 10.1038/s41525-022-00326-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022] Open
Abstract
Genomic sequencing is a powerful diagnostic tool in critically ill infants, but performing exome or genome sequencing (ES/GS) in the context of a research study is different from implementing these tests clinically. We investigated the integration of rapid ES into routine clinical care after a pilot research study in a Level IV Neonatal Intensive Care Unit (NICU). We performed a retrospective cohort analysis of infants admitted with suspected genetic disorders to the NICU from December 1, 2018 to March 31, 2021 and compared results to those obtained from a previous research study cohort (March 1, 2017 to November 30, 2018). Clinical rapid ES was performed in 80/230 infants (35%) with a suspected genetic disorder and identified a genetic diagnosis in 22/80 infants (28%). The majority of diagnoses acutely impacted clinical management (14/22 (64%)). Compared to the previous research study, clinically integrated rapid ES had a significantly lower diagnostic yield and increased time from NICU admission and genetics consult to ES report, but identified four genetic diagnoses that may have been missed by the research study selection criteria. Compared to other genetic tests, rapid ES had similar or higher diagnostic yield and similar or decreased time to result. Overall, rapid ES was utilized in the NICU after the pilot research study, often as the first-tier sequencing test, and could identify the majority of disease-causing variants, shorten the diagnostic odyssey, and impact clinical care. Based on our experience, we have identified strategies to optimize the clinical implementation of rapid ES in the NICU.
Collapse
|
161
|
O'Grady L, Schrier Vergano SA, Hoffman TL, Sarco D, Cherny S, Bryant E, Schultz-Rogers L, Chung WK, Sacharow S, Immken LL, Holder S, Blackwell RR, Buchanan C, Yusupov R, Lecoquierre F, Guerrot AM, Rodan L, de Vries BBA, Kamsteeg EJ, Santos Simarro F, Palomares-Bralo M, Brown N, Pais L, Ferrer A, Klee EW, Babovic-Vuksanovic D, Rhodes L, Person R, Begtrup A, Keller-Ramey J, Santiago-Sim T, Schnur RE, Sweetser DA, Gold NB. Heterozygous variants in PRPF8 are associated with neurodevelopmental disorders. Am J Med Genet A 2022; 188:2750-2759. [PMID: 35543142 DOI: 10.1002/ajmg.a.62772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/22/2022] [Accepted: 04/05/2022] [Indexed: 01/25/2023]
Abstract
The pre-mRNA-processing factor 8, encoded by PRPF8, is a scaffolding component of a spliceosome complex involved in the removal of introns from mRNA precursors. Previously, heterozygous pathogenic variants in PRPF8 have been associated with autosomal dominant retinitis pigmentosa. More recently, PRPF8 was suggested as a candidate gene for autism spectrum disorder due to the enrichment of sequence variants in this gene in individuals with neurodevelopmental disorders. We report 14 individuals with various forms of neurodevelopmental conditions, found to have heterozygous, predominantly de novo, missense, and loss-of-function variants in PRPF8. These individuals have clinical features that may represent a new neurodevelopmental syndrome.
Collapse
Affiliation(s)
- Lauren O'Grady
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, Massachusetts, USA.,MGH Institute of Health Professions, Charlestown, Massachusetts, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughter, Norfolk, Virginia, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Trevor L Hoffman
- Department of Genetics, Southern California Kaiser Permanente Medical Group, Anaheim, California, USA
| | - Dean Sarco
- Department of Neurology, Kaiser Permanente-Los Angeles Medical Center, Los Angeles, California, USA
| | - Sara Cherny
- Division of Cardiology, Ann & Robert H. Lurie Children's Hospital, Chicago, Illinois, USA
| | - Emily Bryant
- Division of Neurology, Ann & Robert H. Lurie Children's Hospital, Chicago, Illinois, USA
| | - Laura Schultz-Rogers
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Stephanie Sacharow
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Ladonna L Immken
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Susan Holder
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Rebecca R Blackwell
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Catherine Buchanan
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Roman Yusupov
- Division of Pediatric Genetics, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, Rouen, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, Rouen, France
| | - Lance Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - Erik Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - Fernando Santos Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Maria Palomares-Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Natasha Brown
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Center for Individualized Medicine, Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | | | | | | | - David A Sweetser
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Nina B Gold
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| |
Collapse
|
162
|
Kaiyrzhanov R, Mohammed SEM, Maroofian R, Husain RA, Catania A, Torraco A, Alahmad A, Dutra-Clarke M, Grønborg S, Sudarsanam A, Vogt J, Arrigoni F, Baptista J, Haider S, Feichtinger RG, Bernardi P, Zulian A, Gusic M, Efthymiou S, Bai R, Bibi F, Horga A, Martinez-Agosto JA, Lam A, Manole A, Rodriguez DP, Durigon R, Pyle A, Albash B, Dionisi-Vici C, Murphy D, Martinelli D, Bugiardini E, Allis K, Lamperti C, Reipert S, Risom L, Laugwitz L, Di Nottia M, McFarland R, Vilarinho L, Hanna M, Prokisch H, Mayr JA, Bertini ES, Ghezzi D, Østergaard E, Wortmann SB, Carrozzo R, Haack TB, Taylor RW, Spinazzola A, Nowikovsky K, Houlden H. Bi-allelic LETM1 variants perturb mitochondrial ion homeostasis leading to a clinical spectrum with predominant nervous system involvement. Am J Hum Genet 2022; 109:1692-1712. [PMID: 36055214 PMCID: PMC9502063 DOI: 10.1016/j.ajhg.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Abstract
Leucine zipper-EF-hand containing transmembrane protein 1 (LETM1) encodes an inner mitochondrial membrane protein with an osmoregulatory function controlling mitochondrial volume and ion homeostasis. The putative association of LETM1 with a human disease was initially suggested in Wolf-Hirschhorn syndrome, a disorder that results from de novo monoallelic deletion of chromosome 4p16.3, a region encompassing LETM1. Utilizing exome sequencing and international gene-matching efforts, we have identified 18 affected individuals from 11 unrelated families harboring ultra-rare bi-allelic missense and loss-of-function LETM1 variants and clinical presentations highly suggestive of mitochondrial disease. These manifested as a spectrum of predominantly infantile-onset (14/18, 78%) and variably progressive neurological, metabolic, and dysmorphic symptoms, plus multiple organ dysfunction associated with neurodegeneration. The common features included respiratory chain complex deficiencies (100%), global developmental delay (94%), optic atrophy (83%), sensorineural hearing loss (78%), and cerebellar ataxia (78%) followed by epilepsy (67%), spasticity (53%), and myopathy (50%). Other features included bilateral cataracts (42%), cardiomyopathy (36%), and diabetes (27%). To better understand the pathogenic mechanism of the identified LETM1 variants, we performed biochemical and morphological studies on mitochondrial K+/H+ exchange activity, proteins, and shape in proband-derived fibroblasts and muscles and in Saccharomyces cerevisiae, which is an important model organism for mitochondrial osmotic regulation. Our results demonstrate that bi-allelic LETM1 variants are associated with defective mitochondrial K+ efflux, swollen mitochondrial matrix structures, and loss of important mitochondrial oxidative phosphorylation protein components, thus highlighting the implication of perturbed mitochondrial osmoregulation caused by LETM1 variants in neurological and mitochondrial pathologies.
Collapse
Affiliation(s)
- Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Sami E M Mohammed
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Reza Maroofian
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Ralf A Husain
- Department of Neuropediatrics, Jena University Hospital, Jena 07747, Germany; Center for Rare Diseases, Jena University Hospital, Jena 07747, Germany
| | - Alessia Catania
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Alessandra Torraco
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Ahmad Alahmad
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; Kuwait Medical Genetics Centre, Al-Sabah Medical Area 80901, Kuwait
| | - Marina Dutra-Clarke
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, the University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Sabine Grønborg
- Center for Rare Diseases, Department of Pediatrics and Department of Genetics, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Annapurna Sudarsanam
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham B15 2TG, UK
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham B15 2TG, UK
| | - Filippo Arrigoni
- Paediatric Radiology and Neuroradiology Department, V. Buzzi Children's Hospital, Milan 20154, Italy
| | - Julia Baptista
- Peninsula Medical School, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
| | - Shahzad Haider
- Paediatrics Wah Medical College NUMS, Wah Cantonment, Punjab 44000, Pakistan
| | - René G Feichtinger
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg 5020, Austria
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, Padova 35131, Italy
| | - Alessandra Zulian
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, Padova 35131, Italy
| | - Mirjana Gusic
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg 85764, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich 81675, Germany; Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | | | - Farah Bibi
- Institute of Biochemistry and Biotechnology, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi 44000, Pakistan
| | - Alejandro Horga
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK; Neuromuscular Diseases Unit, Department of Neurology, Hospital Clinico San Carlos and San Carlos Health Research Institute (IdISSC), Madrid 28040, Spain
| | - Julian A Martinez-Agosto
- Department of Human Genetics, Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amanda Lam
- Neurometabolic Unit, National Hospital for Neurology and Neurosurgery, London, UK; Department of Chemical Pathology, Great Ormond Street Hospital, WC1N 3BG London, UK
| | - Andreea Manole
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Diego-Perez Rodriguez
- Department of Clinical Movement Neurosciences, Royal Free Campus, University College of London, Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Romina Durigon
- Department of Clinical Movement Neurosciences, Royal Free Campus, University College of London, Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
| | - Buthaina Albash
- Kuwait Medical Genetics Centre, Al-Sabah Medical Area 80901, Kuwait
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Diego Martinelli
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | | | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Siegfried Reipert
- Core Facility of Cell Imaging and Ultrastructure Research, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
| | - Lotte Risom
- Department of Genetics, Copenhagen University Hospital Rigshospitalet Blegdamsvej, Copenhagen 2100, Denmark
| | - Lucia Laugwitz
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany; Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, Tübingen 72076, Germany
| | - Michela Di Nottia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Laura Vilarinho
- Unit of Neonatal Screening, Metabolism and Genetics, Department of Human Genetics, National Institute of Health Dr Ricardo Jorge, Porto 4000-055, Portugal
| | - Michael Hanna
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg 85764, Germany; Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany
| | - Johannes A Mayr
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg 5020, Austria
| | - Enrico Silvio Bertini
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan 20122, Italy
| | - Elsebet Østergaard
- Department of Genetics, Copenhagen University Hospital Rigshospitalet Blegdamsvej, Copenhagen 2100, Denmark; Institute for Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Saskia B Wortmann
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg 5020, Austria; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg 85764, Germany; Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany; Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboudumc, Nijmegen 6525 EZ, the Netherlands
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Tobias B Haack
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, Tübingen 72076, Germany; Centre for Rare Diseases, University of Tuebingen, Tübingen 72076, Germany
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Antonella Spinazzola
- Department of Clinical Movement Neurosciences, Royal Free Campus, University College of London, Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Karin Nowikovsky
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine Vienna, Vienna 1210, Austria; Department of Internal Medicine I, ASCTR and Comprehensive Cancer Center, Medical University of Vienna, Vienna 1090, Austria.
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK.
| |
Collapse
|
163
|
Ritter A, Leonard J, Gray C, Izumi K, Levinson K, Nair DR, O'Connor M, Rossano J, Shankar V, Chowns J, Marzolf A, Owens A, Ahrens-Nicklas RC. MYH7 variants cause complex congenital heart disease. Am J Med Genet A 2022; 188:2772-2776. [PMID: 35491958 DOI: 10.1002/ajmg.a.62766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/01/2022] [Accepted: 04/09/2022] [Indexed: 01/25/2023]
Abstract
MYH7, encoding the myosin heavy chain sarcomeric β-myosin heavy chain, is a common cause of both hypertrophic and dilated cardiomyopathy. Additionally, families with left ventricular noncompaction cardiomyopathy (LVNC) and congenital heart disease (CHD), typically septal defects or Ebstein anomaly, have been identified to have heterozygous pathogenic variants in MHY7. One previous case of single ventricle CHD with heart failure due to a MYH7 variant has been identified. Herein, we present a single center's experience of complex CHD due to MYH7 variants. Three probands with a history of CHD, LVNC, and/or arrhythmias were identified to have MYH7 variants through multigene panel testing or exome sequencing. These three patients collectively had 12 affected family members, four with a history of Ebstein anomaly and seven with a history of LVNC. These findings suggest a wider phenotypic spectrum in MYH7-related CHD than previously understood. Further investigation into the possible role of MYH7 in CHD and mechanism of disease is necessary to fully delineate the phenotypic spectrum of MYH7-related cardiac disease. MYH7 should be considered for families with multiple individuals with complex CHD in the setting of a family history of LVNC or arrhythmias.
Collapse
Affiliation(s)
- Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jacqueline Leonard
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christopher Gray
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katharine Levinson
- Division of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Divya R Nair
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew O'Connor
- Division of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joseph Rossano
- Division of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Venkat Shankar
- Division of Cardiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jessica Chowns
- Center for Inherited Cardiovascular Disease, Division of Cardiology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Amy Marzolf
- Center for Inherited Cardiovascular Disease, Division of Cardiology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Anjali Owens
- Center for Inherited Cardiovascular Disease, Division of Cardiology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Rebecca C Ahrens-Nicklas
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
164
|
Dong R, Wei X, Zhang K, Song F, Lv Y, Gao M, Wang D, Ma J, Gai Z, Liu Y. Genotypic and phenotypic characteristics of 12 chinese children with glycogen storage diseases. Front Genet 2022; 13:932760. [PMID: 36105079 PMCID: PMC9465291 DOI: 10.3389/fgene.2022.932760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Glycogen storage diseases (GSDs) are known as a group of disorders characterized by genetic errors leading to accumulation of glycogen in various tissues. Since different types of GSD can sometimes be clinically indistinguishable, next generation sequencing is becoming a powerful tool for clinical diagnosis. Methods: 12 patients with suspected GSDs and their parents were enrolled in this study. The clinical and laboratory data of the patients were reviewed. Causative gene variants were identified in the patients using whole exome sequencing (WES) and verified by Sanger sequencing. Results: Genetic testing and analysis showed that 7 patients were diagnosed with GSD II (Pompe disease), 2 patients with GSD III, 1 patient with GSD VI, and 2 patients with GSD IXα. A total number of 18 variants were identified in 12 patients including 11 variants in GAA gene, 3 variants in AGL gene, 2 variants in PYGL gene and 2 variants in PHKA2 gene, of which 9 variants were reported and 9 variants were novel. SIFT, Polyphen-2, Mutation Taster, and REVEL predicted the novel variants (except GAA c.1052_1075 + 47del) to be disease-causing. The 3D structures of wild/mutant type GAA protein were predicted indicating that variants p. Trp621Gly, p. Pro541Leu, p. Ser800Ile and p. Gly293Trp might affect the proteins function via destroying hydrogen bonds or conformational constraints. Neither liver size nor laboratory findings allow for a differentiation among GSD III, GSD VI and GSD IXα. Conclusion: Our study expanded the variation spectrum of genes associated with GSDs. WES, in combination with clinical, biochemical, and pathological hallmarks, could provide accurate results for diagnosing and sub-typing GSD and related diseases in clinical setting.
Collapse
Affiliation(s)
- Rui Dong
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan, China
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Xuxia Wei
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
- Gastroenterology, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan, China
| | - Kaihui Zhang
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan, China
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Fengling Song
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
- Children’s Health Department, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan, China
| | - Yuqiang Lv
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan, China
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Min Gao
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan, China
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Dong Wang
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan, China
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Jian Ma
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan, China
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Zhongtao Gai
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan, China
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
- *Correspondence: Zhongtao Gai, ; Yi Liu,
| | - Yi Liu
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University (Jinan Children’s Hospital), Jinan, China
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
- *Correspondence: Zhongtao Gai, ; Yi Liu,
| |
Collapse
|
165
|
Pathogenic variants detected by RNA sequencing in Cornelia de Lange syndrome. Genomics 2022; 114:110468. [PMID: 36041635 DOI: 10.1016/j.ygeno.2022.110468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/11/2022] [Accepted: 08/26/2022] [Indexed: 11/23/2022]
Abstract
Recent studies suggest that transcript isoforms significantly overlap (approximately 60%) between brain tissue and Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs). Interestingly, 14 cohesion-related genes with variants that cause Cornelia de Lange Syndrome (CdLS) are highly expressed in the brain and LCLs. In this context, we first performed RNA sequencing of LCLs from 22 solved (with pathogenic variants) and 19 unsolved (with no confirmed variants) CdLS cases. Next, an RNA sequencing pipeline was developed using solved cases with two different methods: short variant analysis (for single-nucleotide and indel variants) and aberrant splicing detection analysis. Then, 19 unsolved cases were subsequently applied to our pipeline, and four pathogenic variants in NIPBL (one inframe deletion and three intronic variants) were newly identified. Two of three intronic variants were located at Alu elements in deep-intronic regions, creating cryptic exons. RNA sequencing with LCLs was useful for identifying hidden variants in exome-negative cases.
Collapse
|
166
|
Flex E, Albadri S, Radio FC, Cecchetti S, Lauri A, Priolo M, Kissopoulos M, Carpentieri G, Fasano G, Venditti M, Magliocca V, Bellacchio E, Welch CL, Colombo PC, Kochav SM, Chang R, Barrick R, Trivisano M, Micalizzi A, Borghi R, Messina E, Mancini C, Pizzi S, De Santis F, Rosello M, Specchio N, Compagnucci C, McWalter K, Chung WK, Del Bene F, Tartaglia M. Dominantly acting KIF5B variants with pleiotropic cellular consequences cause variable clinical phenotypes. Hum Mol Genet 2022; 32:473-488. [PMID: 36018820 PMCID: PMC9851748 DOI: 10.1093/hmg/ddac213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/05/2022] [Accepted: 08/23/2022] [Indexed: 01/25/2023] Open
Abstract
Kinesins are motor proteins involved in microtubule (MT)-mediated intracellular transport. They contribute to key cellular processes, including intracellular trafficking, organelle dynamics and cell division. Pathogenic variants in kinesin-encoding genes underlie several human diseases characterized by an extremely variable clinical phenotype, ranging from isolated neurodevelopmental/neurodegenerative disorders to syndromic phenotypes belonging to a family of conditions collectively termed as 'ciliopathies.' Among kinesins, kinesin-1 is the most abundant MT motor for transport of cargoes towards the plus end of MTs. Three kinesin-1 heavy chain isoforms exist in mammals. Different from KIF5A and KIF5C, which are specifically expressed in neurons and established to cause neurological diseases when mutated, KIF5B is an ubiquitous protein. Three de novo missense KIF5B variants were recently described in four subjects with a syndromic skeletal disorder characterized by kyphomelic dysplasia, hypotonia and DD/ID. Here, we report three dominantly acting KIF5B variants (p.Asn255del, p.Leu498Pro and p.Leu537Pro) resulting in a clinically wide phenotypic spectrum, ranging from dilated cardiomyopathy with adult-onset ophthalmoplegia and progressive skeletal myopathy to a neurodevelopmental condition characterized by severe hypotonia with or without seizures. In vitro and in vivo analyses provide evidence that the identified disease-associated KIF5B variants disrupt lysosomal, autophagosome and mitochondrial organization, and impact cilium biogenesis. All variants, and one of the previously reported missense changes, were shown to affect multiple developmental processes in zebrafish. These findings document pleiotropic consequences of aberrant KIF5B function on development and cell homeostasis, and expand the phenotypic spectrum resulting from altered kinesin-mediated processes.
Collapse
Affiliation(s)
- Elisabetta Flex
- To whom correspondence should be addressed at: Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy. Tel: +39 06 4990 2866; ; Marco Tartaglia, Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Viale di San Paolo 15, 00146 Rome, Italy. Tel: +39 06 6859 3742;
| | | | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Serena Cecchetti
- Core Facilities, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Manuela Priolo
- UOSD Genetica Medica, Grande Ospedale Metropolitano "Bianchi Melacrino Morelli", 89124 Reggio Calabria, Italy
| | - Marta Kissopoulos
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Giovanna Carpentieri
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Giulia Fasano
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Martina Venditti
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Valentina Magliocca
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Carrie L Welch
- Department of Pediatrics, Columbia University Irving Medical Center, NY, New York 10032, USA
| | - Paolo C Colombo
- Department of Medicine, Columbia University Irving Medical Center, NY, New York 10032, USA
| | - Stephanie M Kochav
- Department of Medicine, Columbia University Irving Medical Center, NY, New York 10032, USA
| | - Richard Chang
- Division of Metabolic Disorders, Children's Hospital of Orange County (CHOC), CA, Orange 92868, USA
| | - Rebekah Barrick
- Division of Metabolic Disorders, Children's Hospital of Orange County (CHOC), CA, Orange 92868, USA
| | - Marina Trivisano
- Department of Neuroscience, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Alessia Micalizzi
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Rossella Borghi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Elena Messina
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Cecilia Mancini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Flavia De Santis
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215 Paris, France
| | - Marion Rosello
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 Rue Moreau, F-75012 Paris, France
| | - Nicola Specchio
- Department of Neuroscience, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Claudia Compagnucci
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, NY, New York 10032, USA,Department of Medicine, Columbia University Irving Medical Center, NY, New York 10032, USA
| | | | - Marco Tartaglia
- To whom correspondence should be addressed at: Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy. Tel: +39 06 4990 2866; ; Marco Tartaglia, Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Viale di San Paolo 15, 00146 Rome, Italy. Tel: +39 06 6859 3742;
| |
Collapse
|
167
|
Jia X, Zhang S, Tan S, Du B, He M, Qin H, Chen J, Duan X, Luo J, Chen F, Ouyang L, Wang J, Chen G, Yu B, Zhang G, Zhang Z, Lyu Y, Huang Y, Jiao J, Chen JY(H, Swoboda KJ, Agolini E, Novelli A, Leoni C, Zampino G, Cappuccio G, Brunetti-Pierri N, Gerard B, Ginglinger E, Richer J, McMillan H, White-Brown A, Hoekzema K, Bernier RA, Kurtz-Nelson EC, Earl RK, Meddens C, Alders M, Fuchs M, Caumes R, Brunelle P, Smol T, Kuehl R, Day-Salvatore DL, Monaghan KG, Morrow MM, Eichler EE, Hu Z, Yuan L, Tan J, Xia K, Shen Y, Guo H. De novo variants in genes regulating stress granule assembly associate with neurodevelopmental disorders. SCIENCE ADVANCES 2022; 8:eabo7112. [PMID: 35977029 PMCID: PMC9385150 DOI: 10.1126/sciadv.abo7112] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/06/2022] [Indexed: 05/25/2023]
Abstract
Stress granules (SGs) are cytoplasmic assemblies in response to a variety of stressors. We report a new neurodevelopmental disorder (NDD) with common features of language problems, intellectual disability, and behavioral issues caused by de novo likely gene-disruptive variants in UBAP2L, which encodes an essential regulator of SG assembly. Ubap2l haploinsufficiency in mouse led to social and cognitive impairments accompanied by disrupted neurogenesis and reduced SG formation during early brain development. On the basis of data from 40,853 individuals with NDDs, we report a nominally significant excess of de novo variants within 29 genes that are not implicated in NDDs, including 3 essential genes (G3BP1, G3BP2, and UBAP2L) in the core SG interaction network. We validated that NDD-related de novo variants in newly implicated and known NDD genes, such as CAPRIN1, disrupt the interaction of the core SG network and interfere with SG formation. Together, our findings suggest the common SG pathology in NDDs.
Collapse
Affiliation(s)
- Xiangbin Jia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Shujie Zhang
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Senwei Tan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Bing Du
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Mei He
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Hunan, China
| | - Haisong Qin
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
| | - Jia Chen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Xinyu Duan
- Department of Pediatrics, Daping Hospital, Army Medical University, Chongqing, China
| | - Jingsi Luo
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
| | - Fei Chen
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
| | - Luping Ouyang
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Guodong Chen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Bin Yu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Ge Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Zimin Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Yongqing Lyu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Yi Huang
- Mental Health Center, West China Hospital of Sichuan University, Chengdu 610000, China
| | - Jian Jiao
- Mental Health Center, West China Hospital of Sichuan University, Chengdu 610000, China
| | - Jin Yun (Helen) Chen
- Massachusetts General Hospital Neurogenetics Unit, Department of Neurology, Massachusetts General Brigham, Boston, MA 02114, USA
| | - Kathryn J. Swoboda
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children’s Hospital, IRCCS, Rome 00165, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children’s Hospital, IRCCS, Rome 00165, Italy
| | - Chiara Leoni
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome 00168, Italy
| | - Giuseppe Zampino
- Center for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli-IRCCS, Rome 00168, Italy
- Faculty of Medicine and Surgery, Catholic University of the Sacred Heart, Rome 00168, Italy
- Fondazione Policlinico Universitario Agostino Gemelli Dipartimento Scienze della Salute della Donna e del Bambino, Rome, Italy
- Università Cattolica S. Cuore, Dipartimento Scienze della Vita e Sanità Pubblica, Rome, Italy
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Translational Medicine, Federico II University, Naples, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Translational Medicine, Federico II University, Naples, Italy
| | - Benedicte Gerard
- Institut de Génétique Médicale d’Alsace (IGMA), Laboratoire de Diagnostic Génétique, Hôpitaux universitaires de Strasbourg, Strasbourg, Alsace, France
| | | | - Julie Richer
- Department of Medical Genetics, Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Hugh McMillan
- Department of Pediatrics, Neurology and Neurosurgery, Montreal Children’s Hospital, McGill University, Montreal, Canada
| | - Alexandre White-Brown
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Raphael A. Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Rachel K. Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Claartje Meddens
- Amsterdam University Medical Center, Department of Clinical Genetics, Amsterdam, Netherlands
- University Medical Center Utrecht, Department of Paediatrics, Utrecht, Netherlands
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | | | - Roseline Caumes
- CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000 Lille, France
| | - Perrine Brunelle
- Institut de Génétique Médicale, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000 Lille, France
| | - Thomas Smol
- Institut de Génétique Médicale, Université de Lille, ULR7364 RADEME, CHU Lille, F-59000 Lille, France
| | - Ryan Kuehl
- Department of Medical Genetics and Genomic Medicine, Saint Peter’s University Hospital, New Brunswick, NJ 08901, USA
| | - Debra-Lynn Day-Salvatore
- Department of Medical Genetics and Genomic Medicine, Saint Peter’s University Hospital, New Brunswick, NJ 08901, USA
| | | | | | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Zhengmao Hu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Ling Yuan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Jieqiong Tan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
- CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Chinese Academy of Sciences, Shanghai 200000, China
- Hengyang Medical School, University of South China, Hengyang, China
| | - Yiping Shen
- Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan 410078, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha, Hunan 410078, China
| |
Collapse
|
168
|
Song X, Xu W, Xiao M, Lu Y, Lan X, Tang X, Xu N, Yu G, Zhang H, Wu S. Two novel heterozygous truncating variants in NR4A2 identified in patients with neurodevelopmental disorder and brief literature review. Front Neurosci 2022; 16:956429. [PMID: 35992907 PMCID: PMC9383035 DOI: 10.3389/fnins.2022.956429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/15/2022] [Indexed: 12/05/2022] Open
Abstract
Pathogenic variants in the nuclear receptor superfamily 4 group A member 2 (NR4A2) cause an autosomal dominant neurodevelopmental disorder with or without seizures. Here, we described two patients presenting with developmental delay, language impairment, and attention-deficit hyperactivity disorder. Trio-based whole exome sequencing revealed two novel heterozygous variants, c.1541-2A > C and c.915C > A, in NR4A2. Both variants were identified as de novo and confirmed by Sanger sequencing. In vitro functional analyses were performed to assess their effects on expression of mRNA or protein. The canonical splicing variant c.1541-2A > C caused aberrant splicing, leading to the retention of intron 7 and a truncated protein due to an early termination codon within intron 7 with decreased protein expression, while the variant c.915C > A was shown to result in a shorter protein with increased expression level unexpectedly. The clinical and genetic characteristics of the previously published patients were briefly reviewed for highlighting the potential link between mutations and phenotypes. Our research further confirms that NR4A2 is a disease-causing gene of neurodevelopmental disorders and suggests alterations in different domains of NR4A2 cause various severity of symptoms.
Collapse
Affiliation(s)
- Xiaozhen Song
- Molecular Diagnostic Laboratory, Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wuhen Xu
- Molecular Diagnostic Laboratory, Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Man Xiao
- Molecular Diagnostic Laboratory, Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanfen Lu
- Department of Neurology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoping Lan
- Molecular Diagnostic Laboratory, Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojun Tang
- Molecular Diagnostic Laboratory, Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nanjie Xu
- Research Center of Translational Medicine, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Anatomy and Physiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guangjun Yu
- Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Zhang
- Molecular Diagnostic Laboratory, Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Hong Zhang,
| | - Shengnan Wu
- Molecular Diagnostic Laboratory, Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shengnan Wu,
| |
Collapse
|
169
|
Martinussen J, Chalk M, Elliott J, Gallacher L. Receiving Genomic Sequencing Results through the Victorian Undiagnosed Disease Program: Exploring Parental Experiences. J Pers Med 2022; 12:jpm12081250. [PMID: 36013198 PMCID: PMC9410238 DOI: 10.3390/jpm12081250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/24/2022] [Indexed: 11/16/2022] Open
Abstract
Rare diseases cumulatively affect a significant number of people, and for many, a diagnosis remains elusive. The Victorian Undiagnosed Disease Program (UDP-Vic) utilizes deep phenotyping, advanced genomic sequencing and functional studies to diagnose children with rare diseases for which previous clinical testing has been non-diagnostic. Whereas the diagnostic outcomes of undiagnosed disease programs have been well-described, here, we explore how parents experience participation in the UDP-Vic and the impact of receiving both diagnostic and non-diagnostic genomic sequencing results for their children. Semi-structured interviews ranging in length from 25 to 105 min were conducted with 21 parents of children in the program. Ten participants were parents of children who received a diagnosis through the program, and eleven were parents of children who remain undiagnosed. Although the experiences of families varied, five shared themes emerged from the data: (1) searching for a diagnosis, (2) varied impact of receiving a result, (3) feelings of relief and disappointment, (4) seeking connection and (5) moving towards acceptance. The findings demonstrate the shared experience of parents of children with rare disease both before and after a genomic sequencing result. The results have implications for genetic counselors and clinicians offering genomic sequencing and supporting families of children with rare diseases.
Collapse
Affiliation(s)
- Jo Martinussen
- Department of Paediatrics, The University of Melbourne, Melbourne 3010, Australia; (J.M.); (M.C.)
| | - Michal Chalk
- Department of Paediatrics, The University of Melbourne, Melbourne 3010, Australia; (J.M.); (M.C.)
| | - Justine Elliott
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne 3052, Australia;
| | - Lyndon Gallacher
- Department of Paediatrics, The University of Melbourne, Melbourne 3010, Australia; (J.M.); (M.C.)
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne 3052, Australia;
- Correspondence:
| |
Collapse
|
170
|
Baker EK, Ulm EA, Belonis A, Brightman DS, Hallinan BE, Leslie ND, Miethke AG, Vawter-Lee M, Wu Y, Pena LDM. Clinically available testing options resulting in diagnosis in post-exome clinic at one medical center. Front Genet 2022; 13:887698. [PMID: 35937981 PMCID: PMC9355124 DOI: 10.3389/fgene.2022.887698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/28/2022] [Indexed: 11/27/2022] Open
Abstract
Exome sequencing (ES) became clinically available in 2011 and promised an agnostic, unbiased next-generation sequencing (NGS) platform for patients with symptoms believed to have a genetic etiology. The diagnostic yield of ES has been estimated to be between 25–40% and may be higher in specific clinical scenarios. Those who remain undiagnosed may have no molecular findings of interest on ES, variants of uncertain significance in genes that are linked to human disease, or variants of uncertain significance in candidate genes that are not definitively tied to human disease. Recent evidence suggests that a post-exome evaluation consisting of clinical re-phenotyping, functional studies of candidate variants in known genes, and variant reevaluation can lead to a diagnosis in 5–15% of additional cases. In this brief research study, we present our experience on post-exome evaluations in a cohort of patients who are believed to have a genetic etiology for their symptoms. We have reached a full or partial diagnosis in approximately 18% (6/33) of cases that have completed evaluations to date. We accomplished this by utilizing NGS-based methods that are available on a clinical basis. A sample of these cases highlights the utility of ES reanalysis with updated phenotyping allowing for the discovery of new genes, re-adjudication of known variants, incorporating updated phenotypic information, utilizing functional testing such as targeted RNA sequencing, and deploying other NGS-based testing methods such as gene panels and genome sequencing to reach a diagnosis.
Collapse
Affiliation(s)
- Elizabeth K. Baker
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Elizabeth A. Ulm
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Alyce Belonis
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Diana S. Brightman
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Barbara E. Hallinan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Neurology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Nancy D. Leslie
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Alexander G. Miethke
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Marissa Vawter-Lee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Neurology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Yaning Wu
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Loren D. M. Pena
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- *Correspondence: Loren D. M. Pena,
| |
Collapse
|
171
|
Lesca G, Baumgartner T, Monin P, De Dominicis A, Kunz WS, Specchio N. Genetic causes of rare and common epilepsies: What should the epileptologist know? Eur J Med Genet 2022; 65:104570. [PMID: 35850153 DOI: 10.1016/j.ejmg.2022.104570] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/04/2022] [Accepted: 07/10/2022] [Indexed: 11/03/2022]
Abstract
In past decades, the identification of genes involved in epileptic disorders has grown exponentially. The pace of gene identification in epileptic disorders began to accelerate in the late 2000s, driven by new technologies such as molecular cytogenetics and next-generation sequencing (NGS). These technologies have also been applied to genetic diagnostics, with different configurations, such as gene panels, whole-exome sequencing and whole-genome sequencing. The clinician must be aware that any technology has its limitations and complementary techniques must still be used to establish a diagnosis for specific diseases. In addition, increasing the amount of genetic information available in a larger patient sample also increases the need for rigorous interpretation steps, when taking into account the clinical, electroclinical, and when available, functional data. Local, multidisciplinary discussions have proven valuable in difficult diagnostic situations, especially in cases where precision medicine is being considered. They also serve to improve genetic counseling in complex situations. In this article, we will briefly review the genetic basis of rare and common epilepsies, the current strategies used for molecular diagnosis, including their limitations, and some pitfalls for data interpretation, in the context of etiological diagnosis and genetic counseling.
Collapse
Affiliation(s)
- Gaetan Lesca
- Department of Medical Genetics and Department of Paedaitric Clinical Epileptology, Member of the ERN EpiCARE, University Hospitals of Lyon (HCL), Lyon, France; University Claude Bernard Lyon 1, Lyon, France.
| | - Tobias Baumgartner
- Department of Epileptology, University Hospital Bonn, Member of the ERN EpiCARE, Bonn, Germany
| | - Pauline Monin
- Department of Medical Genetics and Department of Paedaitric Clinical Epileptology, Member of the ERN EpiCARE, University Hospitals of Lyon (HCL), Lyon, France; University Claude Bernard Lyon 1, Lyon, France
| | - Angela De Dominicis
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Wolfram S Kunz
- Department of Epileptology, University Hospital Bonn, Member of the ERN EpiCARE, Bonn, Germany
| | - Nicola Specchio
- Rare and Complex Epilepsy Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Full Member of European Reference Network EpiCARE, Rome, Italy
| |
Collapse
|
172
|
Hsueh HW, Weng WC, Fan PC, Chien YH, Yang FJ, Lee WT, Lin RJ, Hwu WL, Yang CC, Lee NC. The diversity of hereditary neuromuscular diseases: Experiences from molecular diagnosis. J Formos Med Assoc 2022; 121:2574-2583. [PMID: 35821219 DOI: 10.1016/j.jfma.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 03/02/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Hereditary neuromuscular diseases (NMDs) are a group of rare disorders, and the diagnosis of these diseases is a substantial burden for referral centers. Although next-generation sequencing (NGS) has identified a large number of genes associated with hereditary NMDs, the diagnostic rates still vary across centers. METHODS Patients with a suspected hereditary NMD were referred to neuromuscular specialists at the National Taiwan University Hospital. Molecular diagnoses were performed by employing a capture panel containing 194 genes associated with NMDs. RESULTS Among the 50 patients referred, 43 had a suspicion of myopathy, and seven had polyneuropathy. The overall diagnostic rate was 58%. Pathogenic variants in 19 genes were observed; the most frequent pathogenic variant found in this cohort (DYSF) was observed in only four patients, and 10 pathogenic variants were observed in one patient each. One case of motor neuron disease was clinically mistaken for myopathy. A positive family history increased the diagnostic rate (positive: 72.7% vs. negative: 56.3%). Fourteen patients with elevated plasma creatine kinase levels remained without a diagnosis. CONCLUSION The application of NGS in this single-center study proves the great diversity of hereditary NMDs. A capture panel is essential, but high-quality clinical and laboratory evaluations of patients are also indispensable.
Collapse
Affiliation(s)
- Hsueh-Wen Hsueh
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Chin Weng
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pi-Chuan Fan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Feng-Jung Yang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Wang-Tso Lee
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ru-Jen Lin
- Department of Neurology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chih-Chao Yang
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Ni-Chung Lee
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
| |
Collapse
|
173
|
Chin HL, Gazzaz N, Huynh S, Handra I, Warnock L, Moller-Hansen A, Boerkoel P, Jacobsen JOB, du Souich C, Zhang N, Shefchek K, Prentice LM, Washington N, Haendel M, Armstrong L, Clarke L, Li WL, Smedley D, Robinson PN, Boerkoel CF. The Clinical Variant Analysis Tool: Analyzing the evidence supporting reported genomic variation in clinical practice. Genet Med 2022; 24:1512-1522. [PMID: 35442193 PMCID: PMC9363005 DOI: 10.1016/j.gim.2022.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/03/2023] Open
Abstract
PURPOSE Genomic test results, regardless of laboratory variant classification, require clinical practitioners to judge the applicability of a variant for medical decisions. Teaching and standardizing clinical interpretation of genomic variation calls for a methodology or tool. METHODS To generate such a tool, we distilled the Clinical Genome Resource framework of causality and the American College of Medical Genetics/Association of Molecular Pathology and Quest Diagnostic Laboratory scoring of variant deleteriousness into the Clinical Variant Analysis Tool (CVAT). Applying this to 289 clinical exome reports, we compared the performance of junior practitioners with that of experienced medical geneticists and assessed the utility of reported variants. RESULTS CVAT enabled performance comparable to that of experienced medical geneticists. In total, 124 of 289 (42.9%) exome reports and 146 of 382 (38.2%) reported variants supported a diagnosis. Overall, 10.5% (1 pathogenic [P] or likely pathogenic [LP] variant and 39 variants of uncertain significance [VUS]) of variants were reported in genes without established disease association; 20.2% (23 P/LP and 54 VUS) were in genes without sufficient phenotypic concordance; 7.3% (15 P/LP and 13 VUS) conflicted with the known molecular disease mechanism; and 24% (91 VUS) had insufficient evidence for deleteriousness. CONCLUSION Implementation of CVAT standardized clinical interpretation of genomic variation and emphasized the need for collaborative and transparent reporting of genomic variation.
Collapse
Affiliation(s)
- Hui-Lin Chin
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada; Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Nour Gazzaz
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada; Department of Pediatrics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Stephanie Huynh
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Iulia Handra
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Lynn Warnock
- Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Ashley Moller-Hansen
- Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Pierre Boerkoel
- MD Undergraduate Program, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, United Kingdom
| | - Christèle du Souich
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Kent Shefchek
- Oregon Clinical and Translational Science Institute, Oregon Health & Science University, Portland, OR
| | - Leah M Prentice
- Provincial Laboratory Medicine Services, Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | | | - Melissa Haendel
- Oregon Clinical and Translational Science Institute, Oregon Health & Science University, Portland, OR
| | - Linlea Armstrong
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Lorne Clarke
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | | | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, United Kingdom
| | | | - Cornelius F Boerkoel
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
174
|
Wortmann SB, Oud MM, Alders M, Coene KLM, van der Crabben SN, Feichtinger RG, Garanto A, Hoischen A, Langeveld M, Lefeber D, Mayr JA, Ockeloen CW, Prokisch H, Rodenburg R, Waterham HR, Wevers RA, van de Warrenburg BPC, Willemsen MAAP, Wolf NI, Vissers LELM, van Karnebeek CDM. How to proceed after "negative" exome: A review on genetic diagnostics, limitations, challenges, and emerging new multiomics techniques. J Inherit Metab Dis 2022; 45:663-681. [PMID: 35506430 PMCID: PMC9539960 DOI: 10.1002/jimd.12507] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/28/2022]
Abstract
Exome sequencing (ES) in the clinical setting of inborn metabolic diseases (IMDs) has created tremendous improvement in achieving an accurate and timely molecular diagnosis for a greater number of patients, but it still leaves the majority of patients without a diagnosis. In parallel, (personalized) treatment strategies are increasingly available, but this requires the availability of a molecular diagnosis. IMDs comprise an expanding field with the ongoing identification of novel disease genes and the recognition of multiple inheritance patterns, mosaicism, variable penetrance, and expressivity for known disease genes. The analysis of trio ES is preferred over singleton ES as information on the allelic origin (paternal, maternal, "de novo") reduces the number of variants that require interpretation. All ES data and interpretation strategies should be exploited including CNV and mitochondrial DNA analysis. The constant advancements in available techniques and knowledge necessitate the close exchange of clinicians and molecular geneticists about genotypes and phenotypes, as well as knowledge of the challenges and pitfalls of ES to initiate proper further diagnostic steps. Functional analyses (transcriptomics, proteomics, and metabolomics) can be applied to characterize and validate the impact of identified variants, or to guide the genomic search for a diagnosis in unsolved cases. Future diagnostic techniques (genome sequencing [GS], optical genome mapping, long-read sequencing, and epigenetic profiling) will further enhance the diagnostic yield. We provide an overview of the challenges and limitations inherent to ES followed by an outline of solutions and a clinical checklist, focused on establishing a diagnosis to eventually achieve (personalized) treatment.
Collapse
Affiliation(s)
- Saskia B. Wortmann
- Radboud Center for Mitochondrial and Metabolic Medicine, Department of PediatricsAmalia Children's Hospital, Radboud University Medical CenterNijmegenThe Netherlands
- University Children's Hospital, Paracelsus Medical UniversitySalzburgAustria
| | - Machteld M. Oud
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Department of Human GeneticsDonders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
| | - Mariëlle Alders
- Department of Human GeneticsAmsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research InstituteAmsterdamThe Netherlands
| | - Karlien L. M. Coene
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Translational Metabolic Laboratory, Department of Laboratory MedicineRadboud University Medical CenterNijmegenThe Netherlands
| | - Saskia N. van der Crabben
- Department of Human GeneticsAmsterdam University Medical Centers, University of AmsterdamAmsterdamThe Netherlands
| | - René G. Feichtinger
- University Children's Hospital, Paracelsus Medical UniversitySalzburgAustria
| | - Alejandro Garanto
- Radboud Center for Mitochondrial and Metabolic Medicine, Department of PediatricsAmalia Children's Hospital, Radboud University Medical CenterNijmegenThe Netherlands
- Department of PediatricsAmalia Children's Hospital, Radboud Institute for Molecular LifesciencesNijmegenThe Netherlands
- Department of Human GeneticsRadboud Institute for Molecular LifesciencesNijmegenThe Netherlands
| | - Alex Hoischen
- Department of Human Genetics, Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud Institute of Medical Life Sciences, Radboud University Medical CenterNijmegenthe Netherlands
| | - Mirjam Langeveld
- Department of Endocrinology and MetabolismAmsterdam University Medical Centers, location AMC, University of AmsterdamAmsterdamThe Netherlands
| | - Dirk Lefeber
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Translational Metabolic Laboratory, Department of Laboratory MedicineRadboud University Medical CenterNijmegenThe Netherlands
- Department of Neurology, Donders Institute for BrainCognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
| | - Johannes A. Mayr
- University Children's Hospital, Paracelsus Medical UniversitySalzburgAustria
| | - Charlotte W. Ockeloen
- Department of Human GeneticsRadboud Institute for Molecular LifesciencesNijmegenThe Netherlands
| | - Holger Prokisch
- School of MedicineInstitute of Human Genetics, Technical University Munich and Institute of NeurogenomicsNeuherbergGermany
| | - Richard Rodenburg
- Radboud Center for Mitochondrial and Metabolic MedicineTranslational Metabolic Laboratory, Department of Pediatrics, Radboud University Medical CenterNijmegenThe Netherlands
| | - Hans R. Waterham
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Laboratory Genetic Metabolic Diseases, Department of Clinical ChemistryAmsterdam University Medical Centers, location AMC, University of AmsterdamAmsterdamThe Netherlands
| | - Ron A. Wevers
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Translational Metabolic Laboratory, Department of Laboratory MedicineRadboud University Medical CenterNijmegenThe Netherlands
| | - Bart P. C. van de Warrenburg
- Department of Neurology, Donders Institute for BrainCognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
| | - Michel A. A. P. Willemsen
- Departments of Pediatric Neurology and PediatricsAmalia Children's Hospital, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical CenterNijmegenThe Netherlands
| | - Nicole I. Wolf
- Amsterdam Leukodystrophy Center, Department of Child NeurologyEmma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Lisenka E. L. M. Vissers
- Department of Human GeneticsDonders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
| | - Clara D. M. van Karnebeek
- Radboud Center for Mitochondrial and Metabolic Medicine, Department of PediatricsAmalia Children's Hospital, Radboud University Medical CenterNijmegenThe Netherlands
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Department of Human GeneticsAmsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research InstituteAmsterdamThe Netherlands
- Department of Pediatrics, Emma Center for Personalized MedicineAmsterdam University Medical Centers, Amsterdam, Amsterdam Genetics Endocrinology Metabolism Research Institute, University of AmsterdamAmsterdamThe Netherlands
| |
Collapse
|
175
|
Zhao X, Ning H, Wang Y, Zhao G, Mei S, Liu N, Wang C, Cai A, Wei E, Kong X. Genetic analysis and identification of novel variations in Chinese patients with pediatric epilepsy by whole-exome sequencing. Neurol Sci 2022; 43:4439-4451. [DOI: 10.1007/s10072-022-05953-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/12/2022] [Indexed: 11/28/2022]
|
176
|
Tuteja S, Kadri S, Yap KL. A performance evaluation study: Variant annotation tools - The enigma of clinical next generation sequencing (NGS) based genetic testing. J Pathol Inform 2022; 13:100130. [PMID: 36268089 PMCID: PMC9577137 DOI: 10.1016/j.jpi.2022.100130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/03/2022] Open
Abstract
Dramatically expanding our ability for clinical genetic testing for inherited conditions and complex diseases such as cancer, next generation sequencing (NGS) technologies are allowing for rapid interrogation of thousands of genes and identification of millions of variants. Variant annotation, the process of assigning functional information to DNA variants based on the standardized Human Genome Variation Society (HGVS) nomenclature, is a fundamental challenge in the analysis of NGS data that has led to the development of many bioinformatic algorithms. In this study, we evaluated the performance of 3 variant annotation tools: Alamut® Batch, Ensembl Variant Effect Predictor (VEP), and ANNOVAR, benchmarked by a manually curated ground-truth set of 298 variants from the medical exome database at the Molecular Diagnostics Laboratory at Lurie Children's Hospital. Of the 3 tools, VEP produces the most accurate variant annotations (HGVS nomenclature for 297 of the 298 variants) due to usage of updated gene transcript versions within the algorithm. Alamut® Batch called 296 of the 298 variants correctly; strikingly, ANNOVAR exhibited the greatest number of discrepancies (20 of the 298 variants, 93.3% concordance with ground-truth set). Adoption of validated methods of variant annotation is critical in post-analytical phases of clinical testing.
Collapse
Affiliation(s)
- Sachleen Tuteja
- Illinois Mathematics and Science Academy, 1500 Sullivan Road, Aurora, IL 60506, USA
| | - Sabah Kadri
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, 225 E. Chicago Ave, Chicago, IL 60611, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, 420 E. Superior St, Chicago, IL 606011, USA
| | - Kai Lee Yap
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, 225 E. Chicago Ave, Chicago, IL 60611, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, 420 E. Superior St, Chicago, IL 606011, USA
- Corresponding author at: Molecular Diagnostics, Department of Pathology & Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern Feinberg School of Medicine, 225 E. Chicago Ave, Box 82, Chicago, IL 60611, USA.
| |
Collapse
|
177
|
Moradi N, Ohadian Moghadam S, Heidarzadeh S. Application of next-generation sequencing in the diagnosis of gastric cancer. Scand J Gastroenterol 2022; 57:842-855. [PMID: 35293278 DOI: 10.1080/00365521.2022.2041717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Objectives: Gastric cancer (GC) is a disease with high mortality, poor prognosis and numerous risk factors. GC has an asymptomatic nature in early stages of the diseases, making timely diagnosis complicated using common conventional approaches, namely pathological examinations and imaging tests. Recently, molecular profiling of GC using next generation sequencing (NGS) has opened new doors to efficient prognostic, diagnostic, and therapeutic strategies. The current review aims to thoroughly discuss and compare the current NGS techniques and commercial platforms utilized for GC diagnosis and treatment, highlighting the most recent NGS-based GC studies. Furthermore, this review addresses the challenges of clinical implementation of NGS in GC.Materials and methods: This review was conducted according to the eligible studies identified via search of Web of Science, PubMed, Scopus, Embase and the Cochrane Library. In the present study, data on gastric cancer patients and NGS methods used to diagnose the disease were reviewed.Conclusion: Given the ever-rising advancements in NGS technologies, bioinformatics, healthcare guidelines and refined classifications, it is hoped that these technologies can actualize their advantages and optimize GC patients' experience.
Collapse
Affiliation(s)
- Narges Moradi
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Siamak Heidarzadeh
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| |
Collapse
|
178
|
Castillo MI, Freire E, Romero VI, Arias-Almeida B, Reyes C, Hosomichi K. Novel Variation in Acyl-CoA Synthetase Long Chain Family Member 6 (ACSL6) Results in Protein Structural Modification and Multiple Non-Related Neoplasia in a 46-Year-Old: Case Report. Front Oncol 2022; 12:899579. [PMID: 35756649 PMCID: PMC9215171 DOI: 10.3389/fonc.2022.899579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Multiple non-related neoplasia does not have an established approach or benefits for performing whole-exome sequencing (WES) analysis. We report on a 46-year-old woman who developed astrocytoma, thyroid, and breast cancer within 10 years. The WES analysis found a novel missense variant in the ACSL6 gene, and the protein modeling showed altered secondary and tertiary structures, which modify the binding to cofactors and substrates. ACSL6 is involved in lipid metabolism, expressed in the brain, thyroid, and breast tissues, and is associated with diverse types of cancer. Our study demonstrates the benefit of WES analysis compared with commercial panels in patients with non-related neoplasia.
Collapse
Affiliation(s)
| | - Erick Freire
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Vanessa I Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
| | - Benjamín Arias-Almeida
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Carlos Reyes
- Departamento de Genetica, Hospital de Especialidades Eugenio Espejo, Quito, Ecuador
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Kanazawa University, Kanazawa, Japan
| |
Collapse
|
179
|
Sanford Kobayashi EF, Dimmock DP. Better and faster is cheaper. Hum Mutat 2022; 43:1495-1506. [PMID: 35723630 DOI: 10.1002/humu.24422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022]
Abstract
The rapid pace of advancement in genomic sequencing technology has recently reached a new milestone, with a record-setting time to molecular diagnosis of a mere 8 h. The catalyst behind this achievement is the accumulation of evidence indicating that quicker results more often make an impact on patient care and lead to healthcare cost savings. Herein, we review the diagnostic and clinical utility of rapid whole genome and rapid whole exome sequencing, the associated reduction in healthcare costs, and the relationship between these outcome measures and time-to-diagnosis.
Collapse
Affiliation(s)
- Erica F Sanford Kobayashi
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| |
Collapse
|
180
|
Xu L, Zhou Y, Ren X, Xu C, Ren R, Yan X, Li X, Yang H, Xu X, Guo X, Sheng G, Hua Y, Yuan Z, Wang S, Gu W, Sun D, Gao F. Expanding the Phenotypic and Genotypic Spectrum of ARFGEF1-Related Neurodevelopmental Disorder. Front Mol Neurosci 2022; 15:862096. [PMID: 35782386 PMCID: PMC9248374 DOI: 10.3389/fnmol.2022.862096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
Mono-allelic loss-of-function variants in ARFGEF1 have recently caused a developmental delay, intellectual disability, and epilepsy, with varying clinical expressivity. However, given the clinical heterogeneity and low-penetrance mutations of ARFGEF1-related neurodevelopmental disorder, the robustness of the gene-disease association requires additional evidence. In this study, five novel heterozygous ARFGEF1 variants were identified in five unrelated pediatric patients with neurodevelopmental disorders, including one missense change (c.3539T>G), two canonical splice site variants (c.917-1G>T, c.2850+2T>A), and two frameshift (c.2923_c.2924delCT, c.4951delG) mutations resulting in truncation of ARFGEF1. The pathogenic/likely pathogenic variants presented here will be highly beneficial to patients undergoing genetic testing in the future by providing an expanded reference list of disease-causing variants.
Collapse
Affiliation(s)
- Lu Xu
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Youfeng Zhou
- Department of Pediatrics, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiaoyan Ren
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chenlu Xu
- Beijing Chigene Translational Medical Research Centre Co. Ltd., Beijing, China
| | - Rongna Ren
- Department of Pediatrics and Neurosurgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Xuke Yan
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuelian Li
- Department of Pediatric Neurology, Anhui Provincial Children's Hospital, Hefei, China
| | - Huimin Yang
- Department of Pediatric, Inner Mongolia Maternal and Child Health Care Hospital, Hohhot, China
| | - Xuebin Xu
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaotong Guo
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoxia Sheng
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Hua
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhefeng Yuan
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shugang Wang
- Beijing Chigene Translational Medical Research Centre Co. Ltd., Beijing, China
| | - Weiyue Gu
- Beijing Chigene Translational Medical Research Centre Co. Ltd., Beijing, China
- *Correspondence: Weiyue Gu
| | - Dan Sun
- Department of Pediatric Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Dan Sun
| | - Feng Gao
- Department of Neurology, National Clinical Research Centre for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Feng Gao
| |
Collapse
|
181
|
Disease relevance of rare VPS13B missense variants for neurodevelopmental Cohen syndrome. Sci Rep 2022; 12:9686. [PMID: 35690661 PMCID: PMC9188546 DOI: 10.1038/s41598-022-13717-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/13/2022] [Indexed: 12/29/2022] Open
Abstract
Autosomal recessive Cohen syndrome is a neurodevelopmental disorder characterized by postnatal microcephaly, intellectual disability, and a typical facial gestalt. Genetic variants in VPS13B have been found to cause Cohen syndrome, but have also been linked to autism, retinal disease, primary immunodeficiency, and short stature. While it is well established that loss-of-function mutations of VPS13B cause Cohen syndrome, the relevance of missense variants for the pathomechanism remains unexplained. Here, we investigate their pathogenic effect through a systematic re-evaluation of clinical patient information, comprehensive in silico predictions, and in vitro testing of previously published missense variants. In vitro analysis of 10 subcloned VPS13B missense variants resulted in full-length proteins after transient overexpression. 6/10 VPS13B missense variants show reduced accumulation at the Golgi complex in the steady state. The overexpression of these 6/10 VPS13B missense variants did not rescue the Golgi fragmentation after the RNAi-mediated depletion of endogenous VPS13B. These results thus validate 6/10 missense variants as likely pathogenic according to the classification of the American College of Medical Genetics through the integration of clinical, genetic, in silico, and experimental data. In summary, we state that exact variant classification should be the first step towards elucidating the pathomechanisms of genetically inherited neuronal diseases.
Collapse
|
182
|
Rodrigues EDS, Griffith S, Martin R, Antonescu C, Posey JE, Coban‐Akdemir Z, Jhangiani SN, Doheny KF, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Sheffer A, Chong JX, Einhorn Y, Cupak M, Sobreira N. Variant-level matching for diagnosis and discovery: Challenges and opportunities. Hum Mutat 2022; 43:782-790. [PMID: 35191117 PMCID: PMC9133151 DOI: 10.1002/humu.24359] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 11/30/2022]
Abstract
Here we describe MyGene2, Geno2MP, VariantMatcher, and Franklin; databases that provide variant-level information and phenotypic features to researchers, clinicians, healthcare providers and patients. Following the footsteps of the Matchmaker Exchange project that connects exome, genome, and phenotype databases at the gene level, these databases have as one goal to facilitate connection to one another using Data Connect, a standard for discovery and search of biomedical data from the Global Alliance for Genomics and Health (GA4GH).
Collapse
Affiliation(s)
- Eliete da S. Rodrigues
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Sean Griffith
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Renan Martin
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Corina Antonescu
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jennifer E. Posey
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Zeynep Coban‐Akdemir
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Shalini N. Jhangiani
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTexasUSA
| | - Kimberly F. Doheny
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - James R. Lupski
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTexasUSA
- Department of PediatricsBaylor College of MedicineHoustonTexasUSA
- Texas Children's HospitalHoustonTexasUSA
| | - David Valle
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Michael J. Bamshad
- Division of Genetic Medicine, Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | - Ada Hamosh
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | | | - Jessica X. Chong
- Division of Genetic Medicine, Department of PediatricsUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | | | | | - Nara Sobreira
- McKusick‐Nathans Department of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| |
Collapse
|
183
|
Lavelle TA, Feng X, Keisler M, Cohen JT, Neumann PJ, Prichard D, Schroeder BE, Salyakina D, Espinal PS, Weidner SB, Maron JL. Cost-effectiveness of exome and genome sequencing for children with rare and undiagnosed conditions. Genet Med 2022; 24:1349-1361. [PMID: 35396982 DOI: 10.1016/j.gim.2022.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE This study aimed to estimate the cost-effectiveness of exome sequencing (ES) and genome sequencing (GS) for children. METHODS We modeled costs, diagnoses, and quality-adjusted life years (QALYs) for diagnostic strategies for critically ill infants (aged <1 year) and children (aged <18 years) with suspected genetic conditions: (1) standard of care (SOC) testing, (2) ES, (3) GS, (4) SOC followed by ES, (5) SOC followed by GS, (6) ES followed by GS, and (7) SOC followed by ES followed by GS. We calculated the 10-year incremental cost per additional diagnosis, and lifetime incremental cost per QALY gained, from a health care perspective. RESULTS First-line GS costs $15,048 per diagnosis vs SOC for infants and $27,349 per diagnosis for children. If GS is unavailable, ES represents the next most efficient option compared with SOC ($15,543 per diagnosis for infants and $28,822 per diagnosis for children). Other strategies provided the same or fewer diagnoses at a higher incremental cost per diagnosis. Lifetime results depend on the patient's assumed long-term prognosis after diagnosis. For infants, GS ranged from cost-saving (vs all alternatives) to $18,877 per QALY (vs SOC). For children, GS (vs SOC) ranged from $119,705 to $490,047 per QALY. CONCLUSION First-line GS may be the most cost-effective strategy for diagnosing infants with suspected genetic conditions. For all children, GS may be cost-effective under certain assumptions. ES is nearly as efficient as GS and hence is a viable option when GS is unavailable.
Collapse
Affiliation(s)
- Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA.
| | - Xue Feng
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Marlena Keisler
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Joshua T Cohen
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Peter J Neumann
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | | | | | - Daria Salyakina
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, Miami, FL
| | - Paula S Espinal
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, Miami, FL
| | - Samuel B Weidner
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Jill L Maron
- Women & Infants Hospital of Rhode Island, Care New England Health System, Providence, RI
| |
Collapse
|
184
|
Masri AT, Oweis L, Qudah AA, El-Shanti H. Congenital muscle dystrophies: Role of singleton whole exome sequencing in countries with limited resources. Clin Neurol Neurosurg 2022; 217:107271. [DOI: 10.1016/j.clineuro.2022.107271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 12/01/2022]
|
185
|
Al Masseri Z, AlSayed M. Gonadal mosaicism in GNAO1 causing neurodevelopmental disorder with involuntary movements; two additional variants. Mol Genet Metab Rep 2022; 31:100864. [PMID: 35782616 PMCID: PMC9248221 DOI: 10.1016/j.ymgmr.2022.100864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/19/2022] [Accepted: 03/20/2022] [Indexed: 11/25/2022] Open
Abstract
Background GNAO1 encodes an alpha subunit of the heterotrimeric guanine nucleotide-binding proteins (G proteins). Mutations in GNAO1 result in two clinical phenotypes: Early infantile epileptic encephalopathy 17 (EEIE17-OMIM #615473) and Neurodevelopmental disorder with involuntary movements (NEDIM-OMIM #617493). Both are inherited as autosomal dominant disorders and originate mainly as de novo. Only a few are reported as gonadal mosaicism. Materials and methods We recruited and retrospectively reviewed five patients from two families seen at King Faisal Specialist Hospital and Research Centre in Riyadh (KFSHRC). Results All patients presented with severe neurodevelopmental disorder, followed by progressive dystonia and hyperkinetic movements. In addition, none of the patients had seizures which was consistent with NEDIM phenotype. The specific diagnosis was not clinically entertained and was only found on whole exome sequencing (WES), which identified two variants (c.724-8G > A & c.709G > A). Both variants were previously reported as pathogenic de novo in patients with NEDIM, and one was reported as parental gonadal mosaicism. Conclusion We report these variants as additional variants in GNAO1 gene that may be inherited as parental gonadal mosaicism. Both variants resulted in NEDIM with no observed clinical differences in the severity than the reported cases. This noticeable reported association between GNAO1 gene associated disorders and gonadal mosaicism should be considered in reproductive genetic counselling of affected families. Furthermore, in view of these reports, more studies with prospective data collection to explore the association between GNAO1 and gonadal mosaicism and the underlying mechanisms will be necessary.
Collapse
|
186
|
"We've Opened Pandora's Box, Haven't We?" Clinical Geneticists' Views on Ethical Aspects of Genomic Testing in Neonatal Intensive Care. Balkan J Med Genet 2022; 25:5-12. [PMID: 36880043 PMCID: PMC9985353 DOI: 10.2478/bjmg-2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
The increasing use of genomic testing in neonatal intensive care units (NICU) gives rise to ethical issues. Yet little is known regarding what health professionals implementing the testing think about its ethical aspects. We therefore explored the views of Australian clinical geneticists towards ethical issues in the use of genomic testing in the Neonatal Intensive care Unit (NICU). Semi-structured interviews with 11 clinical geneticists were conducted, transcribed and analysed thematically. Four themes were identified: 1) Consent: the craft is in the conversation, which encapsulated the challenges in the consent process, and with pre-test counseling; 2) Whose autonomy and who decides? This illustrates the balancing of clinical utility and potentially harms the test, and how stakeholder interests are balanced; 3) The winds of change and ethical disruption, recognizing that while professional expertise is vital to clinical decision-making and oversight of mainstreaming, participants also expressed concern over the size of the genetics workforce and 4). Finding Solutions - the resources and mechanisms to prevent and resolve ethical dilemmas when they arise, such as quality genetic counseling, working as a team and drawing on external ethics and legal expertise. The findings highlight the ethical complexities associated with genomic testing in the NICU. They suggest the need for a workforce that has the necessary support and skills to navigate the ethical terrain, drawing on relevant ethical concepts and guidelines to balance the interests of neonates, their careers and health professionals.
Collapse
|
187
|
Schmidlen T, Jones CL, Campbell-Salome G, McCormick CZ, Vanenkevort E, Sturm AC. Use of a chatbot to increase uptake of cascade genetic testing. J Genet Couns 2022; 31:1219-1230. [PMID: 35616645 DOI: 10.1002/jgc4.1592] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/26/2022] [Accepted: 05/06/2022] [Indexed: 12/18/2022]
Abstract
Successful proband-mediated family communication and subsequent cascade genetic testing uptake requires interventions that present information clearly, in sufficient detail, and with medical authority. To facilitate family communication for patients receiving clinically actionable results via the MyCode® Community Health Initiative, a Family Sharing Tool (FST) and a cascade chatbot were developed. FST is an electronic mechanism allowing patients to share genetic test results with relatives via chatbot. The cascade chatbot describes the proband's result, associated disease risks, and recommended management and captures whether the user is a blood relative or caregiver, sex, and relationship to the proband. FST and cascade chatbot uptake among MyCode® probands and relatives was tracked from August 2018 through February 2020. Cascade genetic testing uptake was collected from testing laboratories as number of cascades per proband. Fifty-eight percent (316/543) of probands consented to FST; 42% (227/543) declined. Receipt preferences were patient electronic health record (EHR) portal (52%), email (29%), and text (19%). Patient EHR portal users (p < 0.001) and younger patients were more likely to consent (p < 0.001). FST was deployed to 308 probands. Fifty-nine percent (183/308) opened; of those, 56% (102/183) used FST to send a cascade chatbot to relatives. These 102 probands shared a cascade chatbot with 377 relatives. Sixty-two percent (235/377) of relatives opened; of these, 69% (161/235) started, and of these, 57% (92/161) completed the cascade chatbot. Cascade genetic testing uptake was significantly greater among relatives of probands who consented to the FST (M = 2.34 cascades, SD = 2.10) than relatives of probands who declined (M = 1.40 cascades, SD = 0.82, p < 0.001). Proband age was not a significant predictor of cascade genetic testing uptake. Further work is needed to better understand factors impacting proband use of FST and relative use of cascade chatbots.
Collapse
Affiliation(s)
| | - Claire L Jones
- Geisinger, Genomic Medicine Institute, Danville, Pennsylvania, USA
| | | | - Cara Z McCormick
- Geisinger, Genomic Medicine Institute, Danville, Pennsylvania, USA
| | - Erin Vanenkevort
- Geisinger, Genomic Medicine Institute, Danville, Pennsylvania, USA
| | - Amy C Sturm
- Geisinger, Genomic Medicine Institute, Danville, Pennsylvania, USA
| |
Collapse
|
188
|
Schuermans N, Hemelsoet D, Terryn W, Steyaert S, Van Coster R, Coucke PJ, Steyaert W, Callewaert B, Bogaert E, Verloo P, Vanlander AV, Debackere E, Ghijsels J, LeBlanc P, Verdin H, Naesens L, Haerynck F, Callens S, Dermaut B, Poppe B. Shortcutting the diagnostic odyssey: the multidisciplinary Program for Undiagnosed Rare Diseases in adults (UD-PrOZA). Orphanet J Rare Dis 2022; 17:210. [PMID: 35606766 PMCID: PMC9128245 DOI: 10.1186/s13023-022-02365-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/13/2022] [Indexed: 11/23/2022] Open
Abstract
Background In order to facilitate the diagnostic process for adult patients suffering from a rare disease, the Undiagnosed Disease Program (UD-PrOZA) was founded in 2015 at the Ghent University Hospital in Belgium. In this study we report the five-year results of our multidisciplinary approach in rare disease diagnostics. Methods Patients referred by a healthcare provider, in which an underlying rare disease is likely, qualify for a UD-PrOZA evaluation. UD-PrOZA uses a multidisciplinary clinical approach combined with state-of-the-art genomic technologies in close collaboration with research facilities to diagnose patients. Results Between 2015 and 2020, 692 patients (94% adults) were referred of which 329 (48%) were accepted for evaluation. In 18% (60 of 329) of the cases a definite diagnosis was made. 88% (53 of 60) of the established diagnoses had a genetic origin. 65% (39 of 60) of the genetic diagnoses were made through whole exome sequencing (WES). The mean time interval between symptom-onset and diagnosis was 19 years. Key observations included novel genotype–phenotype correlations, new variants in known disease genes and the identification of three new disease genes. In 13% (7 of 53), identifying the molecular cause was associated with therapeutic recommendations and in 88% (53 of 60), gene specific genetic counseling was made possible. Actionable secondary findings were reported in 7% (12 of 177) of the patients in which WES was performed. Conclusion UD-PrOZA offers an innovative interdisciplinary platform to diagnose rare diseases in adults with previously unexplained medical problems and to facilitate translational research. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02365-y.
Collapse
Affiliation(s)
- Nika Schuermans
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium. .,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | | | - Wim Terryn
- Department of Nephrology, Jan Yperman Hospital, Ieper, Belgium
| | - Sanne Steyaert
- Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Rudy Van Coster
- Department of Pediatrics, Division of Pediatric Neurology and Metabolic Diseases, Ghent University Hospital, Ghent, Belgium
| | - Paul J Coucke
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Wouter Steyaert
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Patrick Verloo
- Department of Pediatrics, Division of Pediatric Neurology and Metabolic Diseases, Ghent University Hospital, Ghent, Belgium
| | - Arnaud V Vanlander
- Department of Pediatrics, Division of Pediatric Neurology and Metabolic Diseases, Ghent University Hospital, Ghent, Belgium
| | - Elke Debackere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Jody Ghijsels
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Pontus LeBlanc
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hannah Verdin
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium.,Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Steven Callens
- Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | | |
Collapse
|
189
|
A single center experience of prenatal parent‐fetus trio exome sequencing for pregnancies with congenital anomalies. Prenat Diagn 2022; 42:901-910. [DOI: 10.1002/pd.6170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/07/2022]
|
190
|
Malakootian M, Bagheri Moghaddam M, Kalayinia S, Farrashi M, Maleki M, Sadeghipour P, Amin A. Dilated cardiomyopathy caused by a pathogenic nucleotide variant in RBM20 in an Iranian family. BMC Med Genomics 2022; 15:106. [PMID: 35527250 PMCID: PMC9079971 DOI: 10.1186/s12920-022-01262-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/05/2022] [Indexed: 12/22/2022] Open
Abstract
Abstract
Introduction
Dilated cardiomyopathy (DCM) is characterized by the dilation and impaired contraction of 1 or both ventricles and can be caused by a variety of disorders. Up to 50% of idiopathic DCM cases have heritable familial diseases, and the clinical screening of family members is recommended. Identifying a genetic cause that can explain the DCM risk in the family can help with better screening planning and clinical decision-making. Whole-exome sequencing (WES) has aided significantly in the detection of causative genes in many genetically heterogeneous diseases. In the present study, we applied WES to identify the causative genetic variant in a family with heritable DCM.
Methods
WES was applied to identify genetic variants on a 26-year-old man as the proband of a family with DCM. Subsequently, Sanger sequencing was performed to confirm the variant in the patient and all the available affected and unaffected family members. The pathogenicity of the variant was evaluated through co-segregation analysis in the family and employment of in silico predictive software.
Results
WES demonstrated the missense pathogenic heterozygous nucleotide variant, c.1907G > A, (p.Arg636His, rs267607004, NM_0011343), in exon 9 of the RBM20 gene in the proband. The variant was co-segregated in all the affected family members in a heterozygous form and the unaffected family members. The in silico analysis confirmed the variant as pathogenic.
Conclusion
Pathogenic RBM20 nucleotide variants are associated with arrhythmogenic DCM. We believe that our report is the first to show an RBM20 variant in Iranian descent associated with DCM.
Collapse
|
191
|
Li Q, Ren Z, Cao K, Li MM, Wang K, Zhou Y. CancerVar: An artificial intelligence-empowered platform for clinical interpretation of somatic mutations in cancer. SCIENCE ADVANCES 2022; 8:eabj1624. [PMID: 35544644 PMCID: PMC9075800 DOI: 10.1126/sciadv.abj1624] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 03/21/2022] [Indexed: 05/12/2023]
Abstract
Several knowledgebases are manually curated to support clinical interpretations of thousands of hotspot somatic mutations in cancer. However, discrepancies or even conflicting interpretations are observed among these databases. Furthermore, many previously undocumented mutations may have clinical or functional impacts on cancer but are not systematically interpreted by existing knowledgebases. To address these challenges, we developed CancerVar to facilitate automated and standardized interpretations for 13 million somatic mutations based on the AMP/ASCO/CAP 2017 guidelines. We further introduced a deep learning framework to predict oncogenicity for these variants using both functional and clinical features. CancerVar achieved satisfactory performance when compared to several independent knowledgebases and, using clinically curated datasets, demonstrated practical utility in classifying somatic variants. In summary, by integrating clinical guidelines with a deep learning framework, CancerVar facilitates clinical interpretation of somatic variants, reduces manual work, improves consistency in variant classification, and promotes implementation of the guidelines.
Collapse
Affiliation(s)
- Quan Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G2C1, Canada
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zilin Ren
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kajia Cao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Marilyn M. Li
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yunyun Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| |
Collapse
|
192
|
Bullich G, Matalonga L, Pujadas M, Papakonstantinou A, Piscia D, Tonda R, Artuch R, Gallano P, Garrabou G, González JR, Grinberg D, Guitart M, Laurie S, Lázaro C, Luengo C, Martí R, Milà M, Ovelleiro D, Parra G, Pujol A, Tizzano E, Macaya A, Palau F, Ribes A, Pérez-Jurado LA, Beltran S. Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases. J Mol Diagn 2022; 24:529-542. [PMID: 35569879 DOI: 10.1016/j.jmoldx.2022.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/16/2021] [Accepted: 02/03/2022] [Indexed: 11/26/2022] Open
Abstract
Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive reanalysis efforts that enable collaborative interpretation and future reinterpretation. The Undiagnosed Rare Disease Program of Catalonia project collated previously inconclusive good quality genomic data (panels, exomes, and genomes) and standardized phenotypic profiles from 323 families (543 individuals) with a neurologic rare disease. The data were reanalyzed systematically to identify relatedness, runs of homozygosity, consanguinity, single-nucleotide variants, insertions and deletions, and copy number variants. Data were shared and collaboratively interpreted within the consortium through a customized Genome-Phenome Analysis Platform, which also enables future data reinterpretation. Reanalysis of existing genomic data provided a diagnosis for 20.7% of the patients, including 1.8% diagnosed after the generation of additional genomic data to identify a second pathogenic heterozygous variant. Diagnostic rate was significantly higher for family-based exome/genome reanalysis compared with singleton panels. Most new diagnoses were attributable to recent gene-disease associations (50.8%), additional or improved bioinformatic analysis (19.7%), and standardized phenotyping data integrated within the Undiagnosed Rare Disease Program of Catalonia Genome-Phenome Analysis Platform functionalities (18%).
Collapse
Affiliation(s)
- Gemma Bullich
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Leslie Matalonga
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Montserrat Pujadas
- Genetics Unit, University Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Anastasios Papakonstantinou
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Davide Piscia
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Raúl Tonda
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Pia Gallano
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Genetics Department, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Glòria Garrabou
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Muscle Research and Mitochondrial Function Laboratory, CELLEX-Institut d'Investigació Biomèdica August Pi i Sunyer (IDIBAPS), Internal Medicine Department, Hospital Clinic of Barcelona, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Juan R González
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Daniel Grinberg
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Institute of Biomedicine of the University of Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain
| | - Míriam Guitart
- Genetics Laboratory, Paediatric Unit, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Steven Laurie
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Conxi Lázaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Catalan Institute of Oncology, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Cristina Luengo
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ramon Martí
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montserrat Milà
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, Institut d'Investigació Biomèdica August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - David Ovelleiro
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Genís Parra
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Aurora Pujol
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)-Hospital Duran i Reynals, Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Eduardo Tizzano
- Department of Clinical and Molecular Genetics, Medicine Genetics Group Vall d'Hebron Institut de Recerca (VHIR), European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Universitat Autònoma de Barcelona, Hospital Vall d´Hebron, Barcelona, Spain
| | - Alfons Macaya
- Pediatric Neurology Research Group, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francesc Palau
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Genetic and Molecular Medicine, Pediatric Institute of Rare Diseases (IPER), Hospital Sant Joan de Déu, Clinic Institute of Medicine and Dermatology, Hospital Clínic de Barcelona and Division of Pediatrics, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Antònia Ribes
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Secció d'Errors Congènits del Metabolisme-Institute of Clinical Biochemistry (IBC), Servei de Bioquímica i Genètìca Molecular, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Luis A Pérez-Jurado
- Genetics Unit, University Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Women's and Children's Hospital, South Australian Health and Medical Research Institute and The University of Adelaide, Adelaide, South Australia, Australia
| | - Sergi Beltran
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
| | | |
Collapse
|
193
|
Liu Y, Zhang Q, Wang J, Liu J, Yang W, Yan X, Ouyang Y, Yang H. Both subthalamic and pallidal deep brain stimulation are effective for GNAO1-associated dystonia: three case reports and a literature review. Ther Adv Neurol Disord 2022; 15:17562864221093507. [PMID: 35509770 PMCID: PMC9058460 DOI: 10.1177/17562864221093507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/24/2022] [Indexed: 11/16/2022] Open
Abstract
Background Mutations in the G-protein subunit alpha o1 (GNAO1) gene have recently been shown to be involved in the pathogenesis of early infantile epileptic encephalopathy and movement disorders. The clinical manifestations of GNAO1-associated movement disorders are highly heterogeneous. However, the genotype-phenotype correlations in this disease remain unclear, and the treatments for GNAO1-associated movement disorders are still limited. Objective The objective of this study was to explore diagnostic and therapeutic strategies for GNAO1-associated movement disorders. Methods This study describes the cases of three Chinese patients who had shown severe and progressive dystonia in the absence of epilepsy since early childhood. We performed genetic analyses in these patients. Patients 1 and 2 underwent globus pallidus internus (GPi) deep brain stimulation (DBS) implantation, and Patient 3 underwent subthalamic nucleus (STN) DBS implantation. In addition, on the basis of a literature review, we summarized and discussed the clinical characteristics and outcomes after DBS surgery for all reported patients with GNAO1-associated movement disorders. Results Whole-exome sequencing (WES) analysis revealed de novo variants in the GNAO1 gene for all three patients, including a splice-site variant (c.724-8G > A) in Patients 1 and 3 and a novel heterozygous missense variant (c.124G > A; p. Gly42Arg) in Patient 2. Both GPi and STN DBS were effective in improving the dystonia symptoms of all three patients. Conclusion DBS is effective in ameliorating motor symptoms in patients with GNAO1-associated movement disorders, and both STN DBS and GPi DBS should be considered promptly for patients with sustained refractory GNAO1-associated dystonia.
Collapse
Affiliation(s)
- Ye Liu
- Department of Neurology, The First Hospital of China Medical University, Shenyang, China
| | - Qingping Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jun Wang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Jiyuan Liu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Wuyang Yang
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xuejing Yan
- Department of Neurology, The First Hospital of China Medical University, Shenyang, China
| | - Yi Ouyang
- Department of Neurology, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Haibo Yang
- Department of Pediatric Surgery, Peking University First Hospital, Beijing 100034, China
| |
Collapse
|
194
|
Perl E, Ravisankar P, Beerens ME, Mulahasanovic L, Smallwood K, Sasso MB, Wenzel C, Ryan TD, Komár M, Bove KE, MacRae CA, Weaver KN, Prada CE, Waxman JS. Stx4 is required to regulate cardiomyocyte Ca 2+ handling during vertebrate cardiac development. HGG ADVANCES 2022; 3:100115. [PMID: 35599850 PMCID: PMC9114686 DOI: 10.1016/j.xhgg.2022.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/22/2022] [Indexed: 12/16/2022] Open
Abstract
Requirements for vesicle fusion within the heart remain poorly understood, despite the multitude of processes that necessitate proper intracellular trafficking within cardiomyocytes. Here, we show that Syntaxin 4 (STX4), a target-Soluble N-ethylmaleimide sensitive factor attachment receptor (t-SNARE) protein, is required for normal vertebrate cardiac conduction and vesicular transport. Two patients were identified with damaging variants in STX4. A patient with a homozygous R240W missense variant displayed biventricular dilated cardiomyopathy, ectopy, and runs of non-sustained ventricular tachycardia, sensorineural hearing loss, global developmental delay, and hypotonia, while a second patient displayed severe pleiotropic abnormalities and perinatal lethality. CRISPR/Cas9-generated stx4 mutant zebrafish exhibited defects reminiscent of these patients' clinical presentations, including linearized hearts, bradycardia, otic vesicle dysgenesis, neuronal atrophy, and touch insensitivity by 3 days post fertilization. Imaging of Vamp2+ vesicles within stx4 mutant zebrafish hearts showed reduced docking to the cardiomyocyte sarcolemma. Optical mapping of the embryonic hearts coupled with pharmacological modulation of Ca2+ handling together support that zebrafish stx4 mutants have a reduction in L-type Ca2+ channel modulation. Transgenic overexpression of zebrafish Stx4R241W, analogous to the first patient's STX4R240W variant, indicated that the variant is hypomorphic. Thus, these data show an in vivo requirement for SNAREs in regulating normal embryonic cardiac function and that variants in STX4 are associated with pleiotropic human disease, including cardiomyopathy.
Collapse
Affiliation(s)
- Eliyahu Perl
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA,Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA,Division of Molecular Cardiovascular Biology, The Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Padmapriyadarshini Ravisankar
- Division of Molecular Cardiovascular Biology, The Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Manu E. Beerens
- Cardiovascular Medicine Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lejla Mulahasanovic
- Praxis für Humangenetik, Tübingen, Baden-Württemberg, Germany,CeGaT GmbH, Tübingen, Baden-Württemberg, Germany
| | - Kelly Smallwood
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Marion Bermúdez Sasso
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Saxony, Germany
| | - Carina Wenzel
- Institute of Pathology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Thomas D. Ryan
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA,Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Matej Komár
- Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Saxony, Germany
| | - Kevin E. Bove
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA,Division of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA,Department of Pathology and Laboratory Medicine, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Calum A. MacRae
- Cardiovascular Medicine Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Genetics and Network Medicine Divisions, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Harvard Stem Cell Institute, Boston, MA, USA
| | - K. Nicole Weaver
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA,Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Carlos E. Prada
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA,Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Joshua S. Waxman
- Division of Molecular Cardiovascular Biology, The Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA,Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA,Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA,Corresponding author
| |
Collapse
|
195
|
Cheng HL, Chen YJ, Xue YY, Wu ZY, Li HF, Wang N. Clinical Characterization and Founder Effect Analysis in Chinese Patients with Phospholipase A2-Associated Neurodegeneration. Brain Sci 2022; 12:brainsci12050517. [PMID: 35624904 PMCID: PMC9138368 DOI: 10.3390/brainsci12050517] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 12/04/2022] Open
Abstract
PLA2G6-associated neurodegeneration (PLAN) is a rare autosomal recessive disorder caused by PLA2G6 mutations. This study aimed to investigate the clinical characteristics and mutation spectrum of PLAN and to investigate the founder effects in Chinese PLAN patients. Six Chinese PLAN families were clinically examined in detail and whole-exome sequencing was performed in the probands. Haplotype analysis was performed in five families with the PLA2G6 c.991G > T mutation using 23 single nucleotide polymorphism markers. Furthermore, all previously reported PLA2G6 mutations and patients in China were reviewed to summarize the genetic and clinical features of PLAN. Interestingly, we found that one patient had hereditary spastic paraplegia and showed various atypical clinical characteristics of PLAN, and five patients had a phenotype of parkinsonism. All probands were compound heterozygotes for PLA2G6 variants, including four novel pathogenic/likely pathogenic mutations (c.967G > A, c.1450G > T, c.1631T > C, and c.1915delG) and five known pathogenic mutations. Haplotype analyses revealed that patients carrying PLA2G6 c.991G > T mutations shared a haplotype of 717 kb. The frequencies of psychiatric features, cognitive decline, and myoclonus in Chinese patients with PLA2G6-related parkinsonism were significantly different from those in European patients. Thus, our study expands the clinical and genetic spectrum of PLAN and provides an insightful view of the founder effect to better diagnose and understand the disease.
Collapse
Affiliation(s)
- Hao-Ling Cheng
- Department of Neurology, Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China; (H.-L.C.); (Y.-J.C.)
| | - Yi-Jun Chen
- Department of Neurology, Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China; (H.-L.C.); (Y.-J.C.)
| | - Yan-Yan Xue
- Research Center of Neurology, Key Laboratory of Medical Neurobiology of Zhejiang Province, Department of Neurology, Second Affiliated Hospital of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310000, China; (Y.-Y.X.); (Z.-Y.W.)
| | - Zhi-Ying Wu
- Research Center of Neurology, Key Laboratory of Medical Neurobiology of Zhejiang Province, Department of Neurology, Second Affiliated Hospital of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310000, China; (Y.-Y.X.); (Z.-Y.W.)
| | - Hong-Fu Li
- Research Center of Neurology, Key Laboratory of Medical Neurobiology of Zhejiang Province, Department of Neurology, Second Affiliated Hospital of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310000, China; (Y.-Y.X.); (Z.-Y.W.)
- Correspondence: (H.-F.L.); (N.W.); Tel.: +086-571-87783569 (H.-F.L.); +086-591-87982772 (N.W.)
| | - Ning Wang
- Department of Neurology, Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China; (H.-L.C.); (Y.-J.C.)
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
- Correspondence: (H.-F.L.); (N.W.); Tel.: +086-571-87783569 (H.-F.L.); +086-591-87982772 (N.W.)
| |
Collapse
|
196
|
Walsh M, West K, Taylor JA, Thompson BA, Hopkins A, Sexton A, Ragunathan A, Verma KP, Panetta J, Matotek E, Fahey MC, Christie M, Winship IM, Trainer AH, James PA. Real world outcomes and implementation pathways of exome sequencing in an adult genetic department. Genet Med 2022; 24:1536-1544. [PMID: 35416776 DOI: 10.1016/j.gim.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE This study aimed to correlate the indications and diagnostic yield of exome sequencing (ES) in adult patients across various clinical settings. The secondary aim was to examine the clinical utility of ES in adult patients. METHODS Data on demographics, clinical indications, results, management changes, and cascade testing were collected for 250 consecutive patients who underwent ES through an adult genetics department between 2016 and 2021. Data were analyzed using descriptive and inferential statistics. Testing in which traditional gene panels were in standard use, such as in heritable cancers, was excluded. RESULTS The average age at testing was 43 years (range = 17-80 years). A molecular diagnosis was identified in 29% of patients. Older age at symptom onset did not pre-exclude a substantial diagnostic yield. Patients with syndromic intellectual disability and multiple system disorders had the highest yield. In >50% of patients with an exome diagnosis, the results changed management. Cascade testing occured in at least one family member for 30% of patients with a diagnosis. Diagnostic results had reproductive implications for 26% of patients and 31% of patients' relatives. CONCLUSION ES has a robust diagnostic yield and clear clinical utility in adult patients across a range of ages and phenotypes.
Collapse
Affiliation(s)
- Maie Walsh
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Kirsty West
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Jessica A Taylor
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Adelaide Hopkins
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Adrienne Sexton
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Abiramy Ragunathan
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Kunal P Verma
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Julie Panetta
- Metabolic Diseases Unit (MDU), The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ebony Matotek
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael C Fahey
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael Christie
- Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia; Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Alison H Trainer
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul A James
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
197
|
Nevado J, García-Miñaúr S, Palomares-Bralo M, Vallespín E, Guillén-Navarro E, Rosell J, Bel-Fenellós C, Mori MÁ, Milá M, del Campo M, Barrúz P, Santos-Simarro F, Obregón G, Orellana C, Pachajoa H, Tenorio JA, Galán E, Cigudosa JC, Moresco A, Saleme C, Castillo S, Gabau E, Pérez-Jurado L, Barcia A, Martín MS, Mansilla E, Vallcorba I, García-Murillo P, Cammarata-Scalisi F, Gonçalves Pereira N, Blanco-Lago R, Serrano M, Ortigoza-Escobar JD, Gener B, Seidel VA, Tirado P, Lapunzina P. Variability in Phelan-McDermid Syndrome in a Cohort of 210 Individuals. Front Genet 2022; 13:652454. [PMID: 35495150 PMCID: PMC9044489 DOI: 10.3389/fgene.2022.652454] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/16/2022] [Indexed: 12/18/2022] Open
Abstract
Phelan-McDermid syndrome (PMS, OMIM# 606232) results from either different rearrangements at the distal region of the long arm of chromosome 22 (22q13.3) or pathogenic sequence variants in the SHANK3 gene. SHANK3 codes for a structural protein that plays a central role in the formation of the postsynaptic terminals and the maintenance of synaptic structures. Clinically, patients with PMS often present with global developmental delay, absent or severely delayed speech, neonatal hypotonia, minor dysmorphic features, and autism spectrum disorders (ASD), among other findings. Here, we describe a cohort of 210 patients with genetically confirmed PMS. We observed multiple variant types, including a significant number of small deletions (<0.5 Mb, 64/189) and SHANK3 sequence variants (21 cases). We also detected multiple types of rearrangements among microdeletion cases, including a significant number with post-zygotic mosaicism (9.0%, 17/189), ring chromosome 22 (10.6%, 20/189), unbalanced translocations (de novo or inherited, 6.4%), and additional rearrangements at 22q13 (6.3%, 12/189) as well as other copy number variations in other chromosomes, unrelated to 22q deletions (14.8%, 28/189). We compared the clinical and genetic characteristics among patients with different sizes of deletions and with SHANK3 variants. Our findings suggest that SHANK3 plays an important role in this syndrome but is probably not uniquely responsible for all the spectrum features in PMS. We emphasize that only an adequate combination of different molecular and cytogenetic approaches allows an accurate genetic diagnosis in PMS patients. Thus, a diagnostic algorithm is proposed.
Collapse
Affiliation(s)
- Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Sixto García-Miñaúr
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - María Palomares-Bralo
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Elena Vallespín
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | | | | | - Cristina Bel-Fenellós
- Departamento de Investigación y Psicología en Educación, Facultad de Educación, UCM, Madrid, Spain
- CEE Estudio-3, Afanias, Madrid, Spain
| | - María Ángeles Mori
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | | | | | - Pilar Barrúz
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | | | | | | | - Jair Antonio Tenorio
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Enrique Galán
- Hospital Materno-Infantil Infanta Cristina, Badajoz, Spain
| | | | | | - César Saleme
- Maternity Nuestra Señora de la Merced, Tucumán, Argentina
| | - Silvia Castillo
- Sección Genética, Hospital Clínico Universidad de Chile, Santiago, Chile
- Clínica Alemana, Santiago, Chile
| | | | - Luis Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- Servicio de Genética, Instituto de Investigaciones Médicas Hospital del Mar (IMIM)/Universitat Pompeu Fabra, Barcelona, Spain
| | - Ana Barcia
- Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - Maria Soledad Martín
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Elena Mansilla
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Isabel Vallcorba
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | | | | | | | - Raquel Blanco-Lago
- Servicio de Neuropediatría, Hospital Universitario Central de Asturias, Oviedo (Asturias), Spain
| | - Mercedes Serrano
- Unidad de Neuropediatría, Hospital San Joan de Deu, Barcelona, Spain
| | | | | | | | - Pilar Tirado
- Servicio de Neuropediatría, Hospital Universitario La Paz, Madrid, Spain
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| |
Collapse
|
198
|
Lu S, Hernan R, Marcogliese PC, Huang Y, Gertler TS, Akcaboy M, Liu S, Chung HL, Pan X, Sun X, Oguz MM, Oztoprak U, de Baaij JH, Ivanisevic J, McGinnis E, Guillen Sacoto MJ, Chung WK, Bellen HJ. Loss-of-function variants in TIAM1 are associated with developmental delay, intellectual disability, and seizures. Am J Hum Genet 2022; 109:571-586. [PMID: 35240055 DOI: 10.1016/j.ajhg.2022.01.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
TIAM Rac1-associated GEF 1 (TIAM1) regulates RAC1 signaling pathways that affect the control of neuronal morphogenesis and neurite outgrowth by modulating the actin cytoskeletal network. To date, TIAM1 has not been associated with a Mendelian disorder. Here, we describe five individuals with bi-allelic TIAM1 missense variants who have developmental delay, intellectual disability, speech delay, and seizures. Bioinformatic analyses demonstrate that these variants are rare and likely pathogenic. We found that the Drosophila ortholog of TIAM1, still life (sif), is expressed in larval and adult central nervous system (CNS) and is mainly expressed in a subset of neurons, but not in glia. Loss of sif reduces the survival rate, and the surviving adults exhibit climbing defects, are prone to severe seizures, and have a short lifespan. The TIAM1 reference (Ref) cDNA partially rescues the sif loss-of-function (LoF) phenotypes. We also assessed the function associated with three TIAM1 variants carried by two of the probands and compared them to the TIAM1 Ref cDNA function in vivo. TIAM1 p.Arg23Cys has reduced rescue ability when compared to TIAM1 Ref, suggesting that it is a partial LoF variant. In ectopic expression studies, both wild-type sif and TIAM1 Ref are toxic, whereas the three variants (p.Leu862Phe, p.Arg23Cys, and p.Gly328Val) show reduced toxicity, suggesting that they are partial LoF variants. In summary, we provide evidence that sif is important for appropriate neural function and that TIAM1 variants observed in the probands are disruptive, thus implicating loss of TIAM1 in neurological phenotypes in humans.
Collapse
|
199
|
Guo W, Feng X, Hu M, Shangguan Y, Xia J, Hu W, Li X, Zhang Z, Shi Y, Xu K. The Application of Whole-Exome Sequencing in Patients With FUO. Front Cell Infect Microbiol 2022; 11:783568. [PMID: 35096640 PMCID: PMC8790153 DOI: 10.3389/fcimb.2021.783568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/17/2021] [Indexed: 12/02/2022] Open
Abstract
Background Fever of unknown origin (FUO) is still a challenge for clinicians. Next-generation sequencing technologies, such as whole exome sequencing (WES), can be used to identify genetic defects in patients and assist in diagnosis. In this study, we investigated the application of WES in individuals with FUO. Methods We performed whole-exome sequencing on 15 FUO patients. Clinical information was extracted from the hospital information system. Results In 7/15 samples, we found positive results, including potentially causative mutations across eight different genes: CFTR, CD209, IRF2BP2, ADGRV 1, TYK2, MEFV, THBD and GATA2. Conclusions Our results show that whole-exome sequencing can promote the genetic diagnosis and treatment of patients with FUO.
Collapse
Affiliation(s)
- Wanru Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xuewen Feng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ming Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yanwan Shangguan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jiafeng Xia
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Wenjuan Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaomeng Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zunjing Zhang
- Department of Respiratory Medicine, Lishui Hospital of Traditional Chinese Medicine (TCM), Lishui, China
| | - Yunzhen Shi
- Department of Infectious Diseases,Dongyang People's Hospital, Dongyang, China
| | - Kaijin Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
200
|
Yépez VA, Gusic M, Kopajtich R, Mertes C, Smith NH, Alston CL, Ban R, Beblo S, Berutti R, Blessing H, Ciara E, Distelmaier F, Freisinger P, Häberle J, Hayflick SJ, Hempel M, Itkis YS, Kishita Y, Klopstock T, Krylova TD, Lamperti C, Lenz D, Makowski C, Mosegaard S, Müller MF, Muñoz-Pujol G, Nadel A, Ohtake A, Okazaki Y, Procopio E, Schwarzmayr T, Smet J, Staufner C, Stenton SL, Strom TM, Terrile C, Tort F, Van Coster R, Vanlander A, Wagner M, Xu M, Fang F, Ghezzi D, Mayr JA, Piekutowska-Abramczuk D, Ribes A, Rötig A, Taylor RW, Wortmann SB, Murayama K, Meitinger T, Gagneur J, Prokisch H. Clinical implementation of RNA sequencing for Mendelian disease diagnostics. Genome Med 2022; 14:38. [PMID: 35379322 PMCID: PMC8981716 DOI: 10.1186/s13073-022-01019-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Lack of functional evidence hampers variant interpretation, leaving a large proportion of individuals with a suspected Mendelian disorder without genetic diagnosis after whole genome or whole exome sequencing (WES). Research studies advocate to further sequence transcriptomes to directly and systematically probe gene expression defects. However, collection of additional biopsies and establishment of lab workflows, analytical pipelines, and defined concepts in clinical interpretation of aberrant gene expression are still needed for adopting RNA sequencing (RNA-seq) in routine diagnostics. METHODS We implemented an automated RNA-seq protocol and a computational workflow with which we analyzed skin fibroblasts of 303 individuals with a suspected mitochondrial disease that previously underwent WES. We also assessed through simulations how aberrant expression and mono-allelic expression tests depend on RNA-seq coverage. RESULTS We detected on average 12,500 genes per sample including around 60% of all disease genes-a coverage substantially higher than with whole blood, supporting the use of skin biopsies. We prioritized genes demonstrating aberrant expression, aberrant splicing, or mono-allelic expression. The pipeline required less than 1 week from sample preparation to result reporting and provided a median of eight disease-associated genes per patient for inspection. A genetic diagnosis was established for 16% of the 205 WES-inconclusive cases. Detection of aberrant expression was a major contributor to diagnosis including instances of 50% reduction, which, together with mono-allelic expression, allowed for the diagnosis of dominant disorders caused by haploinsufficiency. Moreover, calling aberrant splicing and variants from RNA-seq data enabled detecting and validating splice-disrupting variants, of which the majority fell outside WES-covered regions. CONCLUSION Together, these results show that streamlined experimental and computational processes can accelerate the implementation of RNA-seq in routine diagnostics.
Collapse
Affiliation(s)
- Vicente A. Yépez
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
- Quantitative Biosciences Munich, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mirjana Gusic
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Robert Kopajtich
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christian Mertes
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Nicholas H. Smith
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP UK
| | - Rui Ban
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Skadi Beblo
- Department of Women and Child Health, Hospital for Children and Adolescents, Center for Pediatric Research Leipzig (CPL), Center for Rare Diseases, University Hospitals, University of Leipzig, Leipzig, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Blessing
- Department for Inborn Metabolic Diseases, Children’s and Adolescents’ Hospital, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Elżbieta Ciara
- Department of Medical Genetics, Children’s Memorial Health Institute, Warsaw, Poland
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Peter Freisinger
- Department of Pediatrics, Klinikum Reutlingen, Reutlingen, Germany
| | - Johannes Häberle
- University Children’s Hospital Zurich and Children’s Research Centre, Zürich, Switzerland
| | - Susan J. Hayflick
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, USA
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, Japan
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Neurologico Carlo Besta, Milan, Italy
| | - Dominic Lenz
- Division of Neuropediatrics and Pediatric Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Christine Makowski
- Department of Pediatrics, Technical University of Munich, Munich, Germany
| | - Signe Mosegaard
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michaela F. Müller
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Gerard Muñoz-Pujol
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Agnieszka Nadel
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Saitama, Japan
- Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Elena Procopio
- Inborn Metabolic and Muscular Disorders Unit, Anna Meyer Children Hospital, Florence, Italy
| | - Thomas Schwarzmayr
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Joél Smet
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Christian Staufner
- Division of Neuropediatrics and Pediatric Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Sarah L. Stenton
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tim M. Strom
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Caterina Terrile
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Frederic Tort
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Rudy Van Coster
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Arnaud Vanlander
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Manting Xu
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Fang Fang
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Neurologico Carlo Besta, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Johannes A. Mayr
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
| | | | - Antonia Ribes
- Section of Inborn Errors of Metabolism-IBC, Department of Biochemistry and Molecular Genetics, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Agnès Rötig
- Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
- NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP UK
| | - Saskia B. Wortmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
- Amalia Children’s Hospital, Radboudumc Nijmegen, Nijmegen, The Netherlands
| | - Kei Murayama
- Department of Metabolism, Chiba Children’s Hospital, Chiba, Japan
| | - Thomas Meitinger
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julien Gagneur
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatric Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| |
Collapse
|