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Kim HH, Kim DW, Woo J, Lee K. Explicable prioritization of genetic variants by integration of rule-based and machine learning algorithms for diagnosis of rare Mendelian disorders. Hum Genomics 2024; 18:28. [PMID: 38509596 PMCID: PMC10956189 DOI: 10.1186/s40246-024-00595-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 03/03/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND In the process of finding the causative variant of rare diseases, accurate assessment and prioritization of genetic variants is essential. Previous variant prioritization tools mainly depend on the in-silico prediction of the pathogenicity of variants, which results in low sensitivity and difficulty in interpreting the prioritization result. In this study, we propose an explainable algorithm for variant prioritization, named 3ASC, with higher sensitivity and ability to annotate evidence used for prioritization. 3ASC annotates each variant with the 28 criteria defined by the ACMG/AMP genome interpretation guidelines and features related to the clinical interpretation of the variants. The system can explain the result based on annotated evidence and feature contributions. RESULTS We trained various machine learning algorithms using in-house patient data. The performance of variant ranking was assessed using the recall rate of identifying causative variants in the top-ranked variants. The best practice model was a random forest classifier that showed top 1 recall of 85.6% and top 3 recall of 94.4%. The 3ASC annotates the ACMG/AMP criteria for each genetic variant of a patient so that clinical geneticists can interpret the result as in the CAGI6 SickKids challenge. In the challenge, 3ASC identified causal genes for 10 out of 14 patient cases, with evidence of decreased gene expression for 6 cases. Among them, two genes (HDAC8 and CASK) had decreased gene expression profiles confirmed by transcriptome data. CONCLUSIONS 3ASC can prioritize genetic variants with higher sensitivity compared to previous methods by integrating various features related to clinical interpretation, including features related to false positive risk such as quality control and disease inheritance pattern. The system allows interpretation of each variant based on the ACMG/AMP criteria and feature contribution assessed using explainable AI techniques.
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Affiliation(s)
- Ho Heon Kim
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea
| | - Dong-Wook Kim
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea
| | - Junwoo Woo
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea
| | - Kyoungyeul Lee
- Research and Development Center, 3billion, 14th floor, 416 Teheran-ro, Gangnam-gu, Seoul, 06193, Republic of Korea.
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2
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Sadrolashrafi K, Mobini N. Zosteriform eruption in an adult male. JAAD Case Rep 2024; 45:79-81. [PMID: 38406622 PMCID: PMC10884772 DOI: 10.1016/j.jdcr.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Affiliation(s)
- Kaviyon Sadrolashrafi
- Department of Internal Medicine, Kirk Kerkorian School of Medicine at the University of Nevada, Las Vegas, Nevada
| | - Narciss Mobini
- Department of Internal Medicine, Kirk Kerkorian School of Medicine at the University of Nevada, Las Vegas, Nevada
- Section of Dermatopathology, Associated Pathologists Chartered and Quest Diagnostics, Las Vegas, Nevada
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3
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Rahit KMTH, Avramovic V, Chong JX, Tarailo-Graovac M. GPAD: a natural language processing-based application to extract the gene-disease association discovery information from OMIM. BMC Bioinformatics 2024; 25:84. [PMID: 38413851 PMCID: PMC10898068 DOI: 10.1186/s12859-024-05693-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Thousands of genes have been associated with different Mendelian conditions. One of the valuable sources to track these gene-disease associations (GDAs) is the Online Mendelian Inheritance in Man (OMIM) database. However, most of the information in OMIM is textual, and heterogeneous (e.g. summarized by different experts), which complicates automated reading and understanding of the data. Here, we used Natural Language Processing (NLP) to make a tool (Gene-Phenotype Association Discovery (GPAD)) that could syntactically process OMIM text and extract the data of interest. RESULTS GPAD applies a series of language-based techniques to the text obtained from OMIM API to extract GDA discovery-related information. GPAD can inform when a particular gene was associated with a specific phenotype, as well as the type of validation-whether through model organisms or cohort-based patient-matching approaches-for such an association. GPAD extracted data was validated with published reports and was compared with large language model. Utilizing GPAD's extracted data, we analysed trends in GDA discoveries, noting a significant increase in their rate after the introduction of exome sequencing, rising from an average of about 150-250 discoveries each year. Contrary to hopes of resolving most GDAs for Mendelian disorders by now, our data indicate a substantial decline in discovery rates over the past five years (2017-2022). This decline appears to be linked to the increasing necessity for larger cohorts to substantiate GDAs. The rising use of zebrafish and Drosophila as model organisms in providing evidential support for GDAs is also observed. CONCLUSIONS GPAD's real-time analyzing capacity offers an up-to-date view of GDA discovery and could help in planning and managing the research strategies. In future, this solution can be extended or modified to capture other information in OMIM and scientific literature.
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Affiliation(s)
- K M Tahsin Hassan Rahit
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Vladimir Avramovic
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Jessica X Chong
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
- Brotman-Baty Institute, Seattle, WA, 98195, USA
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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Chong JX, Childers MC, Marvin CT, Marcello AJ, Gonorazky H, Hazrati LN, Dowling JJ, Al Amrani F, Alanay Y, Nieto Y, Gabriel MÁM, Aylsworth AS, Buckingham KJ, Shively KM, Sommers O, Anderson K, Regnier M, Bamshad MJ. Variants in ACTC1 underlie distal arthrogryposis accompanied by congenital heart defects. HGG Adv 2023; 4:100213. [PMID: 37457373 PMCID: PMC10345160 DOI: 10.1016/j.xhgg.2023.100213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Contraction of the human sarcomere is the result of interactions between myosin cross-bridges and actin filaments. Pathogenic variants in genes such as MYH7, TPM1, and TNNI3 that encode parts of the cardiac sarcomere cause muscle diseases that affect the heart, such as dilated cardiomyopathy and hypertrophic cardiomyopathy. In contrast, pathogenic variants in homologous genes such as MYH2, TPM2, and TNNI2 that encode parts of the skeletal muscle sarcomere cause muscle diseases affecting skeletal muscle, such as distal arthrogryposis (DA) syndromes and skeletal myopathies. To date, there have been few reports of genes (e.g., MYH7) encoding sarcomeric proteins in which the same pathogenic variant affects skeletal and cardiac muscle. Moreover, none of the known genes underlying DA have been found to contain pathogenic variants that also cause cardiac abnormalities. We report five families with DA because of heterozygous missense variants in the gene actin, alpha, cardiac muscle 1 (ACTC1). ACTC1 encodes a highly conserved actin that binds to myosin in cardiac and skeletal muscle. Pathogenic variants in ACTC1 have been found previously to underlie atrial septal defect, dilated cardiomyopathy, hypertrophic cardiomyopathy, and left ventricular noncompaction. Our discovery delineates a new DA condition because of variants in ACTC1 and suggests that some functions of ACTC1 are shared in cardiac and skeletal muscle.
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Affiliation(s)
- Jessica X. Chong
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute, Seattle, WA 98195, USA
| | - Matthew Carter Childers
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- University of Washington Center for Translational Muscle Research, Seattle, WA 98195, USA
| | - Colby T. Marvin
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Anthony J. Marcello
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Hernan Gonorazky
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Lili-Naz Hazrati
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - James J. Dowling
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Departments of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Fatema Al Amrani
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Division of Neurology, Department of Pediatrics, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Yasemin Alanay
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Turkey
| | - Yolanda Nieto
- Department of Basic Bio-Medical Sciences, European University of Madrid, Madrid, Spain
| | - Miguel Á Marín Gabriel
- Department of Pediatrics, Puerta de Hierro-Majadahonda University Hospital, 28221 Madrid, Spain
| | - Arthur S. Aylsworth
- Departments of Pediatrics and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kati J. Buckingham
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Kathryn M. Shively
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Olivia Sommers
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Kailyn Anderson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - University of Washington Center for Mendelian Genomics
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- University of Washington Center for Translational Muscle Research, Seattle, WA 98195, USA
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Departments of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
- Division of Neurology, Department of Pediatrics, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Sultanate of Oman
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Turkey
- Department of Basic Bio-Medical Sciences, European University of Madrid, Madrid, Spain
- Department of Pediatrics, Puerta de Hierro-Majadahonda University Hospital, 28221 Madrid, Spain
- Departments of Pediatrics and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - University of Washington Center for Rare Disease Research
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- University of Washington Center for Translational Muscle Research, Seattle, WA 98195, USA
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Departments of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
- Division of Neurology, Department of Pediatrics, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Sultanate of Oman
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Turkey
- Department of Basic Bio-Medical Sciences, European University of Madrid, Madrid, Spain
- Department of Pediatrics, Puerta de Hierro-Majadahonda University Hospital, 28221 Madrid, Spain
- Departments of Pediatrics and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- University of Washington Center for Translational Muscle Research, Seattle, WA 98195, USA
| | - Michael J. Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute, Seattle, WA 98195, USA
- University of Washington Center for Translational Muscle Research, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
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Frost FG, Morimoto M, Sharma P, Ruaud L, Belnap N, Calame DG, Uchiyama Y, Matsumoto N, Oud MM, Ferreira EA, Narayanan V, Rangasamy S, Huentelman M, Emrick LT, Sato-Shirai I, Kumada S, Wolf NI, Steinbach PJ, Huang Y, Pusey BN, Passemard S, Levy J, Drunat S, Vincent M, Guet A, Agolini E, Novelli A, Digilio MC, Rosenfeld JA, Murphy JL, Lupski JR, Vezina G, Macnamara EF, Adams DR, Acosta MT, Tifft CJ, Gahl WA, Malicdan MCV. Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis. Am J Hum Genet 2023; 110:663-680. [PMID: 36965478 PMCID: PMC10119142 DOI: 10.1016/j.ajhg.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/28/2023] [Indexed: 03/27/2023] Open
Abstract
The vast majority of human genes encode multiple isoforms through alternative splicing, and the temporal and spatial regulation of those isoforms is critical for organismal development and function. The spliceosome, which regulates and executes splicing reactions, is primarily composed of small nuclear ribonucleoproteins (snRNPs) that consist of small nuclear RNAs (snRNAs) and protein subunits. snRNA gene transcription is initiated by the snRNA-activating protein complex (SNAPc). Here, we report ten individuals, from eight families, with bi-allelic, deleterious SNAPC4 variants. SNAPC4 encoded one of the five SNAPc subunits that is critical for DNA binding. Most affected individuals presented with delayed motor development and developmental regression after the first year of life, followed by progressive spasticity that led to gait alterations, paraparesis, and oromotor dysfunction. Most individuals had cerebral, cerebellar, or basal ganglia volume loss by brain MRI. In the available cells from affected individuals, SNAPC4 abundance was decreased compared to unaffected controls, suggesting that the bi-allelic variants affect SNAPC4 accumulation. The depletion of SNAPC4 levels in HeLa cell lines via genomic editing led to decreased snRNA expression and global dysregulation of alternative splicing. Analysis of available fibroblasts from affected individuals showed decreased snRNA expression and global dysregulation of alternative splicing compared to unaffected cells. Altogether, these data suggest that these bi-allelic SNAPC4 variants result in loss of function and underlie the neuroregression and progressive spasticity in these affected individuals.
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Affiliation(s)
- F Graeme Frost
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Marie Morimoto
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Prashant Sharma
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Lyse Ruaud
- APHP.Nord, Robert Debré University Hospital, Department of Genetics, Paris, France; Université Paris Cité, Inserm UMR 1141, NeuroDiderot, 75019 Paris, France
| | - Newell Belnap
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Yuri Uchiyama
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan; Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Machteld M Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elise A Ferreira
- Department of Pediatrics, Emma Children's Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, the Netherlands; United for Metabolic Diseases, Amsterdam, the Netherlands
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sampath Rangasamy
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Matt Huentelman
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Lisa T Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Ikuko Sato-Shirai
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan; Department of Pediatrics, Shimada Ryoiku Medical Center Hachioji for Challenged Children, Tokyo, Japan
| | - Satoko Kumada
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Nicole I Wolf
- Amsterdam Leukodystrophy Center, Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Vrije Universiteit, Amsterdam, the Netherlands
| | - Peter J Steinbach
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yan Huang
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Barbara N Pusey
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Sandrine Passemard
- Université Paris Cité, Inserm UMR 1141, NeuroDiderot, 75019 Paris, France; Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, Paris, France
| | - Jonathan Levy
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France; Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France
| | - Séverine Drunat
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France; Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France; INSERM UMR1141, Neurodiderot, University of Paris, Paris, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, Nantes, France; Inserm, CNRS, University Nantes, l'institut du thorax, Nantes, France
| | - Agnès Guet
- APHP.Nord, Louis Mourier Hospital, Pediatrics Department, Paris, France
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer L Murphy
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - James R Lupski
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Gilbert Vezina
- Department of Diagnostic Radiology and Imaging, Children's National Hospital, Washington, DC, USA
| | - Ellen F Macnamara
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - David R Adams
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria T Acosta
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - William A Gahl
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - May Christine V Malicdan
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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6
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Yang Z, Shikany A, Ni Y, Zhang G, Weaver KN, Chen J. Using deep learning and electronic health records to detect Noonan syndrome in pediatric patients. Genet Med 2022; 24:2329-2337. [PMID: 36098741 DOI: 10.1016/j.gim.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 11/27/2022] Open
Abstract
PURPOSE The variable expressivity and multisystem features of Noonan syndrome (NS) make it difficult for patients to obtain a timely diagnosis. Genetic testing can confirm a diagnosis, but underdiagnosis is prevalent owing to a lack of recognition and referral for testing. Our study investigated the utility of using electronic health records (EHRs) to identify patients at high risk of NS. METHODS Using diagnosis texts extracted from Cincinnati Children's Hospital's EHR database, we constructed deep learning models from 162 NS cases and 16,200 putative controls. Performance was evaluated on 2 independent test sets, one containing patients with NS who were previously diagnosed and the other containing patients with undiagnosed NS. RESULTS Our novel method performed significantly better than the previous method, with the convolutional neural network model achieving the highest area under the precision-recall curve in both test sets (diagnosed: 0.43, undiagnosed: 0.16). CONCLUSION The results suggested the validity of using text-based deep learning methods to analyze EHR and showed the value of this approach as a potential tool to identify patients with features of rare diseases. Given the paucity of medical geneticists, this has the potential to reduce disease underdiagnosis by prioritizing patients who will benefit most from a genetics referral.
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Affiliation(s)
- Zeyu Yang
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati Children's Research Foundation, Cincinnati, OH; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Amy Shikany
- Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Yizhao Ni
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati Children's Research Foundation, Cincinnati, OH; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Ge Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - K Nicole Weaver
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH; Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati Children's Research Foundation, Cincinnati, OH; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.
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7
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Similuk MN, Yan J, Ghosh R, Oler AJ, Franco LM, Setzer M, Kamen M, Jodarski C, DiMaggio T, Davis J, Gore R, Jamal L, Borges A, Gentile N, Niemela J, Lowe C, Jevtich K, Yu Y, Hullfish H, Hsu AP, Hong C, Littel P, Seifert BA, Milner J, Johnston JJ, Cheng X, Li Z, Veltri D, Huang K, Kaladi K, Barnett J, Zhang L, Vlasenko N, Fan Y, Karlins E, Ganakammal SR, Gilmore R, Tran E, Yun A, Mackey J, Yazhuk S, Lack J, Kuram V, Cao W, Huse S, Frank K, Fahle G, Rosenzweig S, Su Y, Hwang S, Bi W, Bennett J, Myles IA, De Ravin SS, Fussm I, Strober W, Bielekova B, Almeida de Jesus A, Goldbach-Mansky R, Williamson P, Kumar K, Dempsy C, Frischmeyer-Guerrerio P, Eisch R, Bolan H, Metcalfe DD, Komarow H, Carter M, Druey KM, Sereti I, Dropulic L, Klion AD, Khoury P, O' Connell EM, Holland-Thomas NC, Brown T, McDermott DH, Murphy PM, Bundy V, Keller MD, Peng C, Kim H, Norman S, Delmonte OM, Kang E, Su HC, Malech H, Freeman A, Zerbe C, Uzel G, Bergerson JRE, Rao VK, Olivier KN, Lyons JJ, Lisco A, Cohen JI, Lionakis MS, Biesecker LG, Xirasagar S, Notarangelo L, Holland SM, Walkiewicz MA. Clinical Exome Sequencing of 1000 Families with Complex Immune Phenotypes: Towards comprehensive genomic evaluations. J Allergy Clin Immunol 2022; 150:947-954. [PMID: 35753512 PMCID: PMC9547837 DOI: 10.1016/j.jaci.2022.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/07/2022] [Accepted: 06/02/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Prospective genetic evaluation of patients at our referral research hospital presents clinical research challenges. OBJECTIVE This study sought not only a single-gene explanation for participants' immune-related presentations, but viewed each participant holistically, with the potential to have multiple genetic contributions to their immune-phenotype and other heritable comorbidities relevant to their presentation and health. METHODS We developed a program integrating exome sequencing, chromosomal microarray, phenotyping, results return with genetic counseling, and reanalysis in 1505 individuals from 1000 families with suspected or known inborn errors of immunity. RESULTS Probands were 50.8% female, 71.5% >18 years, and had diverse immune presentations. Overall, 327/1000 probands (32.7%) received 361 molecular diagnoses. These included 17 probands with diagnostic copy number variants, 32 probands with secondary findings, and 31 probands with multiple molecular diagnoses. Reanalysis added 22 molecular diagnoses, predominantly due to new disease-gene associations (9/22, 40.9%). One-quarter of the molecular diagnoses (92/361) did not involve immune-associated genes. Molecular diagnosis was correlated with younger age, male sex, and a higher number of organ systems involved. This program also facilitated the discovery of new gene-disease associations such as SASH3-related immunodeficiency. A review of treatment options and ClinGen actionability curations suggest that at least 251/361 (69.5%) of these molecular diagnoses could translate into >1 management option. CONCLUSION This program contributes to our understanding of the diagnostic and clinical utility whole exome analysis on a large scale. CLINICAL Implication: Comprehensive analysis of exome data has diagnostic and clinical utility for patients with suspected inborn errors of immunity.
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Affiliation(s)
| | - Jia Yan
- Centralized Sequencing Program
- DIR
- NIAID
| | | | - Andrew J Oler
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Luis M Franco
- Functional Immunogenomics Unit
- Systemic Autoimmunity Branch
- National Institute of Arthritis and Musculoskeletal and Skin Diseases
| | | | | | | | - Thomas DiMaggio
- Fungal Pathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
| | - Joie Davis
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Leila Jamal
- Johns Hopkins/NIH Genetic Counseling Training Program; Genetics Branch, Center for Cancer Research, National Cancer Institute; NIH Clinical Center Department of Bioethics
| | | | | | | | - Chenery Lowe
- Health, Behavior, and Society
- Johns Hopkins Bloomberg School of Public Health
| | - Kathleen Jevtich
- School of Medicine
- Uniformed Services University of Health Sciences
| | | | | | - Amy P Hsu
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Patricia Littel
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | | | | | | | - Xi Cheng
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Zhiwen Li
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Daniel Veltri
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Ke Huang
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Krishnaveni Kaladi
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Jason Barnett
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Lingwen Zhang
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Nikita Vlasenko
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Yongjie Fan
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Eric Karlins
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | | | - Robert Gilmore
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Emily Tran
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Alvin Yun
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Joseph Mackey
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Svetlana Yazhuk
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Vasu Kuram
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Wen Cao
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Susan Huse
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | | | | | | | - Yan Su
- Immunology Service
- Laboratory Medicine
- NIH
| | - SuJin Hwang
- Tumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration
| | - Weimin Bi
- Department of Molecular and Human Genetics
- Baylor Genetics
| | - John Bennett
- Clinical Mycology
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Ian A Myles
- Epithelial Therapeutics Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Suk See De Ravin
- Laboratory of Host Defenses
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Ivan Fussm
- Mucosal Immunity Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Warren Strober
- Mucosal Immunity Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Bibiana Bielekova
- Neuroimmunological Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Adriana Almeida de Jesus
- Translational Autoinflammatory Disease Studies Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Disease Studies Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Peter Williamson
- Translational Mycology Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Caeden Dempsy
- Food Allergy Research Unit
- Laboratory of Allergic Diseases
- NIAID
| | | | - Robin Eisch
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Hyejeong Bolan
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Dean D Metcalfe
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Hirsh Komarow
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Melody Carter
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Kirk M Druey
- Lung and Vascular Inflammation Section
- Laboratory of Allergic Diseases
- NIAID
| | - Irini Sereti
- HIV Pathogenesis Section
- Laboratory of Immunoregulation
- NIAID
| | - Lesia Dropulic
- Medical Virology Section
- Laboratory of Immunoregulation
- NIAID
| | - Amy D Klion
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | - Paneez Khoury
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | | | | | - Thomas Brown
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | | | - Philip M Murphy
- Molecular Signaling Section
- Laboratory of Molecular Immunology
- NIAID
| | - Vanessa Bundy
- Division of Allergy and Immunology
- Children's National Health System
| | - Michael D Keller
- Division of Allergy and Immunology
- Children's National Health System
| | - Christine Peng
- Division of Allergy and Immunology
- Children's National Health System
| | - Helen Kim
- Division of Allergy and Immunology
- Children's National Health System
| | - Stephanie Norman
- Division of Allergy and Immunology
- Children's National Health System
| | - Ottavia M Delmonte
- Immune Deficiency Genetics Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Elizabeth Kang
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | - Helen C Su
- Human Immunological Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Harry Malech
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | - Alexandra Freeman
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Christa Zerbe
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Gulbu Uzel
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Jenna R E Bergerson
- Primary Immune Deficiency Clinic
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - V Koneti Rao
- Primary Immune Deficiency Clinic
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Jonathan J Lyons
- Translational Allergic Immunopathology Unit
- Laboratory of Allergic Diseases
- NIAID
| | - Andrea Lisco
- HIV Pathogenesis Section
- Laboratory of Immunoregulation
- NIAID
| | - Jeffrey I Cohen
- Medical Virology Section
- Laboratory of Infectious Diseases
- NIAID
| | - Michail S Lionakis
- Fungal Pathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
| | | | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Luigi Notarangelo
- Immune Deficiency Genetics Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Steven M Holland
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
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8
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Kim YE, Ki CS, Jang MA. Challenges and Considerations in Sequence Variant Interpretation for Mendelian Disorders. Ann Lab Med 2019; 39:421-429. [PMID: 31037860 PMCID: PMC6502951 DOI: 10.3343/alm.2019.39.5.421] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/28/2018] [Accepted: 04/09/2019] [Indexed: 11/23/2022] Open
Abstract
In 2015, the American College of Medical Genetics and Genomics (ACMG), together with the Association for Molecular Pathology (AMP), published the latest guidelines for the interpretation of sequence variants, which have been widely adopted into clinical practice. Despite these standardized efforts, the degrees of subjectivity and uncertainty allowed by the guidelines can lead to inconsistent variant classification across clinical laboratories, making it difficult to assess the pathogenicity of identified variants. We describe the critical elements of variant interpretation processes and potential pitfalls through practical examples and provide updated information based on a review of recent literature. The variant classification we describe is meant to be applicable to sequence variants for Mendelian disorders, whether identified by single-gene tests, multi-gene panels, exome sequencing, or genome sequencing. Continuing efforts to improve the reproducibility and objectivity of sequence variant interpretation across individuals and laboratories are needed.
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Affiliation(s)
- Young Eun Kim
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, Korea
| | | | - Mi Ae Jang
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea.
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9
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Guo MH, Gregg AR. Estimating yields of prenatal carrier screening and implications for design of expanded carrier screening panels. Genet Med 2019; 21:1940-7. [PMID: 30846881 DOI: 10.1038/s41436-019-0472-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Prenatal genetic carrier screening can identify parents at risk of having a child affected by a recessive condition. However, the conditions/genes most appropriate for screening remain a matter of debate. Estimates of carrier rates across genes are needed to guide construction of carrier screening panels. METHOD We leveraged an exome sequencing database (n = 123,136) to estimate carrier rates across six major ancestries for 415 genes associated with severe recessive conditions. RESULTS We found that 32.6% (East Asian) to 62.9% (Ashkenazi Jewish) of individuals are variant carriers in at least one of the 415 genes. For couples, screening all 415 genes would identify 0.17-2.52% of couples as being at risk for having a child affected by one of these conditions. Screening just the 40 genes with carrier rate >1.0% would identify more than 76% of these at-risk couples. An ancestry-specific panel designed to capture genes with carrier rates >1.0% would include 5 to 28 genes, while a comparable panethnic panel would include 40 genes. CONCLUSION Our work guides the design of carrier screening panels and provides data to assist in counseling prospective parents. Our results highlight a high cumulative carrier rate across genes, underscoring the need for careful selection of genes for screening.
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10
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Chia PH, Zhong FL, Niwa S, Bonnard C, Utami KH, Zeng R, Lee H, Eskin A, Nelson SF, Xie WH, Al-Tawalbeh S, El-Khateeb M, Shboul M, Pouladi MA, Al-Raqad M, Reversade B. A homozygous loss-of-function CAMK2A mutation causes growth delay, frequent seizures and severe intellectual disability. eLife 2018; 7:e32451. [PMID: 29784083 PMCID: PMC5963920 DOI: 10.7554/elife.32451] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/30/2018] [Indexed: 12/02/2022] Open
Abstract
Calcium/calmodulin-dependent protein kinase II (CAMK2) plays fundamental roles in synaptic plasticity that underlies learning and memory. Here, we describe a new recessive neurodevelopmental syndrome with global developmental delay, seizures and intellectual disability. Using linkage analysis and exome sequencing, we found that this disease maps to chromosome 5q31.1-q34 and is caused by a biallelic germline mutation in CAMK2A. The missense mutation, p.His477Tyr is located in the CAMK2A association domain that is critical for its function and localization. Biochemically, the p.His477Tyr mutant is defective in self-oligomerization and unable to assemble into the multimeric holoenzyme.In vivo, CAMK2AH477Y failed to rescue neuronal defects in C. elegans lacking unc-43, the ortholog of human CAMK2A. In vitro, neurons derived from patient iPSCs displayed profound synaptic defects. Together, our data demonstrate that a recessive germline mutation in CAMK2A leads to neurodevelopmental defects in humans and suggest that dysfunctional CAMK2 paralogs may contribute to other neurological disorders.
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Affiliation(s)
| | - Franklin Lei Zhong
- Institute of Medical BiologyImmunosSingapore
- Institute of Molecular and Cell BiologyProteosSingapore
| | - Shinsuke Niwa
- Frontier Research Institute for Interdisciplinary SciencesTohoku UniversitySendaiJapan
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | | | - Kagistia Hana Utami
- Translational Laboratory in Genetic MedicineAgency for Science, Technology and ResearchSingaporeSingapore
| | - Ruizhu Zeng
- Translational Laboratory in Genetic MedicineAgency for Science, Technology and ResearchSingaporeSingapore
| | - Hane Lee
- Department of Pathology and Laboratory MedicineDavid Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
- Department of Human GeneticsDavid Geffen School of Medicine University of California, Los AngelesLos AngelesUnited States
| | - Ascia Eskin
- Department of Pathology and Laboratory MedicineDavid Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
- Department of Human GeneticsDavid Geffen School of Medicine University of California, Los AngelesLos AngelesUnited States
| | - Stanley F Nelson
- Department of Pathology and Laboratory MedicineDavid Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
- Department of Human GeneticsDavid Geffen School of Medicine University of California, Los AngelesLos AngelesUnited States
| | | | - Samah Al-Tawalbeh
- Queen Rania Paediatric HospitalKing Hussein Medical Centre, Royal Medical ServicesAmmanJordan
| | | | | | - Mahmoud A Pouladi
- Translational Laboratory in Genetic MedicineAgency for Science, Technology and ResearchSingaporeSingapore
- Department of Medicine, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Mohammed Al-Raqad
- Queen Rania Paediatric HospitalKing Hussein Medical Centre, Royal Medical ServicesAmmanJordan
| | - Bruno Reversade
- Institute of Medical BiologyImmunosSingapore
- Institute of Molecular and Cell BiologyProteosSingapore
- Department of PaediatricsNational University of SingaporeSingaporeSingapore
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
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11
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Maezawa Y, Kato H, Takemoto M, Watanabe A, Koshizaka M, Ishikawa T, Sargolzaeiaval F, Kuzuya M, Wakabayashi H, Kusaka T, Yokote K, Oshima J. Biallelic WRN Mutations in Newly Identified Japanese Werner Syndrome Patients. Mol Syndromol 2018; 9:214-218. [PMID: 30140198 DOI: 10.1159/000489055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2017] [Indexed: 12/26/2022] Open
Abstract
Werner syndrome (WS) is a rare autosomal recessive disorder characterized by systemic accelerated aging. It is caused by pathogenic variants of the WRN gene that encodes a nuclear helicase. In this report, we describe 4 newly identified WS cases among those referred to the Japanese Werner Consortium, Chiba University, Japan. All 4 cases were compound heterozygotes of the Japanese founder mutation, c.3139-1G>C, and a novel null pathogenic variant, c.1587G>A, c.2448+1G>A, or c.3233+1G>T, or an amino acid substitution variant, c.1720G>A, p.Gly574Arg. These 3 null pathogenic variants were not previously described. The p. Gly574Arg was previously reported in a European patient, and the identification of the second p. Gly574Arg case, with classical WS features, further confirmed the pathogenic nature of this variant. For the case with c.3233+1G>T, we determined the phase of 2 disease-causing mutations and demonstrated that they are on different chromosomes. This assay would be particularly important for those cases with ambiguous clinical diagnosis.
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Affiliation(s)
- Yoshiro Maezawa
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba
| | - Hisaya Kato
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba
| | - Minoru Takemoto
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba.,Department of Medicine, International University of Health and Welfare, Narita
| | - Aki Watanabe
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba
| | - Masaya Koshizaka
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba
| | - Takahiro Ishikawa
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba
| | | | - Masafumi Kuzuya
- Department of Community Healthcare and Geriatrics, Nagoya University Graduate School of Medicine, Nagoya
| | | | - Takashi Kusaka
- Department of Pediatrics, Kagawa University, Kagawa, Japan
| | - Koutaro Yokote
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba
| | - Junko Oshima
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba.,Department of Pathology, University of Washington, Seattle, WA, USA
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12
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Diaz-Horta O, Subasioglu-Uzak A, Grati M, DeSmidt A, Foster J 2nd, Cao L, Bademci G, Tokgoz-Yilmaz S, Duman D, Cengiz FB, Abad C, Mittal R, Blanton S, Liu XZ, Farooq A, Walz K, Lu Z, Tekin M. FAM65B is a membrane-associated protein of hair cell stereocilia required for hearing. Proc Natl Acad Sci U S A 2014; 111:9864-8. [PMID: 24958875 DOI: 10.1073/pnas.1401950111] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a large consanguineous Turkish kindred with recessive nonsyndromic, prelingual, profound hearing loss, we identified in the gene FAM65B (MIM611410) a splice site mutation (c.102-1G>A) that perfectly cosegregates with the phenotype in the family. The mutation leads to exon skipping and deletion of 52-amino acid residues of a PX membrane localization domain. FAM65B is known to be involved in myotube formation and in regulation of cell adhesion, polarization, and migration. We show that wild-type Fam65b is expressed during embryonic and postnatal development stages in murine cochlea, and that the protein localizes to the plasma membranes of the stereocilia of inner and outer hair cells of the inner ear. The wild-type protein targets the plasma membrane, whereas the mutant protein accumulates in cytoplasmic inclusion bodies and does not reach the membrane. In zebrafish, knockdown of fam65b leads to significant reduction of numbers of saccular hair cells and neuromasts and to hearing loss. We conclude that FAM65B is a plasma membrane-associated protein of hair cell stereocilia that is essential for hearing.
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