1
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Sullivan JA, Spillmann RC, Schoch K, Walley N, Alkelai A, Stong N, Shea PR, Petrovski S, Jobanputra V, McConkie-Rosell A, Shashi V. The best of both worlds: Blending cutting-edge research with clinical processes for a productive exome clinic. Clin Genet 2024; 105:62-71. [PMID: 37853563 DOI: 10.1111/cge.14437] [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: 08/11/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Genomic medicine has been transformed by next-generation sequencing (NGS), inclusive of exome sequencing (ES) and genome sequencing (GS). Currently, ES is offered widely in clinical settings, with a less prevalent alternative model consisting of hybrid programs that incorporate research ES along with clinical patient workflows. We were among the earliest to implement a hybrid ES clinic, have provided diagnoses to 45% of probands, and have identified several novel candidate genes. Our program is enabled by a cost-effective investment by the health system and is unique in encompassing all the processes that have been variably included in other hybrid/clinical programs. These include careful patient selection, utilization of a phenotype-agnostic bioinformatics pipeline followed by manual curation of variants and phenotype integration by clinicians, close collaborations between the clinicians and the bioinformatician, pursuit of interesting variants, communication of results to patients in categories that are predicated upon the certainty of a diagnosis, and tracking changes in results over time and the underlying mechanisms for such changes. Due to its effectiveness, scalability to GS and its resource efficiency, specific elements of our paradigm can be incorporated into existing clinical settings, or the entire hybrid model can be implemented within health systems that have genomic medicine programs, to provide NGS in a scientifically rigorous, yet pragmatic setting.
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Affiliation(s)
- Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Nicole Walley
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, USA
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Genomics and Bioinformatics Analysis Resource, Columbia University, New York, New York, USA
| | - Slavè Petrovski
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
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2
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Liu Z, Xin B, Smith IN, Sency V, Szekely J, Alkelai A, Shuldiner A, Efthymiou S, Rajabi F, Coury S, Brownstein CA, Rudnik-Schöneborn S, Bruel AL, Thevenon J, Zeidler S, Jayakar P, Schmidt A, Cremer K, Engels H, Peters SO, Zaki MS, Duan R, Zhu C, Xu Y, Gao C, Sepulveda-Morales T, Maroofian R, Alkhawaja IA, Khawaja M, Alhalasah H, Houlden H, Madden JA, Turchetti V, Marafi D, Agrawal PB, Schatz U, Rotenberg A, Rotenberg J, Mancini GMS, Bakhtiari S, Kruer M, Thiffault I, Hirsch S, Hempel M, Stühn LG, Haack TB, Posey JE, Lupski JR, Lee H, Sarn NB, Eng C, Gonzaga-Jauregui C, Zhang B, Wang H. Hemizygous variants in protein phosphatase 1 regulatory subunit 3F (PPP1R3F) are associated with a neurodevelopmental disorder characterized by developmental delay, intellectual disability and autistic features. Hum Mol Genet 2023; 32:2981-2995. [PMID: 37531237 PMCID: PMC10549786 DOI: 10.1093/hmg/ddad124] [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: 05/12/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023] Open
Abstract
Protein phosphatase 1 regulatory subunit 3F (PPP1R3F) is a member of the glycogen targeting subunits (GTSs), which belong to the large group of regulatory subunits of protein phosphatase 1 (PP1), a major eukaryotic serine/threonine protein phosphatase that regulates diverse cellular processes. Here, we describe the identification of hemizygous variants in PPP1R3F associated with a novel X-linked recessive neurodevelopmental disorder in 13 unrelated individuals. This disorder is characterized by developmental delay, mild intellectual disability, neurobehavioral issues such as autism spectrum disorder, seizures and other neurological findings including tone, gait and cerebellar abnormalities. PPP1R3F variants segregated with disease in affected hemizygous males that inherited the variants from their heterozygous carrier mothers. We show that PPP1R3F is predominantly expressed in brain astrocytes and localizes to the endoplasmic reticulum in cells. Glycogen content in PPP1R3F knockout astrocytoma cells appears to be more sensitive to fluxes in extracellular glucose levels than in wild-type cells, suggesting that PPP1R3F functions in maintaining steady brain glycogen levels under changing glucose conditions. We performed functional studies on nine of the identified variants and observed defects in PP1 binding, protein stability, subcellular localization and regulation of glycogen metabolism in most of them. Collectively, the genetic and molecular data indicate that deleterious variants in PPP1R3F are associated with a new X-linked disorder of glycogen metabolism, highlighting the critical role of GTSs in neurological development. This research expands our understanding of neurodevelopmental disorders and the role of PP1 in brain development and proper function.
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Affiliation(s)
- Zhigang Liu
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Baozhong Xin
- DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA
| | - Iris N Smith
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Valerie Sency
- DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA
| | - Julia Szekely
- DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA
| | - Anna Alkelai
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Alan Shuldiner
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, London WC1N 3BG, UK
| | - Farrah Rajabi
- Division of Genetics & Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Stephanie Coury
- Division of Genetics & Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Catherine A Brownstein
- Division of Genetics & Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Ange-Line Bruel
- Inserm UMR1231 GAD, Génétique des Anomalies du Développement, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne, Dijon 21000, France
- UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon 21000, France
| | - Julien Thevenon
- Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL 33155, USA
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53105 Bonn, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53105 Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53105 Bonn, Germany
| | - Sophia O Peters
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53105 Bonn, Germany
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute National Research Centre, Cairo 12622, Egypt
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Changlian Zhu
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Göteborg 417 56, Sweden
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Chao Gao
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450012, China
| | - Tania Sepulveda-Morales
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro 76226, México
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, London WC1N 3BG, UK
| | - Issam A Alkhawaja
- Al-Bashir Hospital, Pediatric Department, Pediatric Neurology Unit, Amman, Jordan
| | - Mariam Khawaja
- Prince Hamzah Hospital, Amman, Jordan
- Hospital Clínic and Fundació Hospital Sant Joan de Déu de Martorell/Barcelona, Barcelona, Spain
| | | | - Henry Houlden
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, London WC1N 3BG, UK
| | - Jill A Madden
- Division of Genetics & Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Valentina Turchetti
- Department of Neuromuscular Disorders, University College London (UCL) Institute of Neurology, London WC1N 3BG, UK
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City 13060, Kuwait
| | - Pankaj B Agrawal
- Division of Genetics & Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
- Division of Neonatology, Department of Pediatrics, University of Miami School of Medicine and Jackson Health System, Miami, FL 33136, USA
| | - Ulrich Schatz
- Institute for Human Genetics, Medical University Innsbruck, Innsbruck 6020, Austria
| | | | | | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine–Phoenix, Phoenix, AZ 85004, USA
| | - Michael Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine–Phoenix, Phoenix, AZ 85004, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children’s Mercy Kansas City, Children's Mercy Research Institute, Kansas City, MO 64108, USA
| | - Steffen Hirsch
- Institute if Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Maja Hempel
- Institute if Human Genetics, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hyunpil Lee
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Nicholas B Sarn
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro 76226, México
| | - Bin Zhang
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Heng Wang
- DDC Clinic for Special Needs Children, Middlefield, OH 44062, USA
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3
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Rogerson D, Alkelai A, Giordano J, Pantrangi M, Hsiao MC, Nhan-Chang CL, Motelow JE, Aggarwal V, Goldstein D, Wapner R, Shawber CJ. Investigation into the genetics of fetal congenital lymphatic anomalies. Prenat Diagn 2023; 43:703-716. [PMID: 36959127 PMCID: PMC10330091 DOI: 10.1002/pd.6345] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/10/2023] [Accepted: 03/12/2023] [Indexed: 03/25/2023]
Abstract
OBJECTIVE Congenital lymphatic anomalies (LAs) arise due to defects in lymphatic development and often present in utero as pleural effusion, chylothorax, nuchal and soft tissue edema, ascites, or hydrops. Many LAs are caused by single nucleotide variants, which are not detected on routine prenatal testing. METHODS Demographic data were compared between two subcohorts, those with clinically significant fetal edema (CSFE) and isolated fetal edema. A targeted variant analysis of LA genes was performed using American College of Medical Genetics criteria on whole exome sequencing (WES) data generated for 71 fetal edema cases who remained undiagnosed after standard workup. RESULTS CSFE cases had poor outcomes, including preterm delivery, demise, and maternal preeclampsia. Pathogenic and likely pathogenic variants were identified in 7% (5/71) of cases, including variants in RASopathy genes, RASA1, SOS1, PTPN11, and a novel PIEZO1 variant. Variants of uncertain significance (VOUS) were identified in 45% (32/71) of cases. In CSFEs, VOUS were found in CELSR1, EPHB4, TIE1, PIEZO1, ITGA9, RASopathy genes, SOS1, SOS2, and RAF1. CONCLUSIONS WES identified pathogenic and likely pathogenic variants and VOUS in LA genes in 51% of fetal edema cases, supporting WES and expanded hydrops panels in cases of idiopathic fetal hydrops and fluid collections.
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Affiliation(s)
- Daniella Rogerson
- Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Jessica Giordano
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Madhulatha Pantrangi
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Meng-Chang Hsiao
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Chia-Ling Nhan-Chang
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Joshua E. Motelow
- Department of Pediatrics, Columbia University Vagelos College of Physicians andSurgeons, New York, New York, USA
| | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - David Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Ron Wapner
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Carrie J. Shawber
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
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4
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Avnat E, Shapira G, Shoval S, Israel-Elgali I, Alkelai A, Shuldiner AR, Gonzaga-Jauregui C, Zidan J, Maray T, Shomron N, Friedman E. Comprehensive Genetic Analysis of Druze Provides Insights into Carrier Screening. Genes (Basel) 2023; 14:genes14040937. [PMID: 37107695 PMCID: PMC10137689 DOI: 10.3390/genes14040937] [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: 02/18/2023] [Revised: 03/24/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND Druze individuals, like many genetically homogeneous and isolated populations, harbor recurring pathogenic variants (PV) in autosomal recessive (AR) disorders. METHODS Variant calling of whole-genome sequencing (WGS) of 40 Druze from the Human Genome Diversity Project (HGDP) was performed (HGDP-cohort). Additionally, we performed whole exome sequencing (WES) of 118 Druze individuals: 38 trios and 2 couples, representing geographically distinct clans (WES-cohort). Rates of validated PV were compared with rates in worldwide and Middle Eastern populations, from the gnomAD and dbSNP datasets. RESULTS Overall, 34 PVs were identified: 30 PVs in genes underlying AR disorders, 3 additional PVs were associated with autosomal dominant (AD) disorders, and 1 PV with X-linked-dominant inherited disorder in the WES cohort. CONCLUSIONS The newly identified PVs associated with AR conditions should be considered for incorporation into prenatal-screening options offered to Druze individuals after an extension and validation of the results in a larger study.
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Affiliation(s)
- Eden Avnat
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shelly Shoval
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Ifat Israel-Elgali
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Anna Alkelai
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | | | - Claudia Gonzaga-Jauregui
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla 04510, Querétaro, Mexico
| | - Jamal Zidan
- The Oncology Department, Ziv Medical Center, and the Azrieli Faculty of Medicine, Bar-Ilan University, Zefat 13206, Israel
| | - Taiseer Maray
- Golan for Development, Majdal Shams 1243800, Golan Heights
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Eitan Friedman
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- The Meirav High Risk Clinic, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan 52621, Israel
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5
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Spillmann RC, Tan QKG, Reuter C, Schoch K, Kohler J, Bonner D, Zastrow D, Alkelai A, Baugh E, Cope H, Marwaha S, Wheeler MT, Bernstein JA, Shashi V. A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network. Genet Med 2023; 25:100353. [PMID: 36481303 PMCID: PMC10506157 DOI: 10.1016/j.gim.2022.12.001] [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: 08/02/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Next-generation sequencing (NGS) has revolutionized the diagnostic process for rare/ultrarare conditions. However, diagnosis rates differ between analytical pipelines. In the National Institutes of Health-Undiagnosed Diseases Network (UDN) study, each individual's NGS data are concurrently analyzed by the UDN sequencing core laboratory and the clinical sites. We examined the outcomes of this practice. METHODS A retrospective review was performed at 2 UDN clinical sites to compare the variants and diagnoses/candidate genes identified with the dual analyses of the NGS data. RESULTS In total, 95 individuals had 100 diagnoses/candidate genes. There was 59% concordance between the UDN sequencing core laboratories and the clinical sites in identifying diagnoses/candidate genes. The core laboratory provided more diagnoses, whereas the clinical sites prioritized more research variants/candidate genes (P < .001). The clinical sites solely identified 15% of the diagnoses/candidate genes. The differences between the 2 pipelines were more often because of variant prioritization disparities than variant detection. CONCLUSION The unique dual analysis of NGS data in the UDN synergistically enhances outcomes. The core laboratory provided a clinical analysis with more diagnoses and the clinical sites prioritized more research variants/candidate genes. Implementing such concurrent dual analyses in other genomic research studies and clinical settings can improve both variant detection and prioritization.
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Affiliation(s)
- Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Queenie K-G Tan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Chloe Reuter
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Jennefer Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Diane Zastrow
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Anna Alkelai
- Institute for Genome Medicine, Columbia University Medical Center, New York, NY
| | - Evan Baugh
- Institute for Genome Medicine, Columbia University Medical Center, New York, NY
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Shruti Marwaha
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Matthew T Wheeler
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC.
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6
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Alkelai A, Greenbaum L, Shohat S, Povysil G, Malakar A, Ren Z, Motelow JE, Schechter T, Draiman B, Chitrit-Raveh E, Hughes D, Jobanputra V, Shifman S, Goldstein DB, Kohn Y. Genetic insights into childhood-onset schizophrenia: The yield of clinical exome sequencing. Schizophr Res 2023; 252:138-145. [PMID: 36645932 DOI: 10.1016/j.schres.2022.12.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 01/15/2023]
Abstract
Childhood-onset schizophrenia (COS) is a rare form of schizophrenia with an onset prior to 13 years of age. Although genetic factors play a role in COS etiology, only a few causal variants have been reported to date. This study presents a diagnostic exome sequencing (ES) in 37 Israeli Jewish families with a proband diagnosed with COS. By implementing a trio/duo ES approach and applying a well-established diagnostic pipeline, we detected clinically significant variants in 7 probands (19 %). These single nucleotide variants and indels were mostly inherited. The implicated genes were ANKRD11, GRIA2, CHD2, CLCN3, CLTC, IGF1R and MICU1. In a secondary analysis that compared COS patients to 4721 healthy controls, we observed that patients had a significant enrichment of rare loss of function (LoF) variants in LoF intolerant genes associated with developmental diseases. Taken together, ES could be considered as a valuable tool in the genetic workup for COS patients.
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Affiliation(s)
- Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA; Regeneron Genetics Center, Tarrytown, NY, USA.
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tal Aviv University, Tel Aviv, Israel
| | - Shahar Shohat
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Ayan Malakar
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Joshua E Motelow
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA; Department of Pediatrics, Division of Critical Care and Hospital Medicine, Columbia University Irving Medical Center, New York-Presbyterian Morgan Stanley Children's Hospital of New York, New York, NY, USA
| | - Tanya Schechter
- Department of Child and Adolescent Psychiatry, Jerusalem Mental Health Center, Eitanim Psychiatric Hospital, Israel
| | - Benjamin Draiman
- Department of Child and Adolescent Psychiatry, Jerusalem Mental Health Center, Eitanim Psychiatric Hospital, Israel
| | - Eti Chitrit-Raveh
- Department of Child and Adolescent Psychiatry, Jerusalem Mental Health Center, Eitanim Psychiatric Hospital, Israel
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA; New York Genome Center, New York, NY, USA
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Yoav Kohn
- Department of Child and Adolescent Psychiatry, Jerusalem Mental Health Center, Eitanim Psychiatric Hospital, Israel; Hadassah-Hebrew University School of Medicine, Jerusalem, Israel
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7
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Motelow JE, Lippa NC, Hostyk J, Feldman E, Nelligan M, Ren Z, Alkelai A, Milner JD, Gharavi AG, Tang Y, Goldstein DB, Kernie SG. Risk Variants in the Exomes of Children With Critical Illness. JAMA Netw Open 2022; 5:e2239122. [PMID: 36306130 PMCID: PMC9617179 DOI: 10.1001/jamanetworkopen.2022.39122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Diagnostic genetic testing can lead to changes in management in the pediatric intensive care unit. Genetic risk in children with critical illness but nondiagnostic exome sequencing (ES) has not been explored. OBJECTIVE To assess the association between loss-of-function (LOF) variants and pediatric critical illness. DESIGN, SETTING, AND PARTICIPANTS This genetic association study examined ES first screened for causative variants among 267 children at the Morgan Stanley Children's Hospital of NewYork-Presbyterian, of whom 22 were otherwise healthy with viral respiratory failure; 18 deceased children with bronchiolitis from the Office of the Chief Medical Examiner of New York City, of whom 14 were previously healthy; and 9990 controls from the Institute for Genomic Medicine at Columbia University Irving Medical Center. The ES data were generated between January 1, 2015, and December 31, 2020, and analyzed between January 1, 2017, and September 2, 2022. EXPOSURE Critical illness. MAIN OUTCOMES AND MEASURES Odds ratios and P values for genes and gene-sets enriched for rare LOF variants and the loss-of-function observed/expected upper bound fraction (LOEUF) score at which cases have a significant enrichment. RESULTS This study included 285 children with critical illness (median [range] age, 4.1 [0-18.9] years; 148 [52%] male) and 9990 controls. A total of 228 children (80%) did not receive a genetic diagnosis. After quality control (QC), 231 children harbored excess rare LOF variants in genes with a LOEUF score of 0.680 or less (intolerant genes) (P = 1.0 × 10-5). After QC, 176 children without a diagnosis harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 1.8; 95% CI, 1.3-2.5). After QC, 25 children with viral respiratory failure harbored excess ultrarare LOF variants in intolerant genes but only in those without a known disease association (odds ratio, 2.8; 95% CI, 1.1-6.6). A total of 114 undiagnosed children were enriched for de novo LOF variants in genes without a known disease association (observed, 14; expected, 6.8; enrichment, 2.05). CONCLUSIONS AND RELEVANCE In this genetic association study, excess LOF variants were observed among critically ill children despite nondiagnostic ES. Variants lay in genes without a known disease association, suggesting future investigation may connect phenotypes to causative genes.
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Affiliation(s)
- Joshua E. Motelow
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Natalie C. Lippa
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Evin Feldman
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Matthew Nelligan
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York
| | | | - Ali G. Gharavi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, NewYork-Presbyterian, New York, New York
| | - Yingying Tang
- Molecular Genetics Laboratory, New York City Office of Chief Medical Examiner, New York, New York
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Steven G. Kernie
- Division of Critical Care and Hospital Medicine, Department of Pediatrics, Columbia University Irving Medical Center, NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York
- NewYork-Presbyterian Hospital, New York, New York
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8
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Manzali SB, Yu E, Ravona-Springer R, Livny A, Golan S, Ouyang Y, Lesman-Segev O, Liu L, Ganmore I, Alkelai A, Gan-Or Z, Lin HM, Heymann A, Schnaider Beeri M, Greenbaum L. Alzheimer’s Disease Polygenic Risk Score Is Not Associated With Cognitive Decline Among Older Adults With Type 2 Diabetes. Front Aging Neurosci 2022; 14:853695. [PMID: 36110429 PMCID: PMC9468264 DOI: 10.3389/fnagi.2022.853695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivesMultiple risk loci for late-onset Alzheimer’s disease (LOAD) have been identified. Type 2 diabetes (T2D) is a risk factor for cognitive decline, dementia and Alzheimer’s disease (AD). We investigated the association of polygenic risk score (PRS) for LOAD with overall cognitive functioning and longitudinal decline, among older adults with T2D.MethodsThe study included 1046 Jewish participants from the Israel Diabetes and Cognitive Decline (IDCD) study, aged ≥ 65 years, diagnosed with T2D, and cognitively normal at baseline. The PRS included variants from 26 LOAD associated loci (at genome-wide significance level), and was calculated with and without APOE. Outcome measures, assessed in 18 months intervals, were global cognition and the specific domains of episodic memory, attention/working memory, executive functions, and language/semantic categorization. Random coefficient models were used for analysis, adjusting for demographic variables, T2D-related characteristics, and cardiovascular factors. Additionally, in a subsample of 202 individuals, we analyzed the association of PRS with the volumes of total gray matter, frontal lobe, hippocampus, amygdala, and white matter hyperintensities. Last, the association of PRS with amyloid beta (Aβ) burden was examined in 44 participants who underwent an 18F-flutemetamol PET scan.ResultsThe PRS was not significantly associated with overall functioning or decline in global cognition or any of the specific cognitive domains. Similarly, following correction for multiple testing, there was no association with Aβ burden and other brain imaging phenotypes.ConclusionOur results suggest that the cumulative effect of LOAD susceptibility loci is not associated with a greater rate of cognitive decline in older adults with T2D, and other pathways may underlie this link.
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Affiliation(s)
- Sigalit B. Manzali
- Department of Pathology, Sheba Medical Center, Tel Hashomer, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Eric Yu
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Ramit Ravona-Springer
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abigail Livny
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Israel
| | - Sapir Golan
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yuxia Ouyang
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Orit Lesman-Segev
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Israel
| | - Lang Liu
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Ithamar Ganmore
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Hung-Mo Lin
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Anthony Heymann
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Maccabi Healthcare Services, Tel Aviv, Israel
| | - Michal Schnaider Beeri
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Lior Greenbaum
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
- *Correspondence: Lior Greenbaum,
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9
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Alkelai A, Greenbaum L, Docherty AR, Shabalin AA, Povysil G, Malakar A, Hughes D, Delaney SL, Peabody EP, McNamara J, Gelfman S, Baugh EH, Zoghbi AW, Harms MB, Hwang HS, Grossman-Jonish A, Aggarwal V, Heinzen EL, Jobanputra V, Pulver AE, Lerer B, Goldstein DB. The benefit of diagnostic whole genome sequencing in schizophrenia and other psychotic disorders. Mol Psychiatry 2022; 27:1435-1447. [PMID: 34799694 DOI: 10.1038/s41380-021-01383-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 01/04/2023]
Abstract
Schizophrenia has a multifactorial etiology, involving a polygenic architecture. The potential benefit of whole genome sequencing (WGS) in schizophrenia and other psychotic disorders is not well studied. We investigated the yield of clinical WGS analysis in 251 families with a proband diagnosed with schizophrenia (N = 190), schizoaffective disorder (N = 49), or other conditions involving psychosis (N = 48). Participants were recruited in Israel and USA, mainly of Jewish, Arab, and other European ancestries. Trio (parents and proband) WGS was performed for 228 families (90.8%); in the other families, WGS included parents and at least two affected siblings. In the secondary analyses, we evaluated the contribution of rare variant enrichment in particular gene sets, and calculated polygenic risk score (PRS) for schizophrenia. For the primary outcome, diagnostic rate was 6.4%; we found clinically significant, single nucleotide variants (SNVs) or small insertions or deletions (indels) in 14 probands (5.6%), and copy number variants (CNVs) in 2 (0.8%). Significant enrichment of rare loss-of-function variants was observed in a gene set of top schizophrenia candidate genes in affected individuals, compared with population controls (N = 6,840). The PRS for schizophrenia was significantly increased in the affected individuals group, compared to their unaffected relatives. Last, we were also able to provide pharmacogenomics information based on CYP2D6 genotype data for most participants, and determine their antipsychotic metabolizer status. In conclusion, our findings suggest that WGS may have a role in the setting of both research and genetic counseling for individuals with schizophrenia and other psychotic disorders and their families.
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Affiliation(s)
- Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA.
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anna R Docherty
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrey A Shabalin
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Ayan Malakar
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Shannon L Delaney
- New York State Psychiatric Institute, Columbia University, New York City, NY, USA
| | - Emma P Peabody
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - James McNamara
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Sahar Gelfman
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Anthony W Zoghbi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- New York State Psychiatric Institute, Columbia University, New York City, NY, USA
- New York State Psychiatric Institute, Office of Mental Health, New York, NY, USA
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Harms
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
| | - Hann-Shyan Hwang
- Department of Medicine, National Taiwan University School of Medicine, Taipei, Taiwan
| | - Anat Grossman-Jonish
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Erin L Heinzen
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vaidehi Jobanputra
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Ann E Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bernard Lerer
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
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10
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Revah-Politi A, Kushary S(T, Vena N, May H, Lippa N, Bier L, Goldman J, Alkelai A, Baugh E, Zoghbi A, Kayser R, Goldstein D, Simpson HB. eP435: Issues in interpreting results in research genomic testing for common disorders: an example within an OCD cohort. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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11
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Zoghbi AW, Dhindsa RS, Goldberg TE, Mehralizade A, Motelow JE, Wang X, Alkelai A, Harms MB, Lieberman JA, Markx S, Goldstein DB. High-impact rare genetic variants in severe schizophrenia. Proc Natl Acad Sci U S A 2021; 118:e2112560118. [PMID: 34903660 PMCID: PMC8713775 DOI: 10.1073/pnas.2112560118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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] [Accepted: 11/04/2021] [Indexed: 02/04/2023] Open
Abstract
Extreme phenotype sequencing has led to the identification of high-impact rare genetic variants for many complex disorders but has not been applied to studies of severe schizophrenia. We sequenced 112 individuals with severe, extremely treatment-resistant schizophrenia, 218 individuals with typical schizophrenia, and 4,929 controls. We compared the burden of rare, damaging missense and loss-of-function variants between severe, extremely treatment-resistant schizophrenia, typical schizophrenia, and controls across mutation intolerant genes. Individuals with severe, extremely treatment-resistant schizophrenia had a high burden of rare loss-of-function (odds ratio, 1.91; 95% CI, 1.39 to 2.63; P = 7.8 × 10-5) and damaging missense variants in intolerant genes (odds ratio, 2.90; 95% CI, 2.02 to 4.15; P = 3.2 × 10-9). A total of 48.2% of individuals with severe, extremely treatment-resistant schizophrenia carried at least one rare, damaging missense or loss-of-function variant in intolerant genes compared to 29.8% of typical schizophrenia individuals (odds ratio, 2.18; 95% CI, 1.33 to 3.60; P = 1.6 × 10-3) and 25.4% of controls (odds ratio, 2.74; 95% CI, 1.85 to 4.06; P = 2.9 × 10-7). Restricting to genes previously associated with schizophrenia risk strengthened the enrichment with 8.9% of individuals with severe, extremely treatment-resistant schizophrenia carrying a damaging missense or loss-of-function variant compared to 2.3% of typical schizophrenia (odds ratio, 5.48; 95% CI, 1.52 to 19.74; P = 0.02) and 1.6% of controls (odds ratio, 5.82; 95% CI, 3.00 to 11.28; P = 2.6 × 10-8). These results demonstrate the power of extreme phenotype case selection in psychiatric genetics and an approach to augment schizophrenia gene discovery efforts.
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Affiliation(s)
- Anthony W Zoghbi
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX 77030;
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY 10032
- Institute of Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032
- Office of Mental Health, New York State Psychiatric Institute, New York, NY 10032
| | - Ryan S Dhindsa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
- Institute of Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Terry E Goldberg
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY 10032
- Office of Mental Health, New York State Psychiatric Institute, New York, NY 10032
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY 10032
| | - Aydan Mehralizade
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY 10032
- Office of Mental Health, New York State Psychiatric Institute, New York, NY 10032
| | - Joshua E Motelow
- Institute of Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
- Department of Pediatrics, Division of Critical Care and Hospital Medicine, Columbia University Irving Medical Center, New York-Presbyterian Morgan Stanley Children's Hospital of New York, New York, NY 10032
| | - Xinchen Wang
- Institute of Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
- Waypoint Bio, New York, NY 10014
| | - Anna Alkelai
- Institute of Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Matthew B Harms
- Institute of Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY 10032
| | - Jeffrey A Lieberman
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY 10032
- Office of Mental Health, New York State Psychiatric Institute, New York, NY 10032
| | - Sander Markx
- Department of Psychiatry, Columbia University Irving Medical Center, New York State Psychiatric Institute, New York, NY 10032;
- Office of Mental Health, New York State Psychiatric Institute, New York, NY 10032
| | - David B Goldstein
- Institute of Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032;
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
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12
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Rodan LH, Spillmann RC, Kurata HT, Lamothe SM, Maghera J, Jamra RA, Alkelai A, Antonarakis SE, Atallah I, Bar-Yosef O, Bilan F, Bjorgo K, Blanc X, Van Bogaert P, Bolkier Y, Burrage LC, Christ BU, Granadillo JL, Dickson P, Donald KA, Dubourg C, Eliyahu A, Emrick L, Engleman K, Gonfiantini MV, Good JM, Kalser J, Kloeckner C, Lachmeijer G, Macchiaiolo M, Nicita F, Odent S, O'Heir E, Ortiz-Gonzalez X, Pacio-Miguez M, Palomares-Bralo M, Pena L, Platzer K, Quinodoz M, Ranza E, Rosenfeld JA, Roulet-Perez E, Santani A, Santos-Simarro F, Pode-Shakked B, Skraban C, Slaugh R, Superti-Furga A, Thiffault I, van Jaabrsveld RH, Vincent M, Wang HG, Zacher P, Rush E, Pitt GS, Au PYB, Shashi V. Correction: Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations. Genet Med 2021; 23:2016. [PMID: 34522029 DOI: 10.1038/s41436-021-01306-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Lance H Rodan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Harley T Kurata
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Shawn M Lamothe
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Jasmine Maghera
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Omer Bar-Yosef
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Frédéric Bilan
- CHU de Poitiers, Service de Génétique, EA3808 NEUVACOD, Poitiers, France
| | - Kathrine Bjorgo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | | | - Yoav Bolkier
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Pediatric Cardiology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lindsay C Burrage
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Björn U Christ
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Patricia Dickson
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
- University of Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- The Danek Gertner Insitute of Human Genetics, Sheba Medical Center, Tel-Hahsomer, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lisa Emrick
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kendra Engleman
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Jean-Marc Good
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Judith Kalser
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Chiara Kloeckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Guus Lachmeijer
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marina Macchiaiolo
- Rare Diseases and Medical Genetic Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neurosciences and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de référence "Maladies Rares" Anomalies du développement CLAD-Ouest, Hôpital SUD, Échirolles, France
| | - Emily O'Heir
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xilma Ortiz-Gonzalez
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marta Pacio-Miguez
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - María Palomares-Bralo
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Loren Pena
- Cincinnati Children's Hospital and Medical Center Cincinnati, Cincinnati, OH, USA
- University of Cincinnati College of Medicine Cincinnati, Cincinnati, OH, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Avni Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Cara Skraban
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, Nantes, France
| | - Hong-Gang Wang
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Eric Rush
- The Children's Mercy Hospital, Kansas City, MO, USA
- Department of Pediatrics University of Missouri-Kansas City, Kansas City, MO, USA
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Geoffrey S Pitt
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ping Yee Billie Au
- Alberta Children's Hospital Research Institute, Department of Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA.
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13
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Rodan LH, Spillmann RC, Kurata HT, Lamothe SM, Maghera J, Jamra RA, Alkelai A, Antonarakis SE, Atallah I, Bar-Yosef O, Bilan F, Bjorgo K, Blanc X, Van Bogaert P, Bolkier Y, Burrage LC, Christ BU, Granadillo JL, Dickson P, Donald KA, Dubourg C, Eliyahu A, Emrick L, Engleman K, Gonfiantini MV, Good JM, Kalser J, Kloeckner C, Lachmeijer G, Macchiaiolo M, Nicita F, Odent S, O'Heir E, Ortiz-Gonzalez X, Pacio-Miguez M, Palomares-Bralo M, Pena L, Platzer K, Quinodoz M, Ranza E, Rosenfeld JA, Roulet-Perez E, Santani A, Santos-Simarro F, Pode-Shakked B, Skraban C, Slaugh R, Superti-Furga A, Thiffault I, van Jaabrsveld RH, Vincent M, Wang HG, Zacher P, Rush E, Pitt GS, Au PYB, Shashi V. Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations. Genet Med 2021; 23:1922-1932. [PMID: 34163037 PMCID: PMC8488020 DOI: 10.1038/s41436-021-01232-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/14/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE CACNA1C encodes the alpha-1-subunit of a voltage-dependent L-type calcium channel expressed in human heart and brain. Heterozygous variants in CACNA1C have previously been reported in association with Timothy syndrome and long QT syndrome. Several case reports have suggested that CACNA1C variation may also be associated with a primarily neurological phenotype. METHODS We describe 25 individuals from 22 families with heterozygous variants in CACNA1C, who present with predominantly neurological manifestations. RESULTS Fourteen individuals have de novo, nontruncating variants and present variably with developmental delays, intellectual disability, autism, hypotonia, ataxia, and epilepsy. Functional studies of a subgroup of missense variants via patch clamp experiments demonstrated differential effects on channel function in vitro, including loss of function (p.Leu1408Val), neutral effect (p.Leu614Arg), and gain of function (p.Leu657Phe, p.Leu614Pro). The remaining 11 individuals from eight families have truncating variants in CACNA1C. The majority of these individuals have expressive language deficits, and half have autism. CONCLUSION We expand the phenotype associated with CACNA1C variants to include neurodevelopmental abnormalities and epilepsy, in the absence of classic features of Timothy syndrome or long QT syndrome.
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Affiliation(s)
- Lance H Rodan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Harley T Kurata
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Shawn M Lamothe
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Jasmine Maghera
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Omer Bar-Yosef
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Frédéric Bilan
- CHU de Poitiers, Service de Génétique, EA3808 NEUVACOD, Poitiers, France
| | - Kathrine Bjorgo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | | | - Yoav Bolkier
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Pediatric Cardiology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lindsay C Burrage
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Björn U Christ
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Patricia Dickson
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
- University of Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- The Danek Gertner Insitute of Human Genetics, Sheba Medical Center, Tel-Hahsomer, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lisa Emrick
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kendra Engleman
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Jean-Marc Good
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Judith Kalser
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Chiara Kloeckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Guus Lachmeijer
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marina Macchiaiolo
- Rare Diseases and Medical Genetic Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neurosciences and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de référence "Maladies Rares" Anomalies du développement CLAD-Ouest, Hôpital SUD, Échirolles, France
| | - Emily O'Heir
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xilma Ortiz-Gonzalez
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marta Pacio-Miguez
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - María Palomares-Bralo
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Loren Pena
- Cincinnati Children's Hospital and Medical Center Cincinnati, Cincinnati, OH, USA
- University of Cincinnati College of Medicine Cincinnati, Cincinnati, OH, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Avni Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Cara Skraban
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, Nantes, France
| | - Hong-Gang Wang
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Eric Rush
- The Children's Mercy Hospital, Kansas City, MO, USA
- Department of Pediatrics University of Missouri-Kansas City, Kansas City, MO, USA
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Geoffrey S Pitt
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ping Yee Billie Au
- Alberta Children's Hospital Research Institute, Department of Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA.
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14
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Cope H, Barseghyan H, Bhattacharya S, Fu Y, Hoppman N, Marcou C, Walley N, Rehder C, Deak K, Alkelai A, Vilain E, Shashi V. Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey. Mol Genet Genomic Med 2021; 9:e1665. [PMID: 33955715 PMCID: PMC8372083 DOI: 10.1002/mgg3.1665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/26/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Currently available structural variant (SV) detection methods do not span the complete spectrum of disease-causing SVs. Optical genome mapping (OGM), an emerging technology with the potential to resolve diagnostic dilemmas, was performed to investigate clinically-relevant SVs in a 4-year-old male with an epileptic encephalopathy of undiagnosed molecular origin. METHODS OGM was utilized to image long, megabase-size DNA molecules, fluorescently labeled at specific sequence motifs throughout the genome with high sensitivity for detection of SVs greater than 500 bp in size. OGM results were confirmed in a CLIA-certified laboratory via mate-pair sequencing. RESULTS OGM identified a mosaic, de novo 90 kb deletion and inversion on the X chromosome disrupting the CDKL5 gene. Detection of the mosaic deletion, which had been previously undetected by chromosomal microarray, an infantile epilepsy panel including exon-level microarray for CDKL5, exome sequencing as well as genome sequencing, resulted in a diagnosis of X-linked dominant early infantile epileptic encephalopathy-2. CONCLUSION OGM affords an effective technology for the detection of SVs, especially those that are mosaic, since these remain difficult to detect with current NGS technologies and with conventional chromosomal microarrays. Further research in undiagnosed populations with OGM is warranted.
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Affiliation(s)
- Heidi Cope
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Hayk Barseghyan
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
- Bionano Genomics IncSan DiegoCAUSA
| | | | - Yulong Fu
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
| | - Nicole Hoppman
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Cherisse Marcou
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Nicole Walley
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Catherine Rehder
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Kristen Deak
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Anna Alkelai
- Institute for Genomic MedicineColumbia University Medical CenterNew YorkNYUSA
| | - Eric Vilain
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
| | - Vandana Shashi
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
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15
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Kobren SN, Baldridge D, Velinder M, Krier JB, LeBlanc K, Esteves C, Pusey BN, Züchner S, Blue E, Lee H, Huang A, Bastarache L, Bican A, Cogan J, Marwaha S, Alkelai A, Murdock DR, Liu P, Wegner DJ, Paul AJ, Sunyaev SR, Kohane IS. Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases. Genet Med 2021; 23:1075-1085. [PMID: 33580225 PMCID: PMC8187147 DOI: 10.1038/s41436-020-01084-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Genomic sequencing has become an increasingly powerful and relevant tool to be leveraged for the discovery of genetic aberrations underlying rare, Mendelian conditions. Although the computational tools incorporated into diagnostic workflows for this task are continually evolving and improving, we nevertheless sought to investigate commonalities across sequencing processing workflows to reveal consensus and standard practice tools and highlight exploratory analyses where technical and theoretical method improvements would be most impactful. METHODS We collected details regarding the computational approaches used by a genetic testing laboratory and 11 clinical research sites in the United States participating in the Undiagnosed Diseases Network via meetings with bioinformaticians, online survey forms, and analyses of internal protocols. RESULTS We found that tools for processing genomic sequencing data can be grouped into four distinct categories. Whereas well-established practices exist for initial variant calling and quality control steps, there is substantial divergence across sites in later stages for variant prioritization and multimodal data integration, demonstrating a diversity of approaches for solving the most mysterious undiagnosed cases. CONCLUSION The largest differences across diagnostic workflows suggest that advances in structural variant detection, noncoding variant interpretation, and integration of additional biomedical data may be especially promising for solving chronically undiagnosed cases.
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Affiliation(s)
| | - Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Matt Velinder
- Center for Genomic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Joel B Krier
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Cecilia Esteves
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Barbara N Pusey
- National Human Genome Research Institute (NHGRI) at the National Institutes of Health (NIH), Bethesda, MD, USA
| | - Stephan Züchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Health System, Miami, FL, USA
| | - Elizabeth Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hane Lee
- Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
| | - Alden Huang
- Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna Bican
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joy Cogan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shruti Marwaha
- Stanford Center for Undiagnosed Diseases, Stanford, CA, USA
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York City, NY, USA
| | - David R Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Daniel J Wegner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexander J Paul
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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16
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Manzali SB, Ravona-Springer R, Alkelai A, Yu E, Gan-Or Z, Ganmore I, Heymann A, Beeri MS, Greenbaum L. Association of the CD2AP locus with cognitive functioning among middle-aged individuals with a family history of Alzheimer's disease. Neurobiol Aging 2020; 101:50-56. [PMID: 33578194 DOI: 10.1016/j.neurobiolaging.2020.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 11/19/2022]
Abstract
First-degree family history is an established risk factor for Alzheimer's disease (AD). We investigated the association of late-onset AD risk loci with cognitive functioning among 315 offspring of AD patients. Participants were cognitively normal Jewish individuals, aged 40-65 years, from the Israel Registry for Alzheimer's Prevention (IRAP) study. Twenty-two single-nucleotide polymorphisms (SNPs) within these loci and the APOE E4 allele were included in the final analyses, and a polygenic risk score was also calculated. Using linear regression (assuming an additive genetic model), we found a significant association only for SNP rs9473117, located near the CD2-associated protein (CD2AP) gene, with global cognition. Controlling for demographic variables (age, sex, years of education, and ancestry), the late-onset AD risk allele C was associated with lower global cognitive functioning (p = 0.0005), and withstood correction for multiple testing. After adjusting for additional characteristics (APOE E4 status and then also for cardiovascular factors), the results remained essentially unchanged (p = 0.0003 and p = 0.0005, respectively). In secondary analyses examining specific cognitive domains, rs9473117 was similarly associated with episodic memory (p = 0.005), language (p = 0.009), and working memory/attention (p = 0.018) but not with executive functions (p = 0.27). Again, the results were similar after adjusting for APOE E4 status and cardiovascular factors. The polygenic risk score was not associated with global cognitive functioning or with any of the 4 domains. In conclusion, our findings suggest a contribution of the CD2AP locus to cognitive functioning in middle-aged individuals with a parental history of AD. Further validations, including in longitudinal studies, are required.
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Affiliation(s)
- Sigalit Batia Manzali
- Department of Pathology, Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Ramit Ravona-Springer
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Eric Yu
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Ithamar Ganmore
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anthony Heymann
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Maccabi Healthcare Services, Tel Aviv, Israel
| | - Michal Schnaider Beeri
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lior Greenbaum
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.
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17
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Fliedner A, Kirchner P, Wiesener A, van de Beek I, Waisfisz Q, van Haelst M, Scott DA, Lalani SR, Rosenfeld JA, Azamian MS, Xia F, Dutra-Clarke M, Martinez-Agosto JA, Lee H, Noh GJ, Lippa N, Alkelai A, Aggarwal V, Agre KE, Gavrilova R, Mirzaa GM, Straussberg R, Cohen R, Horist B, Krishnamurthy V, McWalter K, Juusola J, Davis-Keppen L, Ohden L, van Slegtenhorst M, de Man SA, Ekici AB, Gregor A, van de Laar I, Zweier C, Nelson SF, Grody WW, Lee H, Deignan JL, Kang SH, Arboleda VA, Senaratne TN, Dorrani N, Dutra-Clarke MS, Kianmahd J, Hinkamp FL, Neustadt AM, Martinez-Agosto JA, Fogel BL, Quintero-Rivera F. Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing. Am J Hum Genet 2020; 107:544-554. [PMID: 32730804 DOI: 10.1016/j.ajhg.2020.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/25/2020] [Indexed: 01/14/2023] Open
Abstract
RNA polymerase II interacts with various other complexes and factors to ensure correct initiation, elongation, and termination of mRNA transcription. One of these proteins is SR-related CTD-associated factor 4 (SCAF4), which is important for correct usage of polyA sites for mRNA termination. Using exome sequencing and international matchmaking, we identified nine likely pathogenic germline variants in SCAF4 including two splice-site and seven truncating variants, all residing in the N-terminal two thirds of the protein. Eight of these variants occurred de novo, and one was inherited. Affected individuals demonstrated a variable neurodevelopmental disorder characterized by mild intellectual disability, seizures, behavioral abnormalities, and various skeletal and structural anomalies. Paired-end RNA sequencing on blood lymphocytes of SCAF4-deficient individuals revealed a broad deregulation of more than 9,000 genes and significant differential splicing of more than 2,900 genes, indicating an important role of SCAF4 in mRNA processing. Knockdown of the SCAF4 ortholog CG4266 in the model organism Drosophila melanogaster resulted in impaired locomotor function, learning, and short-term memory. Furthermore, we observed an increased number of active zones in larval neuromuscular junctions, representing large glutamatergic synapses. These observations indicate a role of CG4266 in nervous system development and function and support the implication of SCAF4 in neurodevelopmental phenotypes. In summary, our data show that heterozygous, likely gene-disrupting variants in SCAF4 are causative for a variable neurodevelopmental disorder associated with impaired mRNA processing.
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18
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Ganmore I, Livny A, Ravona-Springer R, Cooper I, Alkelai A, Shelly S, Tsarfaty G, Heymann A, Schnaider Beeri M, Greenbaum L. TCF7L2 polymorphisms are associated with amygdalar volume in elderly individuals with Type 2 Diabetes. Sci Rep 2019; 9:15818. [PMID: 31676834 PMCID: PMC6825182 DOI: 10.1038/s41598-019-48899-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 08/08/2019] [Indexed: 02/06/2023] Open
Abstract
The association between several Single Nucleotide Polymorphisms (SNPs) within the transcription factor 7-like 2 (TCF7L2) gene and Type 2 Diabetes (T2D) as well as additional T2D-related traits is well established. Since alteration in total and regional brain volumes are consistent findings among T2D individuals, we studied the association of four T2D susceptibility SNPS within TCF7L2 (rs7901695, rs7903146, rs11196205, and rs12255372) with volumes of white matter hyperintensities (WMH), gray matter, and regional volumes of amygdala and hippocampus obtained from structural MRI among 191 T2D elderly Jewish individuals. Under recessive genetic model (controlling for age, sex and intracranial volume), we found that for all four SNPs, carriers of two copies of the T2D risk allele (homozygous genotype) had significantly smaller amygdalar volume: rs7901695- CC genotype vs. CT + TT genotypes, p = 0.002; rs7903146-TT vs. TC + CC, p = 0.003; rs11196205- CC vs. CG + GG, p = 0.0003; and rs12255372- TT vs. TG + GG, p = 0.003. Adjusting also for T2D-related covariates, body mass index (BMI), and ancestry did not change the results substantively (rs7901695, p = 0.003; rs7903146, p = 0.005; rs11196205, p = 0.001; and rs12255372, p = 0.005). Conditional analysis demonstrated that only rs11196205 was independently associated with amygdalar volume at a significant level. Separate analysis of left and right amygdala revealed stronger results for left amygdalar volume. Taken together, we report association of TCF7L2 SNPs with amygdalar volume among T2D elderly Jewish patients. Further studies in other populations are required to support these findings and reach more definitive conclusions.
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Affiliation(s)
- Ithamar Ganmore
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. .,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. .,Memory clinic, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Abigail Livny
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ramit Ravona-Springer
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Memory clinic, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Itzik Cooper
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Shahar Shelly
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Galia Tsarfaty
- Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anthony Heymann
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Maccabi Healthcare Services, Tel Aviv, Israel
| | - Michal Schnaider Beeri
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lior Greenbaum
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
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19
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Greenbaum L, Ravona-Springer R, Livny A, Shelly S, Sharvit-Ginon I, Ganmore I, Alkelai A, Heymann A, Schnaider Beeri M. The CADM2 gene is associated with processing speed performance - evidence among elderly with type 2 diabetes. World J Biol Psychiatry 2019; 20:577-583. [PMID: 28797215 DOI: 10.1080/15622975.2017.1366055] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Objectives: Recent large-scale meta-analysis of genome-wide association studies (GWAS) from multiple cohorts, demonstrated the association of the single nucleotide polymorphism (SNP) rs17518584, with processing speed (measured by the Digit Symbol Substitution Test (DSST) or the Letter Digit Substitution Test (LDST)), at GWAS significance level. This SNP is located within the cell adhesion molecule 2 (CADM2) gene. We aimed to validate this finding in our sample of 944 cognitively normal Jewish elderly individuals with type 2 diabetes (T2D), a population which is at risk for cognitive decline and dementia.Methods: Using linear regression, we studied the association of rs17518584 with DSST performance, adjusting for demographic, T2D-related characteristics and cardiovascular factors. In secondary analyses, associations with performance in four cognitive domains (episodic memory, language/semantic categorisation, attention/working memory and executive function) and overall cognition were examined.Results: Controlling for sex, age at cognitive assessment, years of education and ancestry, we found a significant association of rs17518584 with DSST performance (P = 0.013), consistent with the originally reported effect direction. Results remained significant even when the additional covariates (T2D-related and cardiovascular factors) were included in the analysis (P = 0.034). Moreover, this SNP was significantly associated with performance in the cognitive domains of language/semantic categorisation and executive function, as well as overall cognition.Conclusions: Taken together, irrespective of T2D-related characteristics and cardiovascular factors, our findings provide independent support for the association of CADM2 SNP rs17518584 with processing speed (and demonstrate association with additional cognitive phenotypes), among cognitively normal elderly individuals with T2D.
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Affiliation(s)
- Lior Greenbaum
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
| | - Ramit Ravona-Springer
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abigail Livny
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,Department of Diagnostic Imaging, Sheba Medical Center, Tel Hashomer, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Shelly
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
| | - Inbal Sharvit-Ginon
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,Department of Psychology, Bar-Ilan University, Ramat Gan, Israel
| | - Ithamar Ganmore
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Anthony Heymann
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Maccabi Healthcare Services, Tel Aviv, Israel
| | - Michal Schnaider Beeri
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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20
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Alkelai A, Greenbaum L, Heinzen EL, Baugh EH, Teitelbaum A, Zhu X, Strous RD, Tatarskyy P, Zai CC, Tiwari AK, Tampakeras M, Freeman N, Müller DJ, Voineskos AN, Lieberman JA, Delaney SL, Meltzer HY, Remington G, Kennedy JL, Pulver AE, Peabody EP, Levy DL, Lerer B. New insights into tardive dyskinesia genetics: Implementation of whole-exome sequencing approach. Prog Neuropsychopharmacol Biol Psychiatry 2019; 94:109659. [PMID: 31153890 DOI: 10.1016/j.pnpbp.2019.109659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023]
Abstract
Tardive dyskinesia (TD) is an adverse movement disorder induced by chronic treatment with antipsychotics drugs. The contribution of common genetic variants to TD susceptibility has been investigated in recent years, but with limited success. The aim of the current study was to investigate the potential contribution of rare variants to TD vulnerability. In order to identify TD risk genes, we performed whole-exome sequencing (WES) and gene-based collapsing analysis focusing on rare (allele frequency < 1%) and putatively deleterious variants (qualifying variants). 82 Jewish schizophrenia patients chronically treated with antipsychotics were included and classified as having severe TD or lack of any abnormal movements based on a rigorous definition of the TD phenotype. First, we performed a case-control, exome-wide collapsing analysis comparing 39 schizophrenia patients with severe TD to 3118 unrelated population controls. Then, we checked the potential top candidate genes among 43 patients without any TD manifestations. All the genes that were found to harbor one or more qualifying variants in patients without any TD features were excluded from the final list of candidate genes. Only one gene, regulating synaptic membrane exocytosis 2 (RIMS2), showed significant enrichment of qualifying variants in TD patients compared with unrelated population controls after correcting for multiple testing (Fisher's exact test p = 5.32E-08, logistic regression p = 2.50E-08). Enrichment was caused by a single variant (rs567070433) due to a frameshift in an alternative transcript of RIMS2. None of the TD negative patients had qualifying variants in this gene. In a validation cohort of 140 schizophrenia patients assessed for TD, the variant was also not detected in any individual. Some potentially suggestive TD genes were detected in the TD cohort and warrant follow-up in future studies. No significant enrichment in previously reported TD candidate genes was identified. To the best of our knowledge, this is the first WES study of TD, demonstrating the potential role of rare loss-of-function variant enrichment in this pharmacogenetic phenotype.
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Affiliation(s)
- Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA.
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Alexander Teitelbaum
- Jerusalem Mental Health Center, Kfar Shaul Psychiatric Hospital, Hebrew University-Hadassah School of Medicine, Jerusalem, Israel
| | - Xiaolin Zhu
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Rael D Strous
- Maayenei Hayeshua Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pavel Tatarskyy
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Clement C Zai
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Arun K Tiwari
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Maria Tampakeras
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
| | - Natalie Freeman
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
| | - Daniel J Müller
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Aristotle N Voineskos
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Jeffrey A Lieberman
- Columbia University, New York State Psychiatric Institute, New York City, NY, USA
| | - Shannon L Delaney
- Columbia University, New York State Psychiatric Institute, New York City, NY, USA
| | - Herbert Y Meltzer
- Psychiatry and Behavioral Sciences, Pharmacology and Physiology, Chemistry of Life Processes Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gary Remington
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - James L Kennedy
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Ann E Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emma P Peabody
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Deborah L Levy
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Bernard Lerer
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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21
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Olender T, Keydar I, Pinto JM, Tatarskyy P, Alkelai A, Chien MS, Fishilevich S, Restrepo D, Matsunami H, Gilad Y, Lancet D. The human olfactory transcriptome. BMC Genomics 2016; 17:619. [PMID: 27515280 PMCID: PMC4982115 DOI: 10.1186/s12864-016-2960-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [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: 01/20/2016] [Accepted: 07/21/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-characterized human olfactory epithelial samples and compared the results to novel and published mouse olfactory epithelium as well as 16 human control tissues. RESULTS We identified 194 non-olfactory receptor (OR) genes that are overexpressed in human olfactory tissues vs. CONTROLS The highest overexpression is seen for lipocalins and bactericidal/permeability-increasing (BPI)-fold proteins, which in other species include secreted odorant carriers. Mouse-human discordance in orthologous lipocalin expression suggests different mammalian evolutionary paths in this family. Of the overexpressed genes 36 have documented olfactory function while for 158 there is little or no previous such functional evidence. The latter group includes GPCRs, neuropeptides, solute carriers, transcription factors and biotransformation enzymes. Many of them may be indirectly implicated in sensory function, and ~70 % are over expressed also in mouse olfactory epithelium, corroborating their olfactory role. Nearly 90 % of the intact OR repertoire, and ~60 % of the OR pseudogenes are expressed in the olfactory epithelium, with the latter showing a 3-fold lower expression. ORs transcription levels show a 1000-fold inter-paralog variation, as well as significant inter-individual differences. We assembled 160 transcripts representing 100 intact OR genes. These include 1-4 short 5' non-coding exons with considerable alternative splicing and long last exons that contain the coding region and 3' untranslated region of highly variable length. Notably, we identified 10 ORs with an intact open reading frame but with seemingly non-functional transcripts, suggesting a yet unreported OR pseudogenization mechanism. Analysis of the OR upstream regions indicated an enrichment of the homeobox family transcription factor binding sites and a consensus localization of a specific transcription factor binding site subfamily (Olf/EBF). CONCLUSIONS We provide an overview of expression levels of ORs and auxiliary genes in human olfactory epithelium. This forms a transcriptomic view of the entire OR repertoire, and reveals a large number of over-expressed uncharacterized human non-receptor genes, providing a platform for future discovery.
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Affiliation(s)
- Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Ifat Keydar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jayant M Pinto
- Section of Otolaryngology-Head and Neck Surgery, University of Chicago, Chicago, IL, USA
| | - Pavlo Tatarskyy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Alkelai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ming-Shan Chien
- Department of Molecular Genetics and Microbiology, Department of Neurobiology, Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC, USA
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Diego Restrepo
- Department of Cell and Developmental Biology, Neuroscience Program, and Rocky Mountain Taste and Smell Center, University of Colorado School of Medicine, Aurora, CO, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Department of Neurobiology, Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC, USA
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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22
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Stelzer G, Plaschkes I, Oz-Levi D, Alkelai A, Olender T, Zimmerman S, Twik M, Belinky F, Fishilevich S, Nudel R, Guan-Golan Y, Warshawsky D, Dahary D, Kohn A, Mazor Y, Kaplan S, Iny Stein T, Baris HN, Rappaport N, Safran M, Lancet D. VarElect: the phenotype-based variation prioritizer of the GeneCards Suite. BMC Genomics 2016; 17 Suppl 2:444. [PMID: 27357693 PMCID: PMC4928145 DOI: 10.1186/s12864-016-2722-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [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] [Indexed: 01/28/2023] Open
Abstract
Background Next generation sequencing (NGS) provides a key technology for deciphering the genetic underpinnings of human diseases. Typical NGS analyses of a patient depict tens of thousands non-reference coding variants, but only one or very few are expected to be significant for the relevant disorder. In a filtering stage, one employs family segregation, rarity in the population, predicted protein impact and evolutionary conservation as a means for shortening the variation list. However, narrowing down further towards culprit disease genes usually entails laborious seeking of gene-phenotype relationships, consulting numerous separate databases. Thus, a major challenge is to transition from the few hundred shortlisted genes to the most viable disease-causing candidates. Results We describe a novel tool, VarElect (http://ve.genecards.org), a comprehensive phenotype-dependent variant/gene prioritizer, based on the widely-used GeneCards, which helps rapidly identify causal mutations with extensive evidence. The GeneCards suite offers an effective and speedy alternative, whereby >120 gene-centric automatically-mined data sources are jointly available for the task. VarElect cashes on this wealth of information, as well as on GeneCards’ powerful free-text Boolean search and scoring capabilities, proficiently matching variant-containing genes to submitted disease/symptom keywords. The tool also leverages the rich disease and pathway information of MalaCards, the human disease database, and PathCards, the unified pathway (SuperPaths) database, both within the GeneCards Suite. The VarElect algorithm infers direct as well as indirect links between genes and phenotypes, the latter benefitting from GeneCards’ diverse gene-to-gene data links in GenesLikeMe. Finally, our tool offers an extensive gene-phenotype evidence portrayal (“MiniCards”) and hyperlinks to the parent databases. Conclusions We demonstrate that VarElect compares favorably with several often-used NGS phenotyping tools, thus providing a robust facility for ranking genes, pointing out their likelihood to be related to a patient’s disease. VarElect’s capacity to automatically process numerous NGS cases, either in stand-alone format or in VCF-analyzer mode (TGex and VarAnnot), is indispensable for emerging clinical projects that involve thousands of whole exome/genome NGS analyses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2722-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gil Stelzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,LifeMap Sciences Ltd, Tel Aviv, Israel
| | | | - Danit Oz-Levi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Alkelai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shahar Zimmerman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Twik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Frida Belinky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Nudel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Dvir Dahary
- LifeMap Sciences Ltd, Tel Aviv, Israel.,Toldot Genetics Ltd, Hod Hasharon, Israel
| | - Asher Kohn
- LifeMap Sciences Inc, Marshfield, MA, 02050, USA
| | | | | | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit N Baris
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,Rappaport School of Medicine, Technion, Haifa, Israel
| | - Noa Rappaport
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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23
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Alkelai A, Olender T, Haffner-Krausz R, Tsoory MM, Boyko V, Tatarskyy P, Gross-Isseroff R, Milgrom R, Shushan S, Blau I, Cohn E, Beeri R, Levy-Lahad E, Pras E, Lancet D. A role for TENM1 mutations in congenital general anosmia. Clin Genet 2016; 90:211-9. [PMID: 27040985 DOI: 10.1111/cge.12782] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [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: 10/31/2015] [Revised: 03/26/2016] [Accepted: 03/27/2016] [Indexed: 02/01/2023]
Abstract
Congenital general anosmia (CGA) is a neurological disorder entailing a complete innate inability to sense odors. While the mechanisms underlying vertebrate olfaction have been studied in detail, there are still gaps in our understanding of the molecular genetic basis of innate olfactory disorders. Applying whole-exome sequencing to a family multiply affected with CGA, we identified three members with a rare X-linked missense mutation in the TENM1 (teneurin 1) gene (ENST00000422452:c.C4829T). In Drosophila melanogaster, TENM1 functions in synaptic-partner-matching between axons of olfactory sensory neurons and target projection neurons and is involved in synapse organization in the olfactory system. We used CRISPR-Cas9 system to generate a Tenm1 disrupted mouse model. Tenm1(-/-) and point-mutated Tenm1(A) (/A) adult mice were shown to have an altered ability to locate a buried food pellet. Tenm1(A) (/A) mice also displayed an altered ability to sense aversive odors. Results of our study, that describes a new Tenm1 mouse, agree with the hypothesis that TENM1 has a role in olfaction. However, additional studies should be done in larger CGA cohorts, to provide statistical evidence that loss-of-function mutations in TENM1 can solely cause the disease in our and other CGA cases.
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Affiliation(s)
- A Alkelai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - T Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - R Haffner-Krausz
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - M M Tsoory
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - V Boyko
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - P Tatarskyy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - R Gross-Isseroff
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - R Milgrom
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - S Shushan
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel.,Department of Otolaryngology-Head and Neck Surgery, Edith Wolfson Medical Center, Holon, Israel
| | - I Blau
- Department of Otolaryngology, Meir Medical Center, Kfar Saba, Israel
| | - E Cohn
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - R Beeri
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - E Levy-Lahad
- Department of Otolaryngology, Meir Medical Center, Kfar Saba, Israel
| | - E Pras
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - D Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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24
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Vodo D, Sarig O, Geller S, Ben-Asher E, Olender T, Bochner R, Goldberg I, Nosgorodsky J, Alkelai A, Tatarskyy P, Peled A, Baum S, Barzilai A, Ibrahim SM, Zillikens D, Lancet D, Sprecher E. Identification of a Functional Risk Variant for Pemphigus Vulgaris in the ST18 Gene. PLoS Genet 2016; 12:e1006008. [PMID: 27148741 PMCID: PMC4858139 DOI: 10.1371/journal.pgen.1006008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 04/05/2016] [Indexed: 12/13/2022] Open
Abstract
Pemphigus vulgaris (PV) is a life-threatening autoimmune mucocutaneous blistering disease caused by disruption of intercellular adhesion due to auto-antibodies directed against epithelial components. Treatment is limited to immunosuppressive agents, which are associated with serious adverse effects. The propensity to develop the disease is in part genetically determined. We therefore reasoned that the delineation of PV genetic basis may point to novel therapeutic strategies. Using a genome-wide association approach, we recently found that genetic variants in the vicinity of the ST18 gene confer a significant risk for the disease. Here, using targeted deep sequencing, we identified a PV-associated variant residing within the ST18 promoter region (p<0.0002; odds ratio = 2.03). This variant was found to drive increased gene transcription in a p53/p63-dependent manner, which may explain the fact that ST18 is up-regulated in the skin of PV patients. We then discovered that when overexpressed, ST18 stimulates PV serum-induced secretion of key inflammatory molecules and contributes to PV serum-induced disruption of keratinocyte cell-cell adhesion, two processes previously implicated in the pathogenesis of PV. Thus, the present findings indicate that ST18 may play a direct role in PV and consequently represents a potential target for the treatment of this disease.
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Affiliation(s)
- Dan Vodo
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ofer Sarig
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Shamir Geller
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Edna Ben-Asher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Bochner
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Ilan Goldberg
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Judith Nosgorodsky
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Anna Alkelai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Pavel Tatarskyy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Peled
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Sharon Baum
- Department of Dermatology, Sheba Medical Center, Tel-Hashomer, Israel
| | - Aviv Barzilai
- Department of Dermatology, Sheba Medical Center, Tel-Hashomer, Israel
| | - Saleh M. Ibrahim
- Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Luebeck, Luebeck, Germany
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eli Sprecher
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail:
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Li X, Zhang W, Lencz T, Darvasi A, Alkelai A, Lerer B, Jiang HY, Zhang DF, Yu L, Xu XF, Li M, Yao YG. Common variants of IRF3 conferring risk of schizophrenia. J Psychiatr Res 2015; 64:67-73. [PMID: 25843157 DOI: 10.1016/j.jpsychires.2015.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 01/17/2023]
Abstract
Schizophrenia is a brain disorder with high heritability. Recent studies have implicated genes involved in the immune response pathway in the pathogenesis of schizophrenia. Interferon regulatory factor 3 (IRF3), a virus-immune-related gene, activates the transcription of several interferon-induced genes, and functionally interacts with several schizophrenia susceptibility genes. To test whether IRF3 is a schizophrenia susceptibility gene, we analyzed the associations of its SNPs with schizophrenia in independent population samples as well as reported data from expression quantitative trait loci (eQTL) in healthy individuals. We observed multiple independent SNPs in IRF3 showing nominally significant associations with schizophrenia (P < 0.05); more intriguingly, a SNP (rs11880923), which is significantly correlated with IRF3 expression in independent samples (P < 0.05), is also consistently associated with schizophrenia across different cohorts and in combined samples (odds ratio = 1.075, Pmeta = 2.08 × 10(-5)), especially in Caucasians (odds ratio = 1.078, Pmeta = 2.46 × 10(-5)). These results suggested that IRF3 is likely a risk gene for schizophrenia, at least in Caucasians. Although the clinical associations of IRF3 with diagnosis did not achieve genome-wide level of statistical significance, the observed odds ratio is comparable with other susceptibility loci identified through large-scale genetic association studies on schizophrenia, which could be regarded simply as small but detectable effects.
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Affiliation(s)
- Xiao Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wen Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Todd Lencz
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY, USA; Feinstein Institute for Medical Research, 350 Community Drive Manhasset, NY, USA
| | - Ariel Darvasi
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Anna Alkelai
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Bernard Lerer
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Hong-Yan Jiang
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, China; Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Deng-feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Li Yu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, China
| | - Xiu-Feng Xu
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Ming Li
- Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China; CAS Center for Excellence in Brain Science, Chinese Academy of Sciences, Shanghai, China.
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Oz-Levi D, Ben-Zeev B, Ruzzo EK, Hitomi Y, Gelman A, Pelak K, Anikster Y, Reznik-Wolf H, Bar-Joseph I, Olender T, Alkelai A, Weiss M, Ben-Asher E, Ge D, Shianna KV, Elazar Z, Goldstein DB, Pras E, Lancet D. Mutation in TECPR2 reveals a role for autophagy in hereditary spastic paraparesis. Am J Hum Genet 2012. [PMID: 23176824 DOI: 10.1016/j.ajhg.2012.09.015] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We studied five individuals from three Jewish Bukharian families affected by an apparently autosomal-recessive form of hereditary spastic paraparesis accompanied by severe intellectual disability, fluctuating central hypoventilation, gastresophageal reflux disease, wake apnea, areflexia, and unique dysmorphic features. Exome sequencing identified one homozygous variant shared among all affected individuals and absent in controls: a 1 bp frameshift TECPR2 deletion leading to a premature stop codon and predicting significant degradation of the protein. TECPR2 has been reported as a positive regulator of autophagy. We thus examined the autophagy-related fate of two key autophagic proteins, SQSTM1 (p62) and MAP1LC3B (LC3), in skin fibroblasts of an affected individual, as compared to a healthy control, and found that both protein levels were decreased and that there was a more pronounced decrease in the lipidated form of LC3 (LC3II). siRNA knockdown of TECPR2 showed similar changes, consistent with aberrant autophagy. Our results are strengthened by the fact that autophagy dysfunction has been implicated in a number of other neurodegenerative diseases. The discovered TECPR2 mutation implicates autophagy, a central intracellular mechanism, in spastic paraparesis.
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Affiliation(s)
- Danit Oz-Levi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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Alkelai A, Lupoli S, Greenbaum L, Giegling I, Kohn Y, Sarner-Kanyas K, Ben-Asher E, Lancet D, Rujescu D, Macciardi F, Lerer B. Identification of new schizophrenia susceptibility loci in an ethnically homogeneous, family-based, Arab-Israeli sample. FASEB J 2011; 25:4011-23. [PMID: 21795503 DOI: 10.1096/fj.11-184937] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
While the use of population-based samples is a common strategy in genome-wide association studies (GWASs), family-based samples have considerable advantages, such as robustness against population stratification and false-positive associations, better quality control, and the possibility to check for both linkage and association. In a genome-wide linkage study of schizophrenia in Arab-Israeli families with multiple affected individuals, we previously reported significant evidence for a susceptibility locus at chromosome 6q23.2-q24.1 and suggestive evidence at chromosomes 10q22.3-26.3, 2q36.1-37.3 and 7p21.1-22.3. To identify schizophrenia susceptibility genes, we applied a family-based GWAS strategy in an enlarged, ethnically homogeneous, Arab-Israeli family sample. We performed genome-wide single nucleotide polymorphism (SNP) genotyping and single SNP transmission disequilibrium test association analysis and found genome-wide significant association (best value of P=1.22×10(-11)) for 8 SNPs within or near highly reasonable functional candidate genes for schizophrenia. Of particular interest are a group of SNPs within and flanking the transcriptional factor LRRFIP1 gene. To determine replicability of the significant associations beyond the Arab-Israeli population, we studied the association of the significant SNPs in a German case-control validation sample and found replication of associations near the UGT1 subfamily and EFHD1 genes. Applying an exploratory homozygosity mapping approach as a complementary strategy to identify schizophrenia susceptibility genes in our Arab Israeli sample, we identified 8 putative disease loci. Overall, this GWAS, which emphasizes the important contribution of family based studies, identifies promising candidate genes for schizophrenia.
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Affiliation(s)
- Anna Alkelai
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Greenbaum L, Kanyas KS, Rigbi A, Alkelai A, Kohn Y, Lerer B. Why do young women smoke? VII COMT as a risk modifying gene for Nicotine dependence - role of gene-gene interaction, personality, and environmental factors. Hum Psychopharmacol 2010; 25:536-42. [PMID: 21312287 DOI: 10.1002/hup.1149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 08/11/2010] [Indexed: 01/25/2023]
Abstract
OBJECTIVES Catechol-O-methyltransferase (COMT) may be a risk modifying gene for Nicotine dependence (ND) rather than a direct susceptibility gene for this phenotype. Brain nicotinic cholinergic receptors modulate dopaminergic transmission, and several variants within the neighboring CHRNA5-CHRNA3 genes have been associated with ND. Therefore, it is biologically reasonable to study the interactive contribution of COMT and the CHRNA5 and CHRNA3 genes to ND. METHODS Using a case-control sample of 90 young, Israeli, Jewish female smokers (FTND ≥ 4) and 108 controls (FTND = 0 during heaviest period of smoking), we studied association with ND of 8 COMT tagging SNPs, their interaction with tagging CHRNA5-A3 SNPs and the role of background, personality, and environmental factors. RESULTS None of the COMT SNPs were associated directly with ND. In pairwise interaction analysis of SNPs from the two loci (COMT SNP-CHRNA5-CHRNA3 SNP), the interaction of intronic COMT SNP, rs9332377, with CHRNA3 3'UTR SNP rs660652 was significantly associated with ND (p = 0.0005), withstanding correction for multiple testing. CONCLUSION Addition of the genetic interaction variable into a model of non-genetic ND predictors [parental smoking, novelty seeking (NS), and lifetime history of trauma], substantially increases the percentage of ND variance explained by the model, as well as the percentage of cases correctly identified by it.
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Affiliation(s)
- Lior Greenbaum
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Greenbaum L, Alkelai A, Rigbi A, Kohn Y, Lerer B. Evidence for association of the GLI2
gene with tardive dyskinesia in patients with chronic schizophrenia. Mov Disord 2010; 25:2809-17. [DOI: 10.1002/mds.23377] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Alkelai A, Kohn Y, Olender T, Sarner-Kanyas K, Rigbi A, Hamdan A, Ben-Asher E, Lancet D, Lerer B. Evidence for an interaction of schizophrenia susceptibility loci on chromosome 6q23.3 and 10q24.33-q26.13 in Arab Israeli families. Am J Med Genet B Neuropsychiatr Genet 2009; 150B:914-25. [PMID: 19152384 DOI: 10.1002/ajmg.b.30918] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A genome scan for schizophrenia related loci in Arab Israeli families by Lerer et al. [Lerer et al. (2003); Mol Psychiatry 8:488-498] detected significant evidence for linkage at chromosome 6q23. Subsequent fine mapping [Levi et al. (2005); Eur J Hum Genet 13:763-771], association [Amann-Zalcenstein et al. (2006); Eur J Hum Genet 14:1111-1119] and replication studies [Ingason et al. (2007); Eur J Hum Genet 15:988-991] identified AHI1 as a putative susceptibility gene. The same genome scan revealed suggestive evidence for a schizophrenia susceptibility locus in the 10q23-26 region. Genes at these two loci may act independently in the pathogenesis of the disease in our homogeneous sample of Arab Israeli families or may interact with each other and with other factors in a common biological pathway. The purpose of our current study was to test the hypothesis of genetic interaction between these two loci and to identify the type of interaction between them. The initial stage of our study focused on the 10q23-q26 region which has not been explored further in our sample. The second stage of the study included a test for possible genetic interaction between the 6q23.3 locus and the refined 10q24.33-q26.13 locus. A final candidate region of 19.9 Mb between markers D10S222 (105.3 Mb) and D10S587 (125.2 Mb) was found on chromosome 10 by non-parametric and parametric linkage analyses. These linkage findings are consistent with previous reports in the same chromosomal region. Two-locus multipoint linkage analysis under three complex disease inheritance models (heterogeneity, multiplicative, and additive models) yielded a best maximum LOD score of 7.45 under the multiplicative model suggesting overlapping function of the 6q23.3 and 10q24.33-q26.13 loci.
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Affiliation(s)
- A Alkelai
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Ein Karem, Jerusalem, Israel
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Alkelai A, Baum A, Carless M, Crowley J, Dasbanerjee T, Dempster E, Docherty S, Hare E, Galsworthy MJ, Grover D, Glubb D, Karlsson R, Mill J, Sen S, Quinones MP, Vallender EJ, Verma R, Vijayan NN, Villafuerte S, Voineskos AN, Volk H, Yu L, Zimmermann P, Delisi LE. The XVth World Congress of Psychiatric Genetics, October 7-11, 2007: Rapporteur summaries of oral presentations. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:233-77. [PMID: 18297693 DOI: 10.1002/ajmg.b.30711] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The World Congress of Psychiatric Genetics (WCPG) has become an annual event since the early 1990's sponsored by the International Society of Psychiatric Genetics (ISPG). Each year the latest published and unpublished findings are aired for discussion by representatives of the majority of research programs on this topic world-wide. The 2007 congress was held in New York City and attracted over 1000 researchers. The topics emphasized included results from whole genome association studies, the significance of copy number variation and the important contributions of epigenetic events to psychiatric disorders. There were over 20 oral sessions devoted to these and other topics of interest. Young investigator recipients of travel awards served as rapporteurs to summarize sessions and these summaries follow.
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Affiliation(s)
- Anna Alkelai
- Biological Psychiatry Laboratory, Dept. of Psychiatry, Hadassah - Hebrew University Medical Center, Jerusalem, Israel.
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Basel-Vanagaite L, Attia R, Yahav M, Ferland RJ, Anteki L, Walsh CA, Olender T, Straussberg R, Magal N, Taub E, Drasinover V, Alkelai A, Bercovich D, Rechavi G, Simon AJ, Shohat M. The CC2D1A, a member of a new gene family with C2 domains, is involved in autosomal recessive non-syndromic mental retardation. J Med Genet 2005; 43:203-10. [PMID: 16033914 PMCID: PMC2563235 DOI: 10.1136/jmg.2005.035709] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND The molecular basis of autosomal recessive non-syndromic mental retardation (NSMR) is poorly understood, mostly owing to heterogeneity and absence of clinical criteria for grouping families for linkage analysis. Only two autosomal genes, the PRSS12 gene on chromosome 4q26 and the CRBN on chromosome 3p26, have been shown to cause autosomal recessive NSMR, each gene in only one family. OBJECTIVE To identify the gene causing autosomal recessive NSMR on chromosome 19p13.12. RESULTS The candidate region established by homozygosity mapping was narrowed down from 2.4 Mb to 0.9 Mb on chromosome 19p13.12. A protein truncating mutation was identified in the gene CC2D1A in nine consanguineous families with severe autosomal recessive NSMR. The absence of the wild type protein in the lymphoblastoid cells of the patients was confirmed. CC2D1A is a member of a previously uncharacterised gene family that carries two conserved motifs, a C2 domain and a DM14 domain. The C2 domain is found in proteins which function in calcium dependent phospholipid binding; the DM14 domain is unique to the CC2D1A protein family and its role is unknown. CC2D1A is a putative signal transducer participating in positive regulation of I-kappaB kinase/NFkappaB cascade. Expression of CC2D1A mRNA was shown in the embryonic ventricular zone and developing cortical plate in staged mouse embryos, persisting into adulthood, with highest expression in the cerebral cortex and hippocampus. CONCLUSIONS A previously unknown signal transduction pathway is important in human cognitive development.
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Affiliation(s)
- L Basel-Vanagaite
- Department of Medical Genetics, Rabin Medical Centre, Beilinson Campus, Petah Tikva 49100, Israel.
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Basel-Vanagaite L, Alkelai A, Straussberg R, Magal N, Inbar D, Mahajna M, Shohat M. Mapping of a new locus for autosomal recessive non-syndromic mental retardation in the chromosomal region 19p13.12-p13.2: further genetic heterogeneity. J Med Genet 2003; 40:729-32. [PMID: 14569116 PMCID: PMC1735276 DOI: 10.1136/jmg.40.10.729] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To identify and clinically evaluate four consanguineous families of Israeli Arab origin with non-syndromic mental retardation (NSMR), comprising a total of 10 affected and 24 unaffected individuals. PARTICIPANTS AND METHODS All the families originated from the same small village and had the same family name. Association of the condition in these families with the two known autosomal recessive NSMR loci on chromosomes 3p25-pter and 4q24 (neurotrypsin gene) was excluded. RESULTS Linkage of the disease gene to chromosome 19p13.12-p13.2(Zmax = 7.06 at theta = 0.00) for the marker D19S840 was established. All the affected individuals were found to be homozygous for a common haplotype for the markers cen-RFX1-D19S840-D19S558-D19S221-tel. CONCLUSIONS The results suggest that the disease is caused by a single mutation derived from a single ancestral founder in all the families. Recombination events and a common disease bearing haplotype defined a critical region of 2.4 Mb, between the loci D19S547 proximally and D19S1165 distally.
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Affiliation(s)
- L Basel-Vanagaite
- Department of Medical Genetics, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.
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