4
|
Eger SJ, Le Guen Y, Khan RR, Hall JN, Kennedy G, Zaharchuk G, Couthouis J, Brooks WS, Velakoulis D, Napolioni V, Belloy ME, Dalgard CL, Mormino EC, Gitler AD, Greicius MD. Confirming Pathogenicity of the F386L PSEN1 Variant in a South Asian Family With Early-Onset Alzheimer Disease. Neurol Genet 2021; 8:e647. [PMID: 34901437 PMCID: PMC8655848 DOI: 10.1212/nxg.0000000000000647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/20/2021] [Indexed: 11/15/2022]
Abstract
Objectives The F386L PSEN1 variant has been reported in 1 Japanese family with limited clinical information. We aimed to prove that F386L is pathogenic by demonstrating that it segregates with early-onset Alzheimer disease (AD). Methods Eight individuals in a South Asian family provided DNA for genetic testing and underwent a neurologic examination. Results The female proband was diagnosed with AD at age 45 years and died at age 49 years. She had a CSF biomarker profile consistent with AD, and her florbetaben PET scan was amyloid positive with high uptake in the striatum. Her MRI showed no prominent white matter disease. Her affected relatives had an age at onset range of 38–57 years and had imaging and biomarker profiles similar to hers. Discussion The results presented here, in conjunction with the prior report, confirm the pathogenicity of F386L. Furthermore, our study highlights the importance of studying families from underrepresented populations to identify or confirm the pathogenicity of rare variants that may be specific to certain genetic ancestries.
Collapse
Affiliation(s)
- Sarah J Eger
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Raiyan R Khan
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Jacob N Hall
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Gabriel Kennedy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Greg Zaharchuk
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Julien Couthouis
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - William S Brooks
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Dennis Velakoulis
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Valerio Napolioni
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Michaël E Belloy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Clifton L Dalgard
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Elizabeth C Mormino
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Aaron D Gitler
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, (S.J.E., Y.L.G., G.K., M.E.B., E.C.M., M.D.G.); Department of Computer Science, Columbia University, New York, NY (R.R.K.) the Neurology Center of Southern California, Temecula, CA (J.N.H.); Department of Radiology, Stanford University School of Medicine, Stanford, CA (G.Z.) Department of Genetics, Stanford University School of Medicine, Stanford, CA (J.C., A.D.G.); Neuroscience Research Australia, Randwick NSW 2031, Australia (W.S.B); the University of New South Wales, Sydney NSW 2052, Australia (W.S.B.); Neuropsychiatry Unit, Royal Melbourne Hospital, Parkville VIC 3050, Australia (D.V.); School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy (V.N); Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.); the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD (C.L.D.)
| |
Collapse
|
6
|
Dahary D, Golan Y, Mazor Y, Zelig O, Barshir R, Twik M, Iny Stein T, Rosner G, Kariv R, Chen F, Zhang Q, Shen Y, Safran M, Lancet D, Fishilevich S. Genome analysis and knowledge-driven variant interpretation with TGex. BMC Med Genomics 2019; 12:200. [PMID: 31888639 PMCID: PMC6937949 DOI: 10.1186/s12920-019-0647-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/15/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The clinical genetics revolution ushers in great opportunities, accompanied by significant challenges. The fundamental mission in clinical genetics is to analyze genomes, and to identify the most relevant genetic variations underlying a patient's phenotypes and symptoms. The adoption of Whole Genome Sequencing requires novel capacities for interpretation of non-coding variants. RESULTS We present TGex, the Translational Genomics expert, a novel genome variation analysis and interpretation platform, with remarkable exome analysis capacities and a pioneering approach of non-coding variants interpretation. TGex's main strength is combining state-of-the-art variant filtering with knowledge-driven analysis made possible by VarElect, our highly effective gene-phenotype interpretation tool. VarElect leverages the widely used GeneCards knowledgebase, which integrates information from > 150 automatically-mined data sources. Access to such a comprehensive data compendium also facilitates TGex's broad variant annotation, supporting evidence exploration, and decision making. TGex has an interactive, user-friendly, and easy adaptive interface, ACMG compliance, and an automated reporting system. Beyond comprehensive whole exome sequence capabilities, TGex encompasses innovative non-coding variants interpretation, towards the goal of maximal exploitation of whole genome sequence analyses in the clinical genetics practice. This is enabled by GeneCards' recently developed GeneHancer, a novel integrative and fully annotated database of human enhancers and promoters. Examining use-cases from a variety of TGex users world-wide, we demonstrate its high diagnostic yields (42% for single exome and 50% for trios in 1500 rare genetic disease cases) and critical actionable genetic findings. The platform's support for integration with EHR and LIMS through dedicated APIs facilitates automated retrieval of patient data for TGex's customizable reporting engine, establishing a rapid and cost-effective workflow for an entire range of clinical genetic testing, including rare disorders, cancer predisposition, tumor biopsies and health screening. CONCLUSIONS TGex is an innovative tool for the annotation, analysis and prioritization of coding and non-coding genomic variants. It provides access to an extensive knowledgebase of genomic annotations, with intuitive and flexible configuration options, allows quick adaptation, and addresses various workflow requirements. It thus simplifies and accelerates variant interpretation in clinical genetics workflows, with remarkable diagnostic yield, as exemplified in the described use cases. TGex is available at http://tgex.genecards.org/.
Collapse
Affiliation(s)
- Dvir Dahary
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA.
| | - Yaron Golan
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA
| | - Yaron Mazor
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA
| | - Ofer Zelig
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA
| | - Ruth Barshir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Twik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Rosner
- Department of Gastroenterology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Revital Kariv
- Department of Gastroenterology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Fei Chen
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Qiang Zhang
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Yiping Shen
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China.,Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.,Department of Neurology, Harvard Medical School, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|