1
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Mullegama SV, Kiernan KA, Torti E, Pavlovsky E, Tilton N, Sekula A, Gao H, Alaimo JT, Engleman K, Rush ET, Blocker K, Dipple KM, Fettig VM, Hare H, Glass I, Grange DK, Griffin M, Phornphutkul C, Massingham L, Mehta L, Miller DE, Thies J, Merritt JL, Muller E, Osmond M, Sawyer SL, Slaugh R, Hickey RE, Wolf B, Choudhary S, Simonović M, Zhang Y, Palculict TB, Telegrafi A, Carere DA, Wentzensen IM, Morrow MM, Monaghan KG, Yang J, Juusola J. De novo missense variants in exon 9 of SEPHS1 cause a neurodevelopmental condition with developmental delay, poor growth, hypotonia, and dysmorphic features. Am J Hum Genet 2024; 111:778-790. [PMID: 38531365 PMCID: PMC11023921 DOI: 10.1016/j.ajhg.2024.02.016] [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: 04/04/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Selenophosphate synthetase (SEPHS) plays an essential role in selenium metabolism. Two mammalian SEPHS paralogues, SEPHS1 and SEPHS2, share high sequence identity and structural homology with SEPHS. Here, we report nine individuals from eight families with developmental delay, growth and feeding problems, hypotonia, and dysmorphic features, all with heterozygous missense variants in SEPHS1. Eight of these individuals had a recurrent variant at amino acid position 371 of SEPHS1 (p.Arg371Trp, p.Arg371Gln, and p.Arg371Gly); seven of these variants were known to be de novo. Structural modeling and biochemical assays were used to understand the effect of these variants on SEPHS1 function. We found that a variant at residue Trp352 results in local structural changes of the C-terminal region of SEPHS1 that decrease the overall thermal stability of the enzyme. In contrast, variants of a solvent-exposed residue Arg371 do not impact enzyme stability and folding but could modulate direct protein-protein interactions of SEPSH1 with cellular factors in promoting cell proliferation and development. In neuronal SH-SY5Y cells, we assessed the impact of SEPHS1 variants on cell proliferation and ROS production and investigated the mRNA expression levels of genes encoding stress-related selenoproteins. Our findings provided evidence that the identified SEPHS1 variants enhance cell proliferation by modulating ROS homeostasis. Our study supports the hypothesis that SEPHS1 plays a critical role during human development and provides a basis for further investigation into the molecular mechanisms employed by SEPHS1. Furthermore, our data suggest that variants in SEPHS1 are associated with a neurodevelopmental disorder.
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Affiliation(s)
- Sureni V Mullegama
- GeneDx, Gaithersburg, MD 20877, USA; Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA.
| | - Kaitlyn A Kiernan
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | - Ethan Pavlovsky
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Nicholas Tilton
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Austin Sekula
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Hua Gao
- GeneDx, Gaithersburg, MD 20877, USA
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA; Department of Pediatrics, University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA; Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | - Kendra Engleman
- Department of Pediatrics, University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA; Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA
| | - Eric T Rush
- Department of Pediatrics, University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA; Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA; Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Karli Blocker
- Division of Clinical Genetics, Stanford Children's Health, San Francisco, CA, USA
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Veronica M Fettig
- Center for Inherited Cardiovascular Disease, Cardiovascular Genetics Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Heather Hare
- Northeastern Ontario Medical Genetics Program, Health Sciences, North Sudbury, ON, Canada
| | - Ian Glass
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael Griffin
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Chanika Phornphutkul
- Division of Genetics, Department of Pediatrics, Alpert School of Medicine at Brown University, Providence, RI, USA
| | - Lauren Massingham
- Division of Genetics, Department of Pediatrics, Alpert School of Medicine at Brown University, Providence, RI, USA
| | - Lakshmi Mehta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Jenny Thies
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - J Lawrence Merritt
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Eric Muller
- Division of Clinical Genetics, Stanford Children's Health, San Francisco, CA, USA
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Sarah L Sawyer
- Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel E Hickey
- Department of Pediatrics, Division of Genetics, Birth Defects and Metabolism, Anne & Robert H. Lurie Children's Hospital, Chicago, IL, USA
| | - Barry Wolf
- Department of Pediatrics, Division of Genetics, Birth Defects and Metabolism, Anne & Robert H. Lurie Children's Hospital, Chicago, IL, USA
| | - Sanjeev Choudhary
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | | | | | | | | | | | - Jun Yang
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
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2
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Rehm HL, Alaimo JT, Aradhya S, Bayrak-Toydemir P, Best H, Brandon R, Buchan JG, Chao EC, Chen E, Clifford J, Cohen ASA, Conlin LK, Das S, Davis KW, Del Gaudio D, Del Viso F, DiVincenzo C, Eisenberg M, Guidugli L, Hammer MB, Harrison SM, Hatchell KE, Dyer LH, Hoang LU, Holt JM, Jobanputra V, Karbassi ID, Kearney HM, Kelly MA, Kelly JM, Kluge ML, Komala T, Kruszka P, Lau L, Lebo MS, Marshall CR, McKnight D, McWalter K, Meng Y, Nagan N, Neckelmann CS, Neerman N, Niu Z, Paolillo VK, Paolucci SA, Perry D, Pesaran T, Radtke K, Rasmussen KJ, Retterer K, Saunders CJ, Spiteri E, Stanley C, Szuto A, Taft RJ, Thiffault I, Thomas BC, Thomas-Wilson A, Thorpe E, Tidwell TJ, Towne MC, Zouk H. The landscape of reported VUS in multi-gene panel and genomic testing: Time for a change. Genet Med 2023; 25:100947. [PMID: 37534744 PMCID: PMC10825061 DOI: 10.1016/j.gim.2023.100947] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 04/24/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023] Open
Abstract
PURPOSE Variants of uncertain significance (VUS) are a common result of diagnostic genetic testing and can be difficult to manage with potential misinterpretation and downstream costs, including time investment by clinicians. We investigated the rate of VUS reported on diagnostic testing via multi-gene panels (MGPs) and exome and genome sequencing (ES/GS) to measure the magnitude of uncertain results and explore ways to reduce their potentially detrimental impact. METHODS Rates of inconclusive results due to VUS were collected from over 1.5 million sequencing test results from 19 clinical laboratories in North America from 2020 to 2021. RESULTS We found a lower rate of inconclusive test results due to VUSs from ES/GS (22.5%) compared with MGPs (32.6%; P < .0001). For MGPs, the rate of inconclusive results correlated with panel size. The use of trios reduced inconclusive rates (18.9% vs 27.6%; P < .0001), whereas the use of GS compared with ES had no impact (22.2% vs 22.6%; P = ns). CONCLUSION The high rate of VUS observed in diagnostic MGP testing warrants examining current variant reporting practices. We propose several approaches to reduce reported VUS rates, while directing clinician resources toward important VUS follow-up.
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Affiliation(s)
- Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Pathology, Harvard Medical School, Boston, MA.
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO; Department of Pediatrics, School of Medicine, University of Missouri, Kansas City, MO; Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO
| | - Swaroop Aradhya
- Invitae, San Francisco, CA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA
| | - Pinar Bayrak-Toydemir
- ARUP Laboratories, Salt Lake City, UT; Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Hunter Best
- ARUP Laboratories, Salt Lake City, UT; Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | | | - Jillian G Buchan
- Genetics Division, Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | | | | | | | - Ana S A Cohen
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO; Department of Pediatrics, School of Medicine, University of Missouri, Kansas City, MO; Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO
| | - Laura K Conlin
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA; Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Soma Das
- Human Genetics, University of Chicago, Chicago, IL
| | | | | | - Florencia Del Viso
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO
| | | | - Marcia Eisenberg
- Women's Health and Genetics, Labcorp, Research Triangle Park, NC
| | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | - Monia B Hammer
- Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | | | | | - James M Holt
- HudsonAlpha Clinical Services Lab, LLC, Huntsville, AL
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | | | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Jacob M Kelly
- HudsonAlpha Clinical Services Lab, LLC, Huntsville, AL
| | - Michelle L Kluge
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | | | - Lynette Lau
- Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Matthew S Lebo
- Pathology, Harvard Medical School, Boston, MA; Laboratory for Molecular Medicine, Mass General Brigham, Cambridge, MA
| | - Christian R Marshall
- Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | | | - Yan Meng
- Fulgent Genetics, Temple City, CA
| | | | | | | | - Zhiyv Niu
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Vitoria K Paolillo
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO
| | - Sarah A Paolucci
- Genetics Division, Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | | | | | | | - Kristen J Rasmussen
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO; Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO; Department of Pediatrics and Pathology, School of Medicine, University of Missouri, Kansas City, MO
| | | | | | - Anna Szuto
- Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO; Department of Pediatrics, School of Medicine, University of Missouri, Kansas City, MO; Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO
| | | | | | | | | | | | - Hana Zouk
- Pathology, Harvard Medical School, Boston, MA; Laboratory for Molecular Medicine, Mass General Brigham, Cambridge, MA
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3
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Koop K, Yuan W, Tessadori F, Rodriguez-Polanco WR, Grubbs J, Zhang B, Osmond M, Graham G, Sawyer S, Conboy E, Vetrini F, Treat K, Płoski R, Pienkowski VM, Kłosowska A, Fieg E, Krier J, Mallebranche C, Alban Z, Aldinger KA, Ritter D, Macnamara E, Sullivan B, Herriges J, Alaimo JT, Helbig C, Ellis CA, van Eyk C, Gecz J, Farrugia D, Osei-Owusu I, Adès L, van den Boogaard MJ, Fuchs S, Bakker J, Duran K, Dawson ZD, Lindsey A, Huang H, Baldridge D, Silverman GA, Grant BD, Raizen D, van Haaften G, Pak SC, Rehmann H, Schedl T, van Hasselt P. Macrocephaly and developmental delay caused by missense variants in RAB5C. Hum Mol Genet 2023; 32:3063-3077. [PMID: 37552066 PMCID: PMC10586195 DOI: 10.1093/hmg/ddad130] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/06/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023] Open
Abstract
Rab GTPases are important regulators of intracellular vesicular trafficking. RAB5C is a member of the Rab GTPase family that plays an important role in the endocytic pathway, membrane protein recycling and signaling. Here we report on 12 individuals with nine different heterozygous de novo variants in RAB5C. All but one patient with missense variants (n = 9) exhibited macrocephaly, combined with mild-to-moderate developmental delay. Patients with loss of function variants (n = 2) had an apparently more severe clinical phenotype with refractory epilepsy and intellectual disability but a normal head circumference. Four missense variants were investigated experimentally. In vitro biochemical studies revealed that all four variants were damaging, resulting in increased nucleotide exchange rate, attenuated responsivity to guanine exchange factors and heterogeneous effects on interactions with effector proteins. Studies in C. elegans confirmed that all four variants were damaging in vivo and showed defects in endocytic pathway function. The variant heterozygotes displayed phenotypes that were not observed in null heterozygotes, with two shown to be through a dominant negative mechanism. Expression of the human RAB5C variants in zebrafish embryos resulted in defective development, further underscoring the damaging effects of the RAB5C variants. Our combined bioinformatic, in vitro and in vivo experimental studies and clinical data support the association of RAB5C missense variants with a neurodevelopmental disorder characterized by macrocephaly and mild-to-moderate developmental delay through disruption of the endocytic pathway.
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Affiliation(s)
- Klaas Koop
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, 3584 EA, The Netherlands
| | - Weimin Yuan
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Federico Tessadori
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, The Netherlands
| | - Wilmer R Rodriguez-Polanco
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jeremy Grubbs
- Department of Neurology and the Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bo Zhang
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Matt Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada
| | - Gail Graham
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada
| | - Sarah Sawyer
- Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada
| | - Erin Conboy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kayla Treat
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Rafal Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, 02-106, Poland
| | - Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, 02-106, Poland
- Marseille Medical Genetics U1251, Aix Marseille University, Marseille, 13005, France
| | - Anna Kłosowska
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdańsk, Gdańsk, 80-210, Poland
| | - Elizabeth Fieg
- Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Joel Krier
- Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Coralie Mallebranche
- Unité d'Onco-Hémato-Immunologie pédiatrique, CHU d’Angers, Angers, 49933, France
| | - Ziegler Alban
- Service de génétique, CHU d’Angers, Angers, 49933, France
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, 98195, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Deborah Ritter
- Department of Pediatrics, Oncology Section, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ellen Macnamara
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bonnie Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, 64108, USA
| | - John Herriges
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, MO, 64108, USA
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, MO, 64108, USA
| | - Catherine Helbig
- The Epilepsy Neurogenetics Initiative, Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Colin A Ellis
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, 19104, USA
| | - Clare van Eyk
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5006, Australia
| | - Jozef Gecz
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5006, Australia
| | | | - Ikeoluwa Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lesley Adès
- Department of Clinical Genetics, The Children’s Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, 2145, Australia
| | - Marie-Jose van den Boogaard
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, 3584EA, The Netherlands
| | - Sabine Fuchs
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, 3584 EA, The Netherlands
| | - Jeroen Bakker
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, The Netherlands
| | - Karen Duran
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, The Netherlands
| | - Zachary D Dawson
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Anika Lindsey
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Huiyan Huang
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Dustin Baldridge
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Gary A Silverman
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Barth D Grant
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - David Raizen
- Department of Neurology and the Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, 3584EA, The Netherlands
| | - Stephen C Pak
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Holger Rehmann
- Department of Energy and Biotechnology, Flensburg University of Applied Sciences, 24943, Flensburg, Germany
| | - Tim Schedl
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Peter van Hasselt
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, 3584 EA, The Netherlands
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4
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Wee E, Herriges J, Dileepan K, Tsai SL, Alaimo JT, Paprocki E. Hyperinsulinemic Hypoglycemia and Growth Hormone Deficiency Secondary to 20p11 Deletion. Case Rep Endocrinol 2023; 2023:8658540. [PMID: 37404330 PMCID: PMC10317580 DOI: 10.1155/2023/8658540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 03/30/2023] [Accepted: 06/14/2023] [Indexed: 07/06/2023] Open
Abstract
Hypoglycemia is concerning for neurological complications in infants and children. Determining the cause of hypoglycemia is essential in providing appropriate treatment. Hyperinsulinism and growth hormone deficiency are known causes of hypoglycemia but are not commonly found together. We report a 4-month-old boy who presented with severe hypoglycemia and was found to have both hyperinsulinism and growth hormone deficiency. Treatment with both recombinant human growth hormone and diazoxide led to blood glucose normalization. Subsequently, he was found to have a genetic diagnosis of 20p11.22p11.21 deletion. 20p11 deletions have been associated with hypopituitarism, most commonly seen in growth hormone deficiency causing hypoglycemia. This case is one of a few to report hyperinsulinism as a manifestation of this deletion.
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Affiliation(s)
- Erica Wee
- Division of Pediatric Endocrinology and Diabetes, Children's Mercy Kansas City, Kansas City, MO, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - John Herriges
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Kavitha Dileepan
- Division of Pediatric Endocrinology and Diabetes, Children's Mercy Kansas City, Kansas City, MO, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Sarah L. Tsai
- Division of Pediatric Endocrinology and Diabetes, Children's Mercy Kansas City, Kansas City, MO, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Joseph T. Alaimo
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Emily Paprocki
- Division of Pediatric Endocrinology and Diabetes, Children's Mercy Kansas City, Kansas City, MO, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
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5
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Lansdon LA, Cadieux-Dion M, Herriges JC, Johnston J, Yoo B, Alaimo JT, Thiffault I, Miller N, Cohen ASA, Repnikova EA, Zhang L, Farooqi MS, Farrow EG, Saunders CJ. Clinical Validation of Genome Reference Consortium Human Build 38 in a Laboratory Utilizing Next-Generation Sequencing Technologies. Clin Chem 2022; 68:1177-1183. [DOI: 10.1093/clinchem/hvac113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/31/2022] [Indexed: 01/02/2023]
Abstract
Abstract
Background
Laboratories utilizing next-generation sequencing align sequence data to a standardized human reference genome (HRG). Several updated versions, or builds, have been released since the original HRG in 2001, including the Genome Reference Consortium Human Build 38 (GRCh38) in 2013. However, most clinical laboratories still use GRCh37, which was released in 2009. We report our laboratory’s clinical validation of GRCh38.
Methods
Migration to GRCh38 was validated by comparing the coordinates (lifting over) of 9443 internally curated variants from GRCh37 to GRCh38, globally comparing protein coding sequence variants aligned with GRCh37 vs GRCh38 from 917 exomes, assessing genes with known discrepancies, comparing coverage differences, and establishing the analytic sensitivity and specificity of variant detection using Genome in a Bottle data.
Results
Eight discrepancies, due to strand swap or reference base, were observed. Three clinically relevant variants had the GRCh37 alternate allele as the reference allele in GRCh38. A comparison of 88 295 calls between builds identified 8 disease-associated genes with sequence differences: ABO, BNC2, KIZ, NEFL, NR2E3, PTPRQ, SHANK2, and SRD5A2. Discrepancies in coding regions in GRCh37 were resolved in GRCh38.
Conclusions
There were a small number of clinically significant changes between the 2 genome builds. GRCh38 provided improved detection of nucleotide changes due to the resolution of discrepancies present in GRCh37. Implementation of GRCh38 results in more accurate and consistent reporting.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Maxime Cadieux-Dion
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
| | - John C Herriges
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Jeffrey Johnston
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
| | - Byunggil Yoo
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Neil Miller
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
- Bionano Genomics, Inc. , 9540 Towne Centre Dr., Suite 100, San Diego, CA , USA
| | - Ana S A Cohen
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Elena A Repnikova
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Lei Zhang
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
| | - Midhat S Farooqi
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Emily G Farrow
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
- Department of Pediatrics Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
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6
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Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B, Berrios CD, Biswell RL, Buczkowicz P, Buske O, Chakraborty S, Cheung WA, Coffman KA, Cooper AM, Cross LA, Curran T, Dang TTT, Elfrink MM, Engleman KL, Fecske ED, Fieser C, Fitzgerald K, Fleming EA, Gadea RN, Gannon JL, Gelineau-Morel RN, Gibson M, Goldstein J, Grundberg E, Halpin K, Harvey BS, Heese BA, Hein W, Herd SM, Hughes SS, Ilyas M, Jacobson J, Jenkins JL, Jiang S, Johnston JJ, Keeler K, Korlach J, Kussmann J, Lambert C, Lawson C, Le Pichon JB, Leeder JS, Little VC, Louiselle DA, Lypka M, McDonald BD, Miller N, Modrcin A, Nair A, Neal SH, Oermann CM, Pacicca DM, Pawar K, Posey NL, Price N, Puckett LMB, Quezada JF, Raje N, Rowell WJ, Rush ET, Sampath V, Saunders CJ, Schwager C, Schwend RM, Shaffer E, Smail C, Soden S, Strenk ME, Sullivan BR, Sweeney BR, Tam-Williams JB, Walter AM, Welsh H, Wenger AM, Willig LK, Yan Y, Younger ST, Zhou D, Zion TN, Thiffault I, Pastinen T. Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. Genet Med 2022; 24:1336-1348. [PMID: 35305867 DOI: 10.1016/j.gim.2022.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 10/15/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022] Open
Abstract
PURPOSE This study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program. METHODS Extensive analyses of 960 families with suspected genetic disorders included short-read exome sequencing and short-read genome sequencing (srGS); PacBio HiFi long-read genome sequencing (HiFi-GS); variant calling for single nucleotide variants (SNV), structural variant (SV), and repeat variants; and machine-learning variant prioritization. Structured phenotypes, prioritized variants, and pedigrees were stored in PhenoTips database, with data sharing through controlled access the database of Genotypes and Phenotypes. RESULTS Diagnostic rates ranged from 11% in patients with prior negative genetic testing to 34.5% in naive patients. Incorporating SVs from genome sequencing added up to 13% of new diagnoses in previously unsolved cases. HiFi-GS yielded increased discovery rate with >4-fold more rare coding SVs compared with srGS. Variants and genes of unknown significance remain the most common finding (58% of nondiagnostic cases). CONCLUSION Computational prioritization is efficient for diagnostic SNVs. Thorough identification of non-SNVs remains challenging and is partly mitigated using HiFi-GS sequencing. Importantly, community research is supported by sharing real-time data to accelerate gene validation and by providing HiFi variant (SNV/SV) resources from >1000 human alleles to facilitate implementation of new sequencing platforms for rare disease diagnoses.
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Affiliation(s)
- Ana S A Cohen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Shivarajan M Amudhavalli
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - John T Anderson
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Lalit Bansal
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Lauren Bartik
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Bradley Belden
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Rebecca L Biswell
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | | | | | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Keith A Coffman
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Ashley M Cooper
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Laura A Cross
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Tom Curran
- Children's Mercy Research Institute, Kansas City, MO
| | - Thuy Tien T Dang
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Mary M Elfrink
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Erin D Fecske
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Cynthia Fieser
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Keely Fitzgerald
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Emily A Fleming
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Randi N Gadea
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Rose N Gelineau-Morel
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Margaret Gibson
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Jeffrey Goldstein
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Kelsee Halpin
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Brian S Harvey
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Bryce A Heese
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Wendy Hein
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Suzanne M Herd
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Susan S Hughes
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Mohammed Ilyas
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Jill Jacobson
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Janda L Jenkins
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | - Kathryn Keeler
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Jonas Korlach
- Pacific Biosciences of California, Inc, Menlo Park, CA
| | | | | | - Caitlin Lawson
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | - Vicki C Little
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | | | - Neil Miller
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Allergy Immunology Pulmonary and Sleep Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Ann Modrcin
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Annapoorna Nair
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Shelby H Neal
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Donna M Pacicca
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Kailash Pawar
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Nyshele L Posey
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Nigel Price
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Laura M B Puckett
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Julio F Quezada
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Nikita Raje
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Neonatology, Children's Mercy Kansas City, Kansas City, MO
| | | | - Eric T Rush
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO; Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, MO
| | - Venkatesh Sampath
- Division of Neonatology, Children's Mercy Hospital Kansas City, Kansas City, MO
| | - Carol J Saunders
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Caitlin Schwager
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Richard M Schwend
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Elizabeth Shaffer
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Craig Smail
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Sarah Soden
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Meghan E Strenk
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Brooke R Sweeney
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Adam M Walter
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Holly Welsh
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Laurel K Willig
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Yun Yan
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Scott T Younger
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Dihong Zhou
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Tricia N Zion
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO.
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Children's Mercy Research Institute, Kansas City, MO.
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Hanson J, Brezavar D, Hughes S, Amudhavalli S, Fleming E, Zhou D, Alaimo JT, Bonnen PE. TAB2 variants cause cardiovascular heart disease, connective tissue disorder, and developmental delay. Clin Genet 2022; 101:214-220. [PMID: 34741306 PMCID: PMC8745489 DOI: 10.1111/cge.14085] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 06/02/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 02/03/2023]
Abstract
Congenital heart defects (CHD) are the most commonly occurring birth defect and can occur in isolation or with additional clinical features comprising a genetic syndrome. Autosomal dominant variants in TAB2 are recognized by the American Heart Association as causing nonsyndromic CHD, however, emerging data point to additional, extra-cardiac features associated with TAB2 variants. We identified 15 newly reported individuals with pathogenic TAB2 variants and reviewed an additional 24 subjects with TAB2 variants in the literature. Analysis showed 64% (25/39) of individuals with disease resulting from TAB2 single nucleotide variants (SNV) had syndromic CHD or adult-onset cardiomyopathy with one or more extra-cardiac features. The most commonly co-occurring features with CHD or cardiomyopathy were facial dysmorphism, skeletal and connective tissue defects and most subjects with TAB2 variants present as a connective tissue disorder. Notably, 53% (8/15) of our cohort displayed developmental delay and we suspect this may be a previously unappreciated feature of TAB2 disease. We describe the largest cohort of subjects with TAB2 SNV and show that in addition to heart disease, features across multiple systems are present in most TAB2 cases. In light of our findings, we recommend that TAB2 be included on the list of genes that cause syndromic CHD, adult-onset cardiomyopathy, and connective tissue disorder.
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Affiliation(s)
- Jennifer Hanson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel Brezavar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Susan Hughes
- Division of Clinical Genetics, Children’s Mercy Hospital, Kansas City, Missouri
| | | | - Emily Fleming
- Division of Clinical Genetics, Children’s Mercy Hospital, Kansas City, Missouri
| | - Dihong Zhou
- Division of Clinical Genetics, Children’s Mercy Hospital, Kansas City, Missouri
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, Missouri,University of Missouri-Kansas City, School of Medicine, Kansas City, Missouri
| | - Penelope E Bonnen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA,Correspondence to: Dr. Penelope E Bonnen () 713-798-4256
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8
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Lansdon LA, Cadieux-Dion M, Yoo B, Miller N, Cohen ASA, Zellmer L, Zhang L, Farrow EG, Thiffault I, Repnikova EA, Cooley LD, Alaimo JT, Porath B, Herriges JC, Saunders CJ, Farooqi MS. Factors Affecting Migration to GRCh38 in Laboratories Performing Clinical Next-Generation Sequencing. J Mol Diagn 2021; 23:651-657. [PMID: 33631350 DOI: 10.1016/j.jmoldx.2021.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/30/2021] [Accepted: 02/11/2021] [Indexed: 12/15/2022] Open
Abstract
The most recent build of the human reference genome, GRCh38, was released in 2013. However, many laboratories performing next-generation sequencing (NGS) continue to align to GRCh37. Our aim was to assess the number of clinical diagnostic laboratories that have migrated to GRCh38 and discern factors impeding migration for those still using GRCh37. A brief, five-question survey was electronically administered to 71 clinical laboratories offering constitutional NGS-based testing and analyzed categorically. Twenty-eight responses meeting inclusion criteria were collected from 24 academic and four commercial diagnostic laboratories. Most of these (14; 50%) reported volumes of <500 NGS-based tests in 2019. Only two respondents (7%) had already migrated entirely to GRCh38; most laboratories (15; 54%) had no plans to migrate. The two prevailing reasons for not yet migrating were as follows: laboratories did not feel the benefits outweighed the time and monetary costs (14; 50%); and laboratories had insufficient staff to facilitate the migration (12; 43%). These data, although limited, suggest most clinical molecular laboratories are reluctant to migrate to GRCh38, and there appear to be multiple obstacles to overcome before GRCh38 is widely adopted.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri
| | - Maxime Cadieux-Dion
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri
| | - Byunggil Yoo
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri
| | - Neil Miller
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Ana S A Cohen
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Lee Zellmer
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri
| | - Lei Zhang
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Emily G Farrow
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, Missouri
| | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Elena A Repnikova
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Linda D Cooley
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Binu Porath
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri
| | - John C Herriges
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Midhat S Farooqi
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri.
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9
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Alaimo JT, Saunders CJ. Big Data Strikes Again: Future Utilization of the UK Biobank as a Resource for Clinical Laboratories. Clin Chem 2021; 67:932-934. [PMID: 33550402 DOI: 10.1093/clinchem/hvab005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 11/13/2022]
Affiliation(s)
- Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA.,University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA.,University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA
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10
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Hartin SN, Means JC, Alaimo JT, Younger ST. Expediting rare disease diagnosis: a call to bridge the gap between clinical and functional genomics. Mol Med 2020; 26:117. [PMID: 33238891 PMCID: PMC7691058 DOI: 10.1186/s10020-020-00244-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 07/27/2020] [Accepted: 11/18/2020] [Indexed: 11/10/2022] Open
Abstract
Approximately 400 million people throughout the world suffer from a rare disease. Although advances in whole exome and whole genome sequencing have greatly facilitated rare disease diagnosis, overall diagnostic rates remain below 50%. Furthermore, in cases where accurate diagnosis is achieved the process requires an average of 4.8 years. Reducing the time required for disease diagnosis is among the most critical needs of patients impacted by a rare disease. In this perspective we describe current challenges associated with rare disease diagnosis and discuss several cutting-edge functional genomic screening technologies that have the potential to rapidly accelerate the process of distinguishing pathogenic variants that lead to disease.
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Affiliation(s)
- Samantha N Hartin
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - John C Means
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Joseph T Alaimo
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64110, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Scott T Younger
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA. .,Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA. .,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64110, USA. .,Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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11
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Drivas TG, Li D, Nair D, Alaimo JT, Alders M, Altmüller J, Barakat TS, Bebin EM, Bertsch NL, Blackburn PR, Blesson A, Bouman AM, Brockmann K, Brunelle P, Burmeister M, Cooper GM, Denecke J, Dieux-Coëslier A, Dubbs H, Ferrer A, Gal D, Bartik LE, Gunderson LB, Hasadsri L, Jain M, Karimov C, Keena B, Klee EW, Kloth K, Lace B, Macchiaiolo M, Marcadier JL, Milunsky JM, Napier MP, Ortiz-Gonzalez XR, Pichurin PN, Pinner J, Powis Z, Prasad C, Radio FC, Rasmussen KJ, Renaud DL, Rush ET, Saunders C, Selcen D, Seman AR, Shinde DN, Smith ED, Smol T, Snijders Blok L, Stoler JM, Tang S, Tartaglia M, Thompson ML, van de Kamp JM, Wang J, Weise D, Weiss K, Woitschach R, Wollnik B, Yan H, Zackai EH, Zampino G, Campeau P, Bhoj E. A second cohort of CHD3 patients expands the molecular mechanisms known to cause Snijders Blok-Campeau syndrome. Eur J Hum Genet 2020; 28:1422-1431. [PMID: 32483341 PMCID: PMC7608102 DOI: 10.1038/s41431-020-0654-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 02/27/2020] [Accepted: 04/28/2020] [Indexed: 01/18/2023] Open
Abstract
There has been one previous report of a cohort of patients with variants in Chromodomain Helicase DNA-binding 3 (CHD3), now recognized as Snijders Blok-Campeau syndrome. However, with only three previously-reported patients with variants outside the ATPase/helicase domain, it was unclear if variants outside of this domain caused a clinically similar phenotype. We have analyzed 24 new patients with CHD3 variants, including nine outside the ATPase/helicase domain. All patients were detected with unbiased molecular genetic methods. There is not a significant difference in the clinical or facial features of patients with variants in or outside this domain. These additional patients further expand the clinical and molecular data associated with CHD3 variants. Importantly we conclude that there is not a significant difference in the phenotypic features of patients with various molecular disruptions, including whole gene deletions and duplications, and missense variants outside the ATPase/helicase domain. This data will aid both clinical geneticists and molecular geneticists in the diagnosis of this emerging syndrome.
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Affiliation(s)
- Theodore G. Drivas
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Dong Li
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Divya Nair
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Joseph T. Alaimo
- grid.266756.60000 0001 2179 926XUniversity of Missouri-Kansas City, School of Medicine, Kansas City, MO USA ,grid.239559.10000 0004 0415 5050Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO USA
| | - Mariëlle Alders
- grid.7177.60000000084992262Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Janine Altmüller
- grid.6190.e0000 0000 8580 3777Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Tahsin Stefan Barakat
- grid.5645.2000000040459992XDepartment of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - E. Martina Bebin
- grid.265892.20000000106344187University of Alabama at Birmingham, Birmingham, AL USA
| | - Nicole L. Bertsch
- grid.66875.3a0000 0004 0459 167XDepartment of Clinical Genomics, Mayo Clinic, Rochester, MN 55905 USA
| | - Patrick R. Blackburn
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - Alyssa Blesson
- grid.240023.70000 0004 0427 667XDepartment of Bone and Osteogenesis Imperfecta, Kennedy Krieger Institute, Baltimore, MD 21205 USA
| | - Arjan M. Bouman
- grid.5645.2000000040459992XDepartment of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Knut Brockmann
- grid.411984.10000 0001 0482 5331Pediatrics and Pediatric Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Perrine Brunelle
- grid.503422.20000 0001 2242 6780Univ. Lille, EA 7364—RADEME—Maladies RAres du DEveloppement embryonnaire et du MEtabolisme, F-59000 Lille, France ,grid.410463.40000 0004 0471 8845CHU Lille, Institut de Génétique Médicale, F-59000 Lille, France
| | - Margit Burmeister
- grid.214458.e0000000086837370Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI USA ,grid.214458.e0000000086837370Departments of Computational Medicine & Bioinformatics, Psychiatry and Human Genetics, University of Michigan, Ann Arbor, MI USA
| | - Gregory M. Cooper
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jonas Denecke
- grid.13648.380000 0001 2180 3484Department of Pediatrics, University Medical Center Hamburg, Eppendorf, Germany
| | - Anne Dieux-Coëslier
- grid.503422.20000 0001 2242 6780Univ. Lille, EA 7364—RADEME—Maladies RAres du DEveloppement embryonnaire et du MEtabolisme, F-59000 Lille, France ,grid.410463.40000 0004 0471 8845CHU Lille, Institut de Génétique Médicale, F-59000 Lille, France
| | - Holly Dubbs
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Alejandro Ferrer
- grid.66875.3a0000 0004 0459 167XCenter for Individualized Medicine, Mayo Clinic, Rochester, MN USA
| | - Danna Gal
- grid.6451.60000000121102151The Ruth and Bruce Rappaport Faculty of Medicine, Technion—Israel Institute of Technology, Haifa, 3525433 Israel
| | - Lauren E. Bartik
- grid.266756.60000 0001 2179 926XUniversity of Missouri-Kansas City, School of Medicine, Kansas City, MO USA ,grid.239559.10000 0004 0415 5050Division of Clinical Genetics, Department of Pediatrics, Children’s Mercy Hospital, Kansas City, MO USA
| | - Lauren B. Gunderson
- grid.66875.3a0000 0004 0459 167XDepartment of Clinical Genomics, Mayo Clinic, Rochester, MN 55905 USA
| | - Linda Hasadsri
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - Mahim Jain
- grid.240023.70000 0004 0427 667XDepartment of Bone and Osteogenesis Imperfecta, Kennedy Krieger Institute, Baltimore, MD 21205 USA
| | - Catherine Karimov
- Department of Medical Genetics, , Children’s Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA 90027 USA
| | - Beth Keena
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Eric W. Klee
- grid.66875.3a0000 0004 0459 167XCenter for Individualized Medicine, Mayo Clinic, Rochester, MN USA
| | - Katja Kloth
- grid.13648.380000 0001 2180 3484Institute of Human Genetics, University Medical Center Hamburg, Eppendorf, Germany
| | - Baiba Lace
- grid.411081.d0000 0000 9471 1794Clinical Geneticist Medical Genetics Department, CHUQ-CHUL, Quebec, Canada
| | - Marina Macchiaiolo
- grid.414125.70000 0001 0727 6809Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Julien L. Marcadier
- grid.454131.6Division of Medical Genetics, Alberta Children’s Hospital, Calgary, AB Canada
| | | | - Melanie P. Napier
- grid.39381.300000 0004 1936 8884Department of Pediatrics London Health Sciences Centre and Western University, London, ON Canada
| | - Xilma R. Ortiz-Gonzalez
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Neurology, Pereleman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Pavel N. Pichurin
- grid.66875.3a0000 0004 0459 167XDepartment of Clinical Genomics, Mayo Clinic, Rochester, MN 55905 USA
| | - Jason Pinner
- grid.414009.80000 0001 1282 788XCentre for Clinical Genetics, Sydney Children’s Hospital, Sydney, Australia
| | - Zoe Powis
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA USA
| | - Chitra Prasad
- grid.39381.300000 0004 1936 8884Department of Pediatrics London Health Sciences Centre and Western University, London, ON Canada
| | - Francesca Clementina Radio
- grid.414125.70000 0001 0727 6809Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Kristen J. Rasmussen
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - Deborah L. Renaud
- grid.66875.3a0000 0004 0459 167XDepartment of Clinical Genomics, Mayo Clinic, Rochester, MN 55905 USA
| | - Eric T. Rush
- grid.266756.60000 0001 2179 926XUniversity of Missouri-Kansas City, School of Medicine, Kansas City, MO USA ,grid.239559.10000 0004 0415 5050Division of Clinical Genetics, Department of Pediatrics, Children’s Mercy Hospital, Kansas City, MO USA ,grid.412016.00000 0001 2177 6375Division of Endocrinology, Metabolism, Osteoporosis, and Genetics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS USA
| | - Carol Saunders
- grid.266756.60000 0001 2179 926XUniversity of Missouri-Kansas City, School of Medicine, Kansas City, MO USA ,grid.239559.10000 0004 0415 5050Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO USA ,grid.239559.10000 0004 0415 5050Division of Clinical Genetics, Department of Pediatrics, Children’s Mercy Hospital, Kansas City, MO USA
| | - Duygu Selcen
- grid.66875.3a0000 0004 0459 167XDepartment of Neurology, Mayo Clinic, Rochester, MN 55905 USA
| | - Ann R. Seman
- grid.2515.30000 0004 0378 8438Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA USA
| | | | - Erica D. Smith
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA USA
| | - Thomas Smol
- grid.503422.20000 0001 2242 6780Univ. Lille, EA 7364—RADEME—Maladies RAres du DEveloppement embryonnaire et du MEtabolisme, F-59000 Lille, France ,grid.410463.40000 0004 0471 8845CHU Lille, Institut de Génétique Médicale, F-59000 Lille, France
| | - Lot Snijders Blok
- grid.10417.330000 0004 0444 9382Human Genetics Department, Radboud University Medical Center, Nijmegen, the Netherlands ,grid.419550.c0000 0004 0501 3839Language & Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Joan M. Stoler
- grid.2515.30000 0004 0378 8438Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA USA
| | - Sha Tang
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA USA
| | - Marco Tartaglia
- grid.414125.70000 0001 0727 6809Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michelle L. Thompson
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jiddeke M. van de Kamp
- grid.12380.380000 0004 1754 9227Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jingmin Wang
- grid.411472.50000 0004 1764 1621Department of Pediatrics, Peking University First Hospital, Beijing, China ,grid.11135.370000 0001 2256 9319Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing, China
| | - Dagmar Weise
- grid.411984.10000 0001 0482 5331Pediatrics and Pediatric Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Karin Weiss
- grid.413731.30000 0000 9950 8111The Genetics Institute, Rambam Health Care Campus, 3109601 Haifa, Israel
| | - Rixa Woitschach
- grid.13648.380000 0001 2180 3484Institute of Human Genetics, University Medical Center Hamburg, Eppendorf, Germany
| | - Bernd Wollnik
- grid.411984.10000 0001 0482 5331Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany ,grid.7450.60000 0001 2364 4210Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37073 Göttingen, Germany
| | - Huifang Yan
- grid.214458.e0000000086837370Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI USA ,grid.411472.50000 0004 1764 1621Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Elaine H. Zackai
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Giuseppe Zampino
- grid.414603.4Center for Rare Disease and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Philippe Campeau
- grid.14848.310000 0001 2292 3357Department of Pediatrics, Medical Genetics Division, University of Montreal, Montreal, Canada
| | - Elizabeth Bhoj
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
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12
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Alaimo JT, Glinton KE, Liu N, Xiao J, Yang Y, Reid Sutton V, Elsea SH. Integrated analysis of metabolomic profiling and exome data supplements sequence variant interpretation, classification, and diagnosis. Genet Med 2020; 22:1560-1566. [PMID: 32439973 PMCID: PMC7483344 DOI: 10.1038/s41436-020-0827-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE A primary barrier to improving exome sequencing diagnostic rates is the interpretation of variants of uncertain clinical significance. We aimed to determine the contribution of integrated untargeted metabolomics in the analysis of exome sequencing data by retrospective analysis of patients evaluated by both exome sequencing and untargeted metabolomics within the same clinical laboratory. METHODS Exome sequencing and untargeted metabolomic data were collected and analyzed for 170 patients. Pathogenic variants, likely pathogenic variants, and variants of uncertain significance in genes associated with a biochemical phenotype were extracted. Metabolomic data were evaluated to determine if these variants resulted in biochemical abnormalities that could be used to support their interpretation using current American College of Genetics and Genomics (ACMG) guidelines. RESULTS Metabolomic data contributed to the interpretation of variants in 74 individuals (43.5%) over 73 different genes. The data allowed for the reclassification of 9 variants as likely benign, 15 variants as likely pathogenic, and 3 variants as pathogenic. Metabolomic data confirmed a clinical diagnosis in 21 cases, for a diagnostic rate of 12.3% in this population. CONCLUSION Untargeted metabolomics can serve as a useful adjunct to exome sequencing by providing valuable functional data that may not otherwise be clinically available, resulting in improved variant classification.
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Affiliation(s)
- Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Kevin E Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Jing Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
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13
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Chilton I, Okur V, Vitiello G, Selicorni A, Mariani M, Goldenberg A, Husson T, Campion D, Lichtenbelt KD, van Gassen K, Steinraths M, Rice J, Roeder ER, Littlejohn RO, Srour M, Sebire G, Accogli A, Héron D, Heide S, Nava C, Depienne C, Larson A, Niyazov D, Azage M, Hoganson G, Burton J, Rush ET, Jenkins JL, Saunders CJ, Thiffault I, Alaimo JT, Fleischer J, Groepper D, Gripp KW, Chung WK. De novo heterozygous missense and loss-of-function variants in CDC42BPB are associated with a neurodevelopmental phenotype. Am J Med Genet A 2020; 182:962-973. [PMID: 32031333 DOI: 10.1002/ajmg.a.61505] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 10/08/2019] [Revised: 12/30/2019] [Accepted: 01/12/2020] [Indexed: 11/08/2022]
Abstract
CDC42BPB encodes MRCKβ (myotonic dystrophy-related Cdc42-binding kinase beta), a serine/threonine protein kinase, and a downstream effector of CDC42, which has recently been associated with Takenouchi-Kosaki syndrome, an autosomal dominant neurodevelopmental disorder. We identified 12 heterozygous predicted deleterious variants in CDC42BPB (9 missense, 2 frameshift, and 1 nonsense) in 14 unrelated individuals (confirmed de novo in 11/14) with neurodevelopmental disorders including developmental delay/intellectual disability, autism, hypotonia, and structural brain abnormalities including cerebellar vermis hypoplasia and agenesis/hypoplasia of the corpus callosum. The frameshift and nonsense variants in CDC42BPB are expected to be gene-disrupting and lead to haploinsufficiency via nonsense-mediated decay. All missense variants are located in highly conserved and functionally important protein domains/regions: 3 are found in the protein kinase domain, 2 are in the citron homology domain, and 4 in a 20-amino acid sequence between 2 coiled-coil regions, 2 of which are recurrent. Future studies will help to delineate the natural history and to elucidate the underlying biological mechanisms of the missense variants leading to the neurodevelopmental and behavioral phenotypes.
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Affiliation(s)
- Ilana Chilton
- Department of Pediatrics, Columbia University, New York, New York
| | - Volkan Okur
- Department of Pediatrics, Columbia University, New York, New York
| | | | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Sant'Anna Hospital, Como, Italy
| | - Milena Mariani
- Pediatric Department, ASST Lariana, Sant'Anna Hospital, Como, Italy
| | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Thomas Husson
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Dominique Campion
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Klaske D Lichtenbelt
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Jennifer Rice
- Department of Medical Genetics, University of British Columbia, Canada
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | | | - Myriam Srour
- McGill University Health Center, Montreal Children's Hospital, Canada
| | - Guillaume Sebire
- McGill University Health Center, Montreal Children's Hospital, Canada
| | - Andrea Accogli
- Medical Genetics Unit, IRCCS Ospedale Policlinico San Martino and DINOGMI-Università degli Studi di Genova, Genoa, Italy
| | - Delphine Héron
- Département de Génétique et de Cytogénétique; Centre de Référence Déficiences Intellectuelles de Causes Rares; GRC UPMC, Déficience Intellectuelle et Autisme, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Solveig Heide
- Département de Génétique et de Cytogénétique; Centre de Référence Déficiences Intellectuelles de Causes Rares; GRC UPMC, Déficience Intellectuelle et Autisme, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Caroline Nava
- Département de Génétique et de Cytogénétique; Centre de Référence Déficiences Intellectuelles de Causes Rares; GRC UPMC, Déficience Intellectuelle et Autisme, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.,INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, Paris, France
| | - Christel Depienne
- INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, Paris, France.,Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Austin Larson
- Department of Pediatrics-Clinical Genetics and Metabolism, University of Colorado, Colorado, USA
| | | | - Meron Azage
- Department of Genetics, Ochsner Health System, Louisiana
| | - George Hoganson
- Department of Pediatrics, University of Illinois, Chicago, Illinois, 60612, USA
| | - Jennifer Burton
- Department of Pediatrics, University of Illinois, Chicago, Illinois, 60612, USA
| | - Eric T Rush
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri
| | - Janda L Jenkins
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | - Joseph T Alaimo
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | - Julie Fleischer
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, Illinois, 62702, USA
| | - Daniel Groepper
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, Illinois, 62702, USA
| | - Karen W Gripp
- Division of Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware, 19803, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York.,Department of Medicine, Columbia University, New York, New York
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14
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Alston CL, Veling MT, Heidler J, Taylor LS, Alaimo JT, Sung AY, He L, Hopton S, Broomfield A, Pavaine J, Diaz J, Leon E, Wolf P, McFarland R, Prokisch H, Wortmann SB, Bonnen PE, Wittig I, Pagliarini DJ, Taylor RW. Pathogenic Bi-allelic Mutations in NDUFAF8 Cause Leigh Syndrome with an Isolated Complex I Deficiency. Am J Hum Genet 2020; 106:92-101. [PMID: 31866046 PMCID: PMC7042492 DOI: 10.1016/j.ajhg.2019.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/02/2019] [Indexed: 12/25/2022] Open
Abstract
Leigh syndrome is one of the most common neurological phenotypes observed in pediatric mitochondrial disease presentations. It is characterized by symmetrical lesions found on neuroimaging in the basal ganglia, thalamus, and brainstem and by a loss of motor skills and delayed developmental milestones. Genetic diagnosis of Leigh syndrome is complicated on account of the vast genetic heterogeneity with >75 candidate disease-associated genes having been reported to date. Candidate genes are still emerging, being identified when “omics” tools (genomics, proteomics, and transcriptomics) are applied to manipulated cell lines and cohorts of clinically characterized individuals who lack a genetic diagnosis. NDUFAF8 is one such protein; it has been found to interact with the well-characterized complex I (CI) assembly factor NDUFAF5 in a large-scale protein-protein interaction screen. Diagnostic next-generation sequencing has identified three unrelated pediatric subjects, each with a clinical diagnosis of Leigh syndrome, who harbor bi-allelic pathogenic variants in NDUFAF8. These variants include a recurrent splicing variant that was initially overlooked due to its deep-intronic location. Subject fibroblasts were found to express a complex I deficiency, and lentiviral transduction with wild-type NDUFAF8-cDNA ameliorated both the assembly defect and the biochemical deficiency. Complexome profiling of subject fibroblasts demonstrated a complex I assembly defect, and the stalled assembly intermediates corroborate the role of NDUFAF8 in early complex I assembly. This report serves to expand the genetic heterogeneity associated with Leigh syndrome and to validate the clinical utility of orphan protein characterization. We also highlight the importance of evaluating intronic sequence when a single, definitively pathogenic variant is identified during diagnostic testing.
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15
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Vetrini F, McKee S, Rosenfeld JA, Suri M, Lewis AM, Nugent KM, Roeder E, Littlejohn RO, Holder S, Zhu W, Alaimo JT, Graham B, Harris JM, Gibson JB, Pastore M, McBride KL, Komara M, Al-Gazali L, Al Shamsi A, Fanning EA, Wierenga KJ, Scott DA, Ben-Neriah Z, Meiner V, Cassuto H, Elpeleg O, Lloyd Holder J, Burrage LC, Seaver LH, Van Maldergem L, Mahida S, Soul JS, Marlatt M, Matyakhina L, Vogt J, Gold JA, Park SM, Varghese V, Lampe AK, Kumar A, Lees M, Holder-Espinasse M, McConnell V, Bernhard B, Blair E, Harrison V, Muzny DM, Gibbs RA, Elsea SH, Posey JE, Bi W, Lalani S, Xia F, Yang Y, Eng CM, Lupski JR, Liu P. Correction to: De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. Genome Med 2019; 11:16. [PMID: 30909959 PMCID: PMC6434874 DOI: 10.1186/s13073-019-0630-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 11/23/2022] Open
Affiliation(s)
- Francesco Vetrini
- Baylor Genetics, Houston, TX, 77021, USA.,Present address: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mohnish Suri
- Nottingham Genetics Service, Nottingham City Hospital, Nottingham, UK
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kimberly Margaret Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Rebecca O Littlejohn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Sue Holder
- North West Thames Regional Genetics Service, 759 Northwick Park Hospital, London, UK
| | | | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brett Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jill M Harris
- Dell Children's Medical Group, Austin, TX, 78723, USA
| | | | - Matthew Pastore
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital; and Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH, 43205, USA
| | - Kim L McBride
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital; and Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH, 43205, USA
| | - Makanko Komara
- Department of Pediatrics, College of Medicine & Health Sciences, United Arab University, Al Ain, UAE
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine & Health Sciences, United Arab University, Al Ain, UAE
| | | | - Elizabeth A Fanning
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Klaas J Wierenga
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Present address: Mayo Clinic Florida, Department of Clinical Genomics, Jacksonville, FL, 32224, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ziva Ben-Neriah
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, 91120, Jerusalem, Israel
| | - J Lloyd Holder
- Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurie H Seaver
- Department of Pediatrics, University of Hawaii, Honolulu, HI, 96826, USA
| | | | - Sonal Mahida
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | - Janet S Soul
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | - Margaret Marlatt
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | | | - Julie Vogt
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - June-Anne Gold
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Soo-Mi Park
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Vinod Varghese
- All-Wales Medical Genetics Service, University Hospital of Wales, Cardiff, UK
| | - Anne K Lampe
- South East of Scotland Clinical Genetic Service, Western General Hospital, Edinburgh, UK
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | - Melissa Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | | | - Vivienne McConnell
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Birgitta Bernhard
- North West Thames Regional Genetics Service, 759 Northwick Park Hospital, London, UK
| | - Ed Blair
- Oxford Regional Genetics Service, Oxford University Hospitals, Oxford, UK
| | - Victoria Harrison
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sarah H Elsea
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Weimin Bi
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema Lalani
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Fan Xia
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yaping Yang
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christine M Eng
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Pengfei Liu
- Baylor Genetics, Houston, TX, 77021, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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16
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Le TN, Williams SR, Alaimo JT, Elsea SH. Genotype and phenotype correlation in 103 individuals with 2q37 deletion syndrome reveals incomplete penetrance and supports HDAC4 as the primary genetic contributor. Am J Med Genet A 2019; 179:782-791. [PMID: 30848064 DOI: 10.1002/ajmg.a.61089] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 01/02/2019] [Accepted: 02/05/2019] [Indexed: 12/11/2022]
Abstract
The 2q37 deletion syndrome, also described in the literature as brachydactyly-mental retardation syndrome (MIM 600430), is caused by deletion or haploinsufficiency of the HDAC4 gene, which encodes the histone deacetylase 4 protein. Although the most commonly described hallmark features of the 2q37 deletion syndrome include brachydactyly type E, developmental delay, obesity, autistic features, and craniofacial or skeletal dysmorphism, a literature review of 101 published cases plus two newly reported individuals indicates that there is a high degree of variability in the presence of some of the features that are considered the most characteristic of the syndrome: overweight and obesity (34%), cognitive-behavioral issues (79%), dysmorphic craniofacial features (86%), and type E brachydactyly (48%). These features overlap with other neurodevelopmental conditions, including Smith-Magenis syndrome (SMS), and may be incompletely penetrant or demonstrate variable expressivity, depending on the specific chromosomal anomaly. With the advent of fluorescence in situ hybridization (FISH), array-based comparative genomic hybridization, and next-generation DNA sequencing, more detailed molecular diagnoses are possible than in years past, enabling refined characterization of the genotype-phenotype correlation for subjects with 2q37 deletions. In addition, investigations into molecular and gene expression networks are expanding in neurodevelopmental conditions, and we surveyed HDAC4 downstream gene expression by quantitative real-time polymerase chain reaction, further implicating HDAC4 in its role in the regulation of RAI1. Correlation of clinical data defining the impact on downstream gene expression and the potential clinical associations across neurodevelopment will improve our understanding of these complex conditions and potentially lead to common therapeutic approaches.
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Affiliation(s)
- Trang N Le
- Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, Virginia.,Department of Internal Medicine, Division of Endocrinology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Stephen R Williams
- Department of Neurology, University of Virginia, Charlottesville, Virginia
| | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Sarah H Elsea
- Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, Virginia.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
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17
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Vetrini F, McKee S, Rosenfeld JA, Suri M, Lewis AM, Nugent KM, Roeder E, Littlejohn RO, Holder S, Zhu W, Alaimo JT, Graham B, Harris JM, Gibson JB, Pastore M, McBride KL, Komara M, Al-Gazali L, Al Shamsi A, Fanning EA, Wierenga KJ, Scott DA, Ben-Neriah Z, Meiner V, Cassuto H, Elpeleg O, Holder JL, Burrage LC, Seaver LH, Van Maldergem L, Mahida S, Soul JS, Marlatt M, Matyakhina L, Vogt J, Gold JA, Park SM, Varghese V, Lampe AK, Kumar A, Lees M, Holder-Espinasse M, McConnell V, Bernhard B, Blair E, Harrison V, Muzny DM, Gibbs RA, Elsea SH, Posey JE, Bi W, Lalani S, Xia F, Yang Y, Eng CM, Lupski JR, Liu P. De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. Genome Med 2019; 11:12. [PMID: 30819258 PMCID: PMC6393995 DOI: 10.1186/s13073-019-0623-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 10/27/2018] [Accepted: 02/15/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Neurodevelopmental disorders are genetically and phenotypically heterogeneous encompassing developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), structural brain abnormalities, and neurological manifestations with variants in a large number of genes (hundreds) associated. To date, a few de novo mutations potentially disrupting TCF20 function in patients with ID, ASD, and hypotonia have been reported. TCF20 encodes a transcriptional co-regulator structurally related to RAI1, the dosage-sensitive gene responsible for Smith-Magenis syndrome (deletion/haploinsufficiency) and Potocki-Lupski syndrome (duplication/triplosensitivity). METHODS Genome-wide analyses by exome sequencing (ES) and chromosomal microarray analysis (CMA) identified individuals with heterozygous, likely damaging, loss-of-function alleles in TCF20. We implemented further molecular and clinical analyses to determine the inheritance of the pathogenic variant alleles and studied the spectrum of phenotypes. RESULTS We report 25 unique inactivating single nucleotide variants/indels (1 missense, 1 canonical splice-site variant, 18 frameshift, and 5 nonsense) and 4 deletions of TCF20. The pathogenic variants were detected in 32 patients and 4 affected parents from 31 unrelated families. Among cases with available parental samples, the variants were de novo in 20 instances and inherited from 4 symptomatic parents in 5, including in one set of monozygotic twins. Two pathogenic loss-of-function variants were recurrent in unrelated families. Patients presented with a phenotype characterized by developmental delay, intellectual disability, hypotonia, variable dysmorphic features, movement disorders, and sleep disturbances. CONCLUSIONS TCF20 pathogenic variants are associated with a novel syndrome manifesting clinical characteristics similar to those observed in Smith-Magenis syndrome. Together with previously described cases, the clinical entity of TCF20-associated neurodevelopmental disorders (TAND) emerges from a genotype-driven perspective.
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Affiliation(s)
- Francesco Vetrini
- Baylor Genetics, Houston, TX, 77021, USA.,Present address: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mohnish Suri
- Nottingham Genetics Service, Nottingham City Hospital, Nottingham, UK
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kimberly Margaret Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Rebecca O Littlejohn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Sue Holder
- North West Thames Regional Genetics Service, 759 Northwick Park Hospital, London, UK
| | | | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brett Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jill M Harris
- Dell Children's Medical Group, Austin, TX, 78723, USA
| | | | - Matthew Pastore
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital; and Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH, 43205, USA
| | - Kim L McBride
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital; and Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH, 43205, USA
| | - Makanko Komara
- Department of Pediatrics, College of Medicine & Health Sciences, United Arab University, Al Ain, UAE
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine & Health Sciences, United Arab University, Al Ain, UAE
| | | | - Elizabeth A Fanning
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Klaas J Wierenga
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Present address: Mayo Clinic Florida, Department of Clinical Genomics, Jacksonville, FL, 32224, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ziva Ben-Neriah
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, 91120, Jerusalem, Israel
| | - J Lloyd Holder
- Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurie H Seaver
- Department of Pediatrics, University of Hawaii, Honolulu, HI, 96826, USA
| | | | - Sonal Mahida
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | - Janet S Soul
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | - Margaret Marlatt
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | | | - Julie Vogt
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners; and Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - June-Anne Gold
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Soo-Mi Park
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Vinod Varghese
- All-Wales Medical Genetics Service, University Hospital of Wales, Cardiff, UK
| | - Anne K Lampe
- South East of Scotland Clinical Genetic Service, Western General Hospital, Edinburgh, UK
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | - Melissa Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | | | - Vivienne McConnell
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Birgitta Bernhard
- North West Thames Regional Genetics Service, 759 Northwick Park Hospital, London, UK
| | - Ed Blair
- Oxford Regional Genetics Service, Oxford University Hospitals, Oxford, UK
| | - Victoria Harrison
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sarah H Elsea
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Weimin Bi
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema Lalani
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Fan Xia
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yaping Yang
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christine M Eng
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Pengfei Liu
- Baylor Genetics, Houston, TX, 77021, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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18
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Abstract
The advent of next-generation sequencing has enabled clinicians to assess many genes simultaneously and at high resolution. This is advantageous for diagnosing patients in whom a genetic disorder is suspected but who have a nonspecific or atypical phenotype or when the disorder has significant genetic heterogeneity. Herein, we describe common clinical applications of next-generation sequencing technology, as well as their respective benefits and limitations. We then discuss key considerations of variant interpretation and reporting, clinical utility, pre- and posttest genetic counseling, and ethical challenges. We will present these topics with an emphasis on their applicability to the reproductive medicine setting.
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Affiliation(s)
- Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Baylor Genetics Laboratory, Baylor College of Medicine, Houston, Texas
| | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Baylor Genetics Laboratory, Baylor College of Medicine, Houston, Texas
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas.
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19
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Alaimo JT, Besse A, Alston CL, Pang K, Appadurai V, Samanta M, Smpokou P, McFarland R, Taylor RW, Bonnen PE. Loss-of-function mutations in ISCA2 disrupt 4Fe-4S cluster machinery and cause a fatal leukodystrophy with hyperglycinemia and mtDNA depletion. Hum Mutat 2018; 39:537-549. [PMID: 29297947 PMCID: PMC5839994 DOI: 10.1002/humu.23396] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 10/10/2016] [Revised: 12/09/2017] [Accepted: 12/27/2017] [Indexed: 12/26/2022]
Abstract
Iron–sulfur (Fe–S) clusters are essential cofactors for proteins that participate in fundamental cellular processes including metabolism, DNA replication and repair, transcriptional regulation, and the mitochondrial electron transport chain (ETC). ISCA2 plays a role in the biogenesis of Fe–S clusters and a recent report described subjects displaying infantile‐onset leukodystrophy due to bi‐allelic mutation of ISCA2. We present two additional unrelated cases, and provide a more complete clinical description that includes hyperglycinemia, leukodystrophy of the brainstem with longitudinally extensive spinal cord involvement, and mtDNA deficiency. Additionally, we characterize the role of ISCA2 in mitochondrial bioenergetics and Fe–S cluster assembly using subject cells and ISCA2 cellular knockdown models. Loss of ISCA2 diminished mitochondrial membrane potential, the mitochondrial network, basal and maximal respiration, ATP production, and activity of ETC complexes II and IV. We specifically tested the impact of loss of ISCA2 on 2Fe–2S proteins versus 4Fe–4S proteins and observed deficits in the functioning of 4Fe–4S but not 2Fe–2S proteins. Together these data indicate loss of ISCA2 impaired function of 4Fe–4S proteins resulting in a fatal encephalopathy accompanied by a relatively unusual combination of features including mtDNA depletion alongside complex II deficiency and hyperglycinemia that may facilitate diagnosis of ISCA2 deficiency patients.
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Affiliation(s)
- Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Arnaud Besse
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Ki Pang
- Royal Victoria Infirmary, Great North Children's Hospital, Newcastle upon Tyne, Newcastle Upon Tyne, UK
| | - Vivek Appadurai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Monisha Samanta
- Division of Genetics & Metabolism, Children's National Health System, Washington, District of Columbia
| | - Patroula Smpokou
- Division of Genetics & Metabolism, Children's National Health System, Washington, District of Columbia.,Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Penelope E Bonnen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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20
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Chen L, Jensik PJ, Alaimo JT, Walkiewicz M, Berger S, Roeder E, Faqeih EA, Bernstein JA, Smith ACM, Mullegama SV, Saffen DW, Elsea SH. Functional analysis of novel DEAF1 variants identified through clinical exome sequencing expands DEAF1-associated neurodevelopmental disorder (DAND) phenotype. Hum Mutat 2017; 38:1774-1785. [PMID: 28940898 DOI: 10.1002/humu.23339] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 05/07/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 11/06/2022]
Abstract
Deformed epidermal autoregulatory factor-1 (DEAF1), a transcription factor essential for central nervous system and early embryonic development, has recently been implicated in a series of intellectual disability-related neurodevelopmental anomalies termed, in this study, as DEAF1-associated neurodevelopmental disorder (DAND). We identified six potentially deleterious DEAF1 variants in a cohort of individuals with DAND via clinical exome sequencing (CES) and in silico analysis, including two novel de novo variants: missense variant c.634G > A p.Gly212Ser in the SAND domain and deletion variant c.913_915del p.Lys305del in the NLS domain, as well as c.676C > T p.Arg226Trp, c.700T > A p.Trp234Arg, c.737G > C p.Arg246Thr, and c.791A > C p.Gln264Pro. Luciferase reporter, immunofluorescence staining, and electrophoretic mobility shift assays revealed that these variants had decreased transcriptional repression activity at the DEAF1 promoter and reduced affinity to consensus DEAF1 DNA binding sequences. In addition, c.913_915del p.K305del localized primarily to the cytoplasm and interacted with wild-type DEAF1. Our results demonstrate that variants located within the SAND or NLS domains significantly reduce DEAF1 transcriptional regulatory activities and are thus, likely to contribute to the underlying clinical concerns in DAND patients. These findings illustrate the importance of experimental characterization of variants with uncertain significance identified by CES to assess their potential clinical significance and possible use in diagnosis.
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Affiliation(s)
- Li Chen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Philip J Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois
| | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics Laboratory, Houston, Texas
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics Laboratory, Houston, Texas
| | - Seth Berger
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Departments of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | - Eissa A Faqeih
- Department of Pediatrics Subspecialty, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Ann C M Smith
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - David W Saffen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Institutes of Brain Science, Fudan University, Shanghai, China.,State Key Laboratory for Medical Neurobiology, Fudan University, Shanghai, China
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics Laboratory, Houston, Texas
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21
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Perkins T, Rosenberg JM, Le Coz C, Alaimo JT, Trofa M, Mullegama SV, Antaya RJ, Jyonouchi S, Elsea SH, Utz PJ, Meffre E, Romberg N. Smith-Magenis Syndrome Patients Often Display Antibody Deficiency but Not Other Immune Pathologies. J Allergy Clin Immunol Pract 2017; 5:1344-1350.e3. [PMID: 28286158 PMCID: PMC5591748 DOI: 10.1016/j.jaip.2017.01.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/03/2017] [Accepted: 01/21/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND Smith-Magenis syndrome (SMS) is a complex neurobehavioral disorder associated with recurrent otitis. Most SMS cases result from heterozygous interstitial chromosome 17p11.2 deletions that encompass not only the intellectual disability gene retinoic acid-induced 1 but also other genes associated with immunodeficiency, autoimmunity, and/or malignancy. OBJECTIVES The goals of this study were to describe the immunological consequence of 17p11.2 deletions by determining the prevalence of immunological diseases in subjects with SMS and by assessing their immune systems via laboratory methods. METHODS We assessed clinical histories of 76 subjects with SMS with heterozygous 17p11.2 deletions and performed in-depth immunological testing on 25 representative cohort members. Laboratory testing included determination of serum antibody concentrations, vaccine titers, and lymphocyte subset frequencies. Detailed reactivity profiles of SMS serum antibodies were performed using custom-made antigen microarrays. RESULTS Of 76 subjects with SMS, 74 reported recurrent infections including otitis (88%), pneumonia (47%), sinusitis (42%), and gastroenteritis (34%). Infections were associated with worsening SMS-related neurobehavioral symptoms. The prevalence of autoimmune and atopic diseases was not increased. Malignancy was not reported. Laboratory evaluation revealed most subjects with SMS to be deficient of isotype-switched memory B cells and many to lack protective antipneumococcal antibodies. SMS antibodies were not more reactive than control antibodies to self-antigens. CONCLUSIONS Patients with SMS with heterozygous 17p.11.2 deletions display an increased susceptibility to sinopulmonary infections, but not to autoimmune, allergic, or malignant diseases. SMS sera display an antibody reactivity profile favoring neither recognition of pathogen-associated antigens nor self-antigens. Prophylactic strategies to prevent infections may also provide neurobehavioral benefits to selected patients with SMS.
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Affiliation(s)
- Tiffany Perkins
- Department of Pediatrics, Yale University School of Medicine, New Haven, Conn
| | - Jacob M Rosenberg
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Carole Le Coz
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Penn
| | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Melissa Trofa
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Penn
| | - Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Richard J Antaya
- Department of Pediatrics, Yale University School of Medicine, New Haven, Conn; Department of Dermatology, Yale University School of Medicine, New Haven, Conn
| | - Soma Jyonouchi
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Penn
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Paul J Utz
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, Conn; Department of Internal Medicine, Yale University School of Medicine, New Haven, Conn
| | - Neil Romberg
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Penn.
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22
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Adkins AE, Hack LM, Bigdeli TB, Williamson VS, McMichael GO, Mamdani M, Edwards AC, Aliev F, Chan RF, Bhandari P, Raabe RC, Alaimo JT, Blackwell GG, Moscati A, Poland RS, Rood B, Patterson DG, Walsh D, Whitfield JB, Zhu G, Montgomery GW, Henders AK, Martin NG, Heath AC, Madden PAF, Frank J, Ridinger M, Wodarz N, Soyka M, Zill P, Ising M, Nöthen MM, Kiefer F, Rietschel M, Gelernter J, Sherva R, Koesterer R, Almasy L, Zhao H, Kranzler HR, Farrer LA, Maher BS, Prescott CA, Dick DM, Bacanu SA, Mathies LD, Davies AG, Vladimirov VI, Grotewiel M, Bowers MS, Bettinger JC, Webb BT, Miles MF, Kendler KS, Riley BP. Genomewide Association Study of Alcohol Dependence Identifies Risk Loci Altering Ethanol-Response Behaviors in Model Organisms. Alcohol Clin Exp Res 2017; 41:911-928. [PMID: 28226201 DOI: 10.1111/acer.13362] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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: 08/20/2016] [Accepted: 02/16/2017] [Indexed: 01/23/2023]
Abstract
BACKGROUND Alcohol dependence (AD) shows evidence for genetic liability, but genes influencing risk remain largely unidentified. METHODS We conducted a genomewide association study in 706 related AD cases and 1,748 unscreened population controls from Ireland. We sought replication in 15,496 samples of European descent. We used model organisms (MOs) to assess the role of orthologous genes in ethanol (EtOH)-response behaviors. We tested 1 primate-specific gene for expression differences in case/control postmortem brain tissue. RESULTS We detected significant association in COL6A3 and suggestive association in 2 previously implicated loci, KLF12 and RYR3. None of these signals are significant in replication. A suggestive signal in the long noncoding RNA LOC339975 is significant in case:control meta-analysis, but not in a population sample. Knockdown of a COL6A3 ortholog in Caenorhabditis elegans reduced EtOH sensitivity. Col6a3 expression correlated with handling-induced convulsions in mice. Loss of function of the KLF12 ortholog in C. elegans impaired development of acute functional tolerance (AFT). Klf12 expression correlated with locomotor activation following EtOH injection in mice. Loss of function of the RYR3 ortholog reduced EtOH sensitivity in C. elegans and rapid tolerance in Drosophila. The ryanodine receptor antagonist dantrolene reduced motivation to self-administer EtOH in rats. Expression of LOC339975 does not differ between cases and controls but is reduced in carriers of the associated rs11726136 allele in nucleus accumbens (NAc). CONCLUSIONS We detect association between AD and COL6A3, KLF12, RYR3, and LOC339975. Despite nonreplication of COL6A3, KLF12, and RYR3 signals, orthologs of these genes influence behavioral response to EtOH in MOs, suggesting potential involvement in human EtOH response and AD liability. The associated LOC339975 allele may influence gene expression in human NAc. Although the functions of long noncoding RNAs are poorly understood, there is mounting evidence implicating these genes in multiple brain functions and disorders.
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Affiliation(s)
- Amy E Adkins
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Laura M Hack
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Tim B Bigdeli
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Vernell S Williamson
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - G Omari McMichael
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Mohammed Mamdani
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Alexis C Edwards
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Fazil Aliev
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Robin F Chan
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Poonam Bhandari
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Richard C Raabe
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Joseph T Alaimo
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - GinaMari G Blackwell
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Arden Moscati
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Ryan S Poland
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Benjamin Rood
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | | | | | | | - John B Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Gu Zhu
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Grant W Montgomery
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Anjali K Henders
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Royal Brisbane and Women's Hospital, Brisbane, Qld, Australia
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Pamela A F Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Monika Ridinger
- Department of Psychiatry, University Hospital Regensburg, University of Regensburg, Regensburg, Germany
| | - Norbert Wodarz
- Department of Psychiatry, University Hospital Regensburg, University of Regensburg, Regensburg, Germany
| | - Michael Soyka
- Privatklinik Meiringen, Meiringen, Switzerland.,Department of Psychiatry and Psychotherapy, University of Munich, Munich, Germany
| | - Peter Zill
- Department of Psychiatry and Psychotherapy, University of Munich, Munich, Germany
| | - Marcus Ising
- Department of Molecular Psychology, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Falk Kiefer
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | | | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.,Department of Neurobiology, Yale University School of Medicine, New Haven, Connecticut.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut.,Department of Psychiatry, VA CT Healthcare Center, West Haven, Connecticut
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
| | - Ryan Koesterer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
| | - Laura Almasy
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut.,Department of Biostatistics, Yale University School of Medicine, New Haven, Connecticut
| | - Henry R Kranzler
- Department of Psychiatry, Treatment Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Philadelphia VA Medical Center, VISN 4 MIRECC, Philadelphia, Pennsylvania
| | - Lindsay A Farrer
- Department of Psychiatry, VA CT Healthcare Center, West Haven, Connecticut.,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts.,Department of Neurology, Boston University School of Medicine, Boston, Massachusetts.,Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts.,Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts.,Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Brion S Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Carol A Prescott
- Department of Psychology, University of Southern California, Los Angeles, California
| | - Danielle M Dick
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Silviu A Bacanu
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Laura D Mathies
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Andrew G Davies
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Vladimir I Vladimirov
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia.,Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, Maryland.,Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Mike Grotewiel
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - M Scott Bowers
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia.,Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Jill C Bettinger
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Bradley T Webb
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Michael F Miles
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia.,Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, Virginia
| | - Kenneth S Kendler
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
| | - Brien P Riley
- Virginia Commonwealth University Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia.,Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia
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23
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Mullegama SV, Alaimo JT, Fountain MD, Burns B, Balog AH, Chen L, Elsea SH. RAI1 Overexpression Promotes Altered Circadian Gene Expression and Dyssomnia in Potocki-Lupski Syndrome. J Pediatr Genet 2017; 6:155-164. [PMID: 28794907 DOI: 10.1055/s-0037-1599147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 11/22/2016] [Accepted: 01/17/2017] [Indexed: 12/22/2022]
Abstract
Retinoic acid induced 1 ( RAI1 ) encodes a dosage-sensitive gene that when haploinsufficient results in Smith-Magenis syndrome (SMS) and when overexpressed results in Potocki-Lupski syndrome (PTLS). Phenotypic and molecular evidence illustrates that haploinsufficiency of RAI1 disrupts circadian rhythm through the dysregulation of the master circadian regulator, circadian locomotor output cycles kaput ( CLOCK) , and other core circadian components, contributing to prominent sleep disturbances in SMS. However, the phenotypic and molecular characterization of sleep features in PTLS has not been elucidated. Using the Pittsburgh Sleep Quality Index (PSQI), caregivers of 15 school-aged children with PTLS reported difficulties in initiating sleep. Indeed, more than 70% of individuals manifested moderate to severe sleep latency, as defined by the PSQI. Moreover, these individuals manifested difficulties in sleep maintenance, with middle of the night and early morning awakenings. When assessing daytime sleepiness through the Epworth Sleepiness Scale, approximately 21% of the individuals manifested excessive daytime somnolence. This indicates that mild dyssomnia characterizes the majority of the sleep phenotype, with occasionally problematic daytime somnolence, a phenotype different than that expressed by individuals with SMS, where daytime sleepiness is a chronic problem. Gene expression analysis of the core circadian machinery in the hypothalamus of the PTLS mouse model ( Rai1 -Tg) found significant dysregulation of the transcriptional activators, Clock and Arntl , and the transcriptional repressors, Per1-3 and Cry1/2 , during both light and dark phases. These findings suggest a partial loss of circadian entrainment typically evoked by environmental photic cues. Examination of circadian clock gene expression in the Rai1- Tg mouse heart, liver, and kidney found unchanged expression of Clock and most of its downstream targets during both light and dark phases, suggesting an asynchronized circadian rhythm. Furthermore, examination of circadian gene expression in synchronized PTLS lymphoblasts revealed reduced transcripts of the Period ( PER1-3 ) family and normal expression of CRY1/2 . The finding that central circadian gene expression was altered while many peripheral circadian components were intact suggests a tissue-specific circadian uncoupling of the circadian machinery due to Rai1 overexpression. Overall, our results demonstrate that overexpression of RAI1 results in sleep deficiencies in individuals with PTLS due to a lack of properly regulated circadian machinery gene expression and highlight the importance of evaluating sleep concerns in individuals with PTLS.
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Affiliation(s)
- Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.,Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California, United States
| | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Michael D Fountain
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Brooke Burns
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States
| | - Amanda Hebert Balog
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States
| | - Li Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.,Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.,Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California, United States.,Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States
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24
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Alaimo JT, Barton LV, Mullegama SV, Wills RD, Foster RH, Elsea SH. Individuals with Smith-Magenis syndrome display profound neurodevelopmental behavioral deficiencies and exhibit food-related behaviors equivalent to Prader-Willi syndrome. Res Dev Disabil 2015; 47:27-38. [PMID: 26323055 DOI: 10.1016/j.ridd.2015.08.011] [Citation(s) in RCA: 18] [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] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 08/08/2015] [Accepted: 08/10/2015] [Indexed: 05/25/2023]
Abstract
Smith-Magenis syndrome (SMS) is a neurodevelopmental disorder associated with intellectual disability, sleep disturbances, early onset obesity and vast behavioral deficits. We used the Behavior Problems Inventory-01 to categorize the frequency and severity of behavioral abnormalities in a SMS cohort relative to individuals with intellectual disability of heterogeneous etiology. Self-injurious, stereotyped, and aggressive/destructive behavioral scores indicated that both frequency and severity were significantly higher among individuals with SMS relative to those with intellectual disability. Next, we categorized food behaviors in our SMS cohort across age using the Food Related Problems Questionnaire (FRPQ) and found that problems began to occur in SMS children as early as 5-11 years old, but children 12-18 years old and adults manifested the most severe problems. Furthermore, we evaluated the similarities of SMS adult food-related behaviors to those with intellectual disability and found that SMS adults had more severe behavioral problems. Many neurodevelopmental disorders exhibit syndromic obesity including SMS. Prader-Willi syndrome (PWS) is the most frequent neurodevelopmental disorder with syndromic obesity and has a well-established management and treatment plan. Using the FRPQ we found that SMS adults had similar scores relative to PWS adults. Both syndromes manifest weight gain early in development, and the FRPQ scores highlight specific areas in which behavioral similarities exist, including preoccupation with food, impaired satiety, and negative behavioral responses. SMS food-related behavior treatment paradigms are not as refined as PWS, suggesting that current PWS treatments for prevention of obesity may be beneficial for individuals with SMS.
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Affiliation(s)
- Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Laura V Barton
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel D Wills
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca H Foster
- Department of Psychology, St. Louis Children's Hospital, St. Louis, MO 63110, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA.
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25
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Alaimo JT, Mullegama SV, Thomas MA, Elsea SH. Copy number loss upstream of RAI1 uncovers gene expression regulatory region that may impact Potocki-Lupski syndrome diagnosis. Mol Cytogenet 2015; 8:75. [PMID: 26442755 PMCID: PMC4594966 DOI: 10.1186/s13039-015-0179-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 07/20/2015] [Accepted: 09/23/2015] [Indexed: 02/07/2023] Open
Abstract
The identification of structural variants of uncertain clinical significance is increasing; however, studies delineating the functional consequence of these variants in the pathogenicity of phenotypic features are lacking. Understanding the consequence of structural variants such as copy number alterations and their role in gene expression changes is paramount in order to perform a comprehensive analysis of genetic effects on phenotypic variation and disease. RAI1 is a dosage-sensitive essential neurodevelopmental gene. Copy number loss of RAI1 results in Smith-Magenis syndrome while copy number gain results in Potocki-Lupski syndrome. Here, we present a case of a six year old female with a newly identified maternally inherited copy number loss that lies within the Smith-Magenis syndrome common deletion region, but RAI1 copy number is normal. Integration of the Encyclopedia of DNA Elements (ENCODE) data at the affected region suggests that the deletion disrupts several cis-acting regulatory elements upstream of RAI1, such as multiple repressor sites and an insulator region. Gene expression studies revealed that both the proband and the mother have significantly elevated RAI1 mRNA levels suggesting that the structural variant alters gene expression regulation. The proband and the mother both have some features of Potocki-Lupski syndrome, while the child appears to be more affected with autistic-like features. Overall, our work demonstrates that the integration of ENCODE data with structural variants of uncertain significance aids in delineating a functional consequence to a genomic aberration and subsequent diagnosis.
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Affiliation(s)
- Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, NAB2015, Houston, TX 77030 USA
| | - Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, NAB2015, Houston, TX 77030 USA
| | - Mary Ann Thomas
- Department of Medical Genetics, Alberta Children's Hospital, University of Calgary, Calgary, AB CA T2N 1N4 Canada
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, NAB2015, Houston, TX 77030 USA
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26
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Chen L, Mullegama SV, Alaimo JT, Elsea SH. Smith-Magenis syndrome and its circadian influence on development, behavior, and obesity - own experience. Dev Period Med 2015; 19:149-156. [PMID: 26384114] [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] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Smith-Magenis syndrome (SMS) is a complex genetic disorder characterized by sleep disturbance, multiple developmental anomalies, psychiatric behavior, and obesity. It is caused by a heterozygous 17p11.2 microdeletion containing the retinoic acid-induced 1 (RAI1) gene or mutation within RAI1. Sleep disorder is one of the most penetrant features of SMS. Molecular genetic studies indicate that RAI1 regulates circadian rhythm genes and when haploinsucient, causes a distorted molecular circadian network that may be the cause of the sleep disturbance and the inverted rhythm of melatonin present in most individuals with SMS. RAI1 also regulates genes involved in development, neurobehavior, and lipid metabolism. Sleep debt, daytime melatonin secretion, and environmental stress often contribute to negative behavior in persons with SMS, and food entrained circadian rhythm also influences food intake behavior and humoral signals, which also affect development and neurobehavior. The cross-talk between circadian rhythm, development, metabolism and behaviors affect the multiple phenotypic outcomes in Smith-Magenis syndrome. These findings shed light on possible effective and personalized drug treatments for SMS patients in the future.
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Affiliation(s)
- Li Chen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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27
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Alaimo JT, Hahn NH, Mullegama SV, Elsea SH. Dietary regimens modify early onset of obesity in mice haploinsufficient for Rai1. PLoS One 2014; 9:e105077. [PMID: 25127133 PMCID: PMC4134272 DOI: 10.1371/journal.pone.0105077] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/18/2014] [Indexed: 01/10/2023] Open
Abstract
Smith-Magenis syndrome is a complex genomic disorder in which a majority of individuals are obese by adolescence. While an interstitial deletion of chromosome 17p11.2 is the leading cause, mutation or deletion of the RAI1 gene alone results in most features of the disorder. Previous studies have shown that heterozygous knockout of Rai1 results in an obese phenotype in mice and that Smith-Magenis syndrome mouse models have a significantly reduced fecundity and an altered transmission pattern of the mutant Rai1 allele, complicating large, extended studies in these models. In this study, we show that breeding C57Bl/6J Rai1+/− mice with FVB/NJ to create F1 Rai1+/− offspring in a mixed genetic background ameliorates both fecundity and Rai1 allele transmission phenotypes. These findings suggest that the mixed background provides a more robust platform for breeding and larger phenotypic studies. We also characterized the effect of dietary intake on Rai1+/− mouse growth during adolescent and early adulthood developmental stages. Animals fed a high carbohydrate or a high fat diet gained weight at a significantly faster rate than their wild type littermates. Both high fat and high carbohydrate fed Rai1+/− mice also had an increase in body fat and altered fat distribution patterns. Interestingly, Rai1+/− mice fed different diets did not display altered fasting blood glucose levels. These results suggest that dietary regimens are extremely important for individuals with Smith- Magenis syndrome and that food high in fat and carbohydrates may exacerbate obesity outcomes.
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Affiliation(s)
- Joseph T. Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Natalie H. Hahn
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Sureni V. Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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28
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Zhang Z, Tang QY, Alaimo JT, Davies AG, Bettinger JC, Logothetis DE. SLO-2 isoforms with unique Ca(2+) - and voltage-dependence characteristics confer sensitivity to hypoxia in C. elegans. Channels (Austin) 2013; 7:194-205. [PMID: 23590941 DOI: 10.4161/chan.24492] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Slo channels are large conductance K (+) channels that display marked differences in their gating by intracellular ions. Among them, the Slo1 and C. elegans SLO-2 channels are gated by calcium (Ca ( 2+) ), while mammalian Slo2 channels are activated by both sodium (Na (+) ) and chloride (Cl (-) ). Here, we report that SLO-2 channels, SLO-2a and a novel N-terminal variant isoform, SLO-2b, are activated by Ca ( 2+) and voltage, but in contrast to previous reports they do not exhibit Cl (-) sensitivity. Most importantly, SLO-2 provides a unique case in the Slo family for sensing Ca ( 2+) with the high-affinity Ca ( 2+) regulatory site in the RCK1 but not the RCK2 domain, formed through interactions with residues E319 and E487 (that correspond to D362 and E535 of Slo1, respectively). The SLO-2 RCK2 domain lacks the Ca ( 2+) bowl structure and shows minimal Ca ( 2+) dependence. In addition, in contrast to SLO-1, SLO-2 loss-of-function mutants confer resistance to hypoxia in C. elegans. Thus, the C. elegans SLO-2 channels possess unique biophysical and functional properties.
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Affiliation(s)
- Zhe Zhang
- Department of Physiology and Biophysics, Virginia Commonwealth University, Medical College of Virginia Campus, Richmond, VA, USA.
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Alaimo JT, Davis SJ, Song SS, Burnette CR, Grotewiel M, Shelton KL, Pierce-Shimomura JT, Davies AG, Bettinger JC. Ethanol metabolism and osmolarity modify behavioral responses to ethanol in C. elegans. Alcohol Clin Exp Res 2012; 36:1840-50. [PMID: 22486589 DOI: 10.1111/j.1530-0277.2012.01799.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 02/10/2012] [Indexed: 12/29/2022]
Abstract
BACKGROUND Ethanol (EtOH) is metabolized by a 2-step process in which alcohol dehydrogenase (ADH) oxidizes EtOH to acetaldehyde, which is further oxidized to acetate by aldehyde dehydrogenase (ALDH). Although variation in EtOH metabolism in humans strongly influences the propensity to chronically abuse alcohol, few data exist on the behavioral effects of altered EtOH metabolism. Here, we used the nematode Caenorhabditis elegans to directly examine how changes in EtOH metabolism alter behavioral responses to alcohol during an acute exposure. Additionally, we investigated EtOH solution osmolarity as a potential explanation for contrasting published data on C. elegans EtOH sensitivity. METHODS We developed a gas chromatography assay and validated a spectrophotometric method to measure internal EtOH in EtOH-exposed worms. Further, we tested the effects of mutations in ADH and ALDH genes on EtOH tissue accumulation and behavioral sensitivity to the drug. Finally, we tested the effects of EtOH solution osmolarity on behavioral responses and tissue EtOH accumulation. RESULTS Only a small amount of exogenously applied EtOH accumulated in the tissues of C. elegans and consequently their tissue concentrations were similar to those that intoxicate humans. Independent inactivation of an ADH-encoding gene (sodh-1) or an ALDH-encoding gene (alh-6 or alh-13) increased the EtOH concentration in worms and caused hypersensitivity to the acute sedative effects of EtOH on locomotion. We also found that the sensitivity to the depressive effects of EtOH on locomotion is strongly influenced by the osmolarity of the exogenous EtOH solution. CONCLUSIONS Our results indicate that EtOH metabolism via ADH and ALDH has a statistically discernable but surprisingly minor influence on EtOH sedation and internal EtOH accumulation in worms. In contrast, the osmolarity of the medium in which EtOH is delivered to the animals has a more substantial effect on the observed sensitivity to EtOH.
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Affiliation(s)
- Joseph T Alaimo
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
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Bhandari P, Hill JS, Farris SP, Costin B, Martin I, Chan CL, Alaimo JT, Bettinger JC, Davies AG, Miles MF, Grotewiel M. Chloride intracellular channels modulate acute ethanol behaviors in Drosophila, Caenorhabditis elegans and mice. Genes Brain Behav 2012; 11:387-97. [PMID: 22239914 DOI: 10.1111/j.1601-183x.2012.00765.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Identifying genes that influence behavioral responses to alcohol is critical for understanding the molecular basis of alcoholism and ultimately developing therapeutic interventions for the disease. Using an integrated approach that combined the power of the Drosophila, Caenorhabditis elegans and mouse model systems with bioinformatics analyses, we established a novel, conserved role for chloride intracellular channels (CLICs) in alcohol-related behavior. CLIC proteins might have several biochemical functions including intracellular chloride channel activity, modulation of transforming growth factor (TGF)-β signaling, and regulation of ryanodine receptors and A-kinase anchoring proteins. We initially identified vertebrate Clic4 as a candidate ethanol-responsive gene via bioinformatic analysis of data from published microarray studies of mouse and human ethanol-related genes. We confirmed that Clic4 expression was increased by ethanol treatment in mouse prefrontal cortex and also uncovered a correlation between basal expression of Clic4 in prefrontal cortex and the locomotor activating and sedating properties of ethanol across the BXD mouse genetic reference panel. Furthermore, we found that disruption of the sole Clic Drosophila orthologue significantly blunted sensitivity to alcohol in flies, that mutations in two C. elegans Clic orthologues, exc-4 and exl-1, altered behavioral responses to acute ethanol in worms and that viral-mediated overexpression of Clic4 in mouse brain decreased the sedating properties of ethanol. Together, our studies demonstrate key roles for Clic genes in behavioral responses to acute alcohol in Drosophila, C. elegans and mice.
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Affiliation(s)
- P Bhandari
- Department of Human and Molecular Genetics, Department of Pharmacology and Toxicology, Virginia Commonwealth University Alcohol Research Center, Richmond, VA, USA
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