1
|
Lee B, Nasanovsky L, Shen L, Maglinte DT, Pan Y, Gai X, Schmidt RJ, Raca G, Biegel JA, Roytman M, An P, Saunders CJ, Farrow EG, Shams S, Ji J. Significance Associated with Phenotype Score Aids in Variant Prioritization for Exome Sequencing Analysis. J Mol Diagn 2024; 26:337-348. [PMID: 38360210 DOI: 10.1016/j.jmoldx.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/04/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Several in silico annotation-based methods have been developed to prioritize variants in exome sequencing analysis. This study introduced a novel metric Significance Associated with Phenotypes (SAP) score, which generates a statistical score by comparing an individual's observed phenotypes against existing gene-phenotype associations. To evaluate the SAP score, a retrospective analysis was performed on 219 exomes. Among them, 82 family-based and 35 singleton exomes had at least one disease-causing variant that explained the patient's clinical features. SAP scores were calculated, and the rank of the disease-causing variant was compared with a known method, Exomiser. Using the SAP score, the known causative variant was ranked in the top 10 retained variants for 94% (77 of 82) of the family-based exomes and in first place for 73% of these cases. For singleton exomes, the SAP score analysis ranked the known pathogenic variants within the top 10 for 80% (28 of 35) of cases. The SAP score, which is independent of detected variants, demonstrates comparable performance with Exomiser, which considers both phenotype and variant-level evidence simultaneously. Among 102 cases with negative results or variants of uncertain significance, SAP score analysis revealed two cases with a potential new diagnosis based on rank. The SAP score, a phenotypic quantitative metric, can be used in conjunction with standard variant filtration and annotation to enhance variant prioritization in exome analysis.
Collapse
Affiliation(s)
- Brian Lee
- Bionano Genomics, San Diego, California
| | | | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Dennis T Maglinte
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Yachen Pan
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ryan J Schmidt
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Gordana Raca
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jaclyn A Biegel
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | - Paul An
- Bionano Genomics, San Diego, California
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Emily G Farrow
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | | | - Jianling Ji
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California.
| |
Collapse
|
2
|
Saunders CJ, Brunelli L, Deem MJ, Farrow EG, Hegde M, Stark Z. More Than a Decade of Rapid Genomic Sequencing: Where Are We Now? Clin Chem 2024; 70:577-583. [PMID: 38565214 PMCID: PMC10987227 DOI: 10.1093/clinchem/hvae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/07/2024] [Indexed: 04/04/2024]
Affiliation(s)
- Carol J Saunders
- Director, Division of Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Mercy-Kansas City, Professor of Pediatrics and Pathology, University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
| | - Luca Brunelli
- Professor of Pediatrics, Division of Neonatology, Department of Pediatrics, University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, UT, United States
| | - Michael J Deem
- Associate Professor, Department of Human Genetics, Core Faculty, Center for Bioethics & Health Law, University of Pittsburgh, Pittsburgh, PA, United States
| | - Emily G Farrow
- Director of Genomics Operations, Division of Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children’s Mercy-Kansas City, Associate Professor of Pediatrics and Pathology, University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
| | - Madhuri Hegde
- Vice President and Chief Scientific Officer, Revvity Inc., Waltham, MA, United States
| | - Zornitza Stark
- Professor, Department of Paediatrics, University of Melbourne; Australian Genomics; Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Smallwood K, Watt KEN, Ide S, Baltrunaite K, Brunswick C, Inskeep K, Capannari C, Adam MP, Begtrup A, Bertola DR, Demmer L, Demo E, Devinsky O, Gallagher ER, Guillen Sacoto MJ, Jech R, Keren B, Kussmann J, Ladda R, Lansdon LA, Lunke S, Mardy A, McWalters K, Person R, Raiti L, Saitoh N, Saunders CJ, Schnur R, Skorvanek M, Sell SL, Slavotinek A, Sullivan BR, Stark Z, Symonds JD, Wenger T, Weber S, Whalen S, White SM, Winkelmann J, Zech M, Zeidler S, Maeshima K, Stottmann RW, Trainor PA, Weaver KN. POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies. Am J Hum Genet 2023; 110:809-825. [PMID: 37075751 PMCID: PMC10183370 DOI: 10.1016/j.ajhg.2023.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 10/26/2022] [Accepted: 03/21/2023] [Indexed: 04/21/2023] Open
Abstract
Heterozygous pathogenic variants in POLR1A, which encodes the largest subunit of RNA Polymerase I, were previously identified as the cause of acrofacial dysostosis, Cincinnati-type. The predominant phenotypes observed in the cohort of 3 individuals were craniofacial anomalies reminiscent of Treacher Collins syndrome. We subsequently identified 17 additional individuals with 12 unique heterozygous variants in POLR1A and observed numerous additional phenotypes including neurodevelopmental abnormalities and structural cardiac defects, in combination with highly prevalent craniofacial anomalies and variable limb defects. To understand the pathogenesis of this pleiotropy, we modeled an allelic series of POLR1A variants in vitro and in vivo. In vitro assessments demonstrate variable effects of individual pathogenic variants on ribosomal RNA synthesis and nucleolar morphology, which supports the possibility of variant-specific phenotypic effects in affected individuals. To further explore variant-specific effects in vivo, we used CRISPR-Cas9 gene editing to recapitulate two human variants in mice. Additionally, spatiotemporal requirements for Polr1a in developmental lineages contributing to congenital anomalies in affected individuals were examined via conditional mutagenesis in neural crest cells (face and heart), the second heart field (cardiac outflow tract and right ventricle), and forebrain precursors in mice. Consistent with its ubiquitous role in the essential function of ribosome biogenesis, we observed that loss of Polr1a in any of these lineages causes cell-autonomous apoptosis resulting in embryonic malformations. Altogether, our work greatly expands the phenotype of human POLR1A-related disorders and demonstrates variant-specific effects that provide insights into the underlying pathogenesis of ribosomopathies.
Collapse
Affiliation(s)
- Kelly Smallwood
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Kristina Baltrunaite
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Chad Brunswick
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Katherine Inskeep
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Corrine Capannari
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Margaret P Adam
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | | | - Laurie Demmer
- Atrium Health's Levine Children's Hospital, Charlotte, NC, USA
| | - Erin Demo
- Sibley Heart Center, Atlanta, GA, USA
| | - Orrin Devinsky
- Department of Neurology, Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Emily R Gallagher
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Boris Keren
- Genetic Department, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Jennifer Kussmann
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Roger Ladda
- Department of Pediatrics, Penn State Health Children's Hospital, Hershey, PA, USA
| | - Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy Research Institute, 2401 Gillham Road, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, USA
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Anne Mardy
- Department of Women's Health, University of Texas Austin Dell Medical Center, Austin, TX, USA
| | | | | | - Laura Raiti
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia
| | | | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy Research Institute, 2401 Gillham Road, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, USA
| | | | - Matej Skorvanek
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic; Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Susan L Sell
- Department of Pediatrics, Penn State Health Children's Hospital, Hershey, PA, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Joseph D Symonds
- Paediatric Neuroscience Research Group, Royal Hospital for Children, Glasgow G667AB, UK
| | - Tara Wenger
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sacha Weber
- CCA-AHU de génétique clinique et de neurogénétique, Service de Génétique et de Neurologie, CHU de Caen, Caen, France
| | - Sandra Whalen
- Genetic Department, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Rolf W Stottmann
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - K Nicole Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| |
Collapse
|
5
|
Schmid CM, Gregor A, Costain G, Morel CF, Massingham L, Schwab J, Quélin C, Faoucher M, Kaplan J, Procopio R, Saunders CJ, Cohen ASA, Lemire G, Sacharow S, O'Donnell-Luria A, Segal RJ, Shamshoni JK, Schweitzer D, Ebrahimi-Fakhari D, Monaghan K, Palculict TB, Napier MP, Tao A, Isidor B, Moradkhani K, Reis A, Sticht H, Chung WK, Zweier C. LHX2 haploinsufficiency causes a variable neurodevelopmental disorder. Genet Med 2023; 25:100839. [PMID: 37057675 DOI: 10.1016/j.gim.2023.100839] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023] Open
Abstract
PURPOSE LHX2 encodes the LIM homeobox 2 transcription factor (LHX2), which is highly expressed in brain and well conserved across species, but has not been clearly linked to neurodevelopmental disorders (NDD) to date. METHODS Through international collaboration, we identified 19 individuals from 18 families with variable neurodevelopmental phenotypes, carrying a small chromosomal deletion, likely gene-disrupting or missense variants in LHX2. Functional consequences of missense variants were investigated in cellular systems. RESULTS Affected individuals presented with developmental and/or behavioral abnormalities, autism-spectrum disorder, variable intellectual disability, and microcephaly. We observed nucleolar accumulation for two missense variants located within the DNA-binding HOX domain, impaired interaction with co-factor LDB1 for another variant located in the protein-protein interaction mediating LIM domain, and impaired transcriptional activation by luciferase assay for four missense variants. CONCLUSION We implicate LHX2 haploinsufficiency by deletion and likely gene-disrupting variants as causative for a variable NDD. Our findings suggest a loss-of-function mechanism also for likely pathogenic LHX2 missense variants. Together, our observations underscore the importance of LHX2 in nervous system and for variable neurodevelopmental phenotypes.
Collapse
Affiliation(s)
- Cosima M Schmid
- Department of Human Genetics, Inselspital Bern, University of Bern, 3010 Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, 3010 Bern, Switzerland
| | - Anne Gregor
- Department of Human Genetics, Inselspital Bern, University of Bern, 3010 Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, 3010 Bern, Switzerland; Bern Center for Precision Medicine (BCPM), University of Bern, 3010 Bern, Switzerland
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Chantal F Morel
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, ON, M5T 3L9, Canada; Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Lauren Massingham
- Division of Human Genetics, Department of Pediatrics, Warren Alpert Medical School of Brown University, Hasbro Children's Hospital/Rhode Island Hospital, Providence, RI 02905, USA
| | - Jennifer Schwab
- Division of Human Genetics, Department of Pediatrics, Warren Alpert Medical School of Brown University, Hasbro Children's Hospital/Rhode Island Hospital, Providence, RI 02905, USA
| | - Chloé Quélin
- Clinical Genetics Department, CHU Hôspital Sud, Rennes 35203, France
| | - Marie Faoucher
- Service de Génétique Moléculaire et Génomique, CHU, Rennes 35033, France; Univ Rennes, CNRS, IGDR, UMR 6290, Rennes 35000, France
| | - Julie Kaplan
- Division of Genetics, Department of Pediatrics, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Rebecca Procopio
- Division of Genetics, Department of Pediatrics, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Carol J Saunders
- Genomic Medicine Center, Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Ana S A Cohen
- Genomic Medicine Center, Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Gabrielle Lemire
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stephanie Sacharow
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anne O'Donnell-Luria
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ranit Jaron Segal
- Schneider Children's Medical Center of Israel, Petach Tikvah 49100, Israel
| | - Jessica Kianmahd Shamshoni
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Daniela Schweitzer
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Darius Ebrahimi-Fakhari
- Movement Disorders Program, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Alice Tao
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Bertrand Isidor
- Department of Medical Genetics, CHU Nantes, 44093 Nantes, France
| | | | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; Centre for Rare Diseases Erlangen (ZSEER), University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Heinrich Sticht
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Christiane Zweier
- Department of Human Genetics, Inselspital Bern, University of Bern, 3010 Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, 3010 Bern, Switzerland; Bern Center for Precision Medicine (BCPM), University of Bern, 3010 Bern, Switzerland.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Lebaron S, O’Donohue M, Smith SC, Engleman KL, Juusola J, Safina NN, Thiffault I, Saunders CJ, Gleizes P. Functionally impaired
RPL8
variants associated with Diamond‐Blackfan anemia and a Diamond‐Blackfan anemia‐like phenotype. Hum Mutat 2021; 43:389-402. [DOI: 10.1002/humu.24323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Simon Lebaron
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI) University of Toulouse, CNRS, UT3 Toulouse France
| | - Marie‐Françoise O’Donohue
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI) University of Toulouse, CNRS, UT3 Toulouse France
| | - Scott C. Smith
- Department of Pathology and Laboratory Medicine Children's Mercy Hospital Kansas City MO USA
- Current address: SUNY Upstate Medical University Syracuse NY USA
| | - Kendra L. Engleman
- Division of Clinical Genetics Children's Mercy Hospital Kansas City MO USA
- Department of Pediatrics Children’s Mercy Hospital Kansas City MO USA
| | | | - Nicole N. Safina
- Division of Clinical Genetics Children's Mercy Hospital Kansas City MO USA
- Department of Pediatrics Children’s Mercy Hospital Kansas City MO USA
- Current address: Division of Medical Genetics and Genomics, Stead Family University of Iowa Children’s Hospital, The University of Iowa Carver College of Medicine Iowa City IA USA
| | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine Children's Mercy Hospital Kansas City MO USA
- 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
| | - Carol J. Saunders
- Department of Pathology and Laboratory Medicine Children's Mercy Hospital Kansas City MO USA
- 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
| | - Pierre‐Emmanuel Gleizes
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI) University of Toulouse, CNRS, UT3 Toulouse France
| |
Collapse
|
9
|
Lansdon LA, Chen D, Rush ET, Engleman K, Zhang L, Saunders CJ, Oroszi G. A novel likely pathogenic variant in a patient with Hermansky-Pudlak syndrome. Cold Spring Harb Mol Case Stud 2021; 7:a006110. [PMID: 34362826 PMCID: PMC8559624 DOI: 10.1101/mcs.a006110] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/28/2021] [Indexed: 11/24/2022] Open
Abstract
Hermansky-Pudlak syndrome (HPS) is a genetic disorder characterized by oculocutaneous albinism and variable pulmonary fibrosis, granulomatous colitis, or immunodeficiency. The diagnosis relies on clinical findings, platelet transmission electron microscopy studies showing absent dense granules, or the identification of a pathogenic genotype in one of 11 associated genes, including HPS1 We report a 2-wk-old male with significant iris transillumination defects, a pale fundus, and mild corectopia found by clinical exome sequencing to have a previously reported pathogenic variant, c.972dupC p.(Met325HisfsTer128), and a variant of uncertain significance, c.1846G>A p.(Glu616Lys), in HPS1 To determine whether his phenotype was consistent with HPS, follow-up studies of whole blood lumiaggregometry and platelet transmission electron microscopy were performed that revealed absent or markedly reduced platelet ATP secretion and virtually absent platelet dense granules, thus confirming the diagnosis. To the best of our knowledge, our case is the first in which the c.1846G>A p.(Glu616Lys) variant is identified in a patient with HPS. In addition, the case also highlights the importance of leveraging appropriate confirmatory clinical testing and reverse phenotyping, which allowed the care team to establish the clinical diagnosis of HPS and reclassify the previously reported variant of uncertain significance in HPS1 to likely pathogenic.
Collapse
Affiliation(s)
- Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, Missouri 64108, USA
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri 64108, USA
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City, School of Medicine, Kansas City, Missouri 64110, USA
| | - Dong Chen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55901, USA
| | - Eric T Rush
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, Missouri 64108, USA
- Department of Pediatrics, University of Missouri-Kansas City, School of Medicine, Kansas City, Missouri 64110, USA
- Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, Kansas 66160, USA
| | - Kendra Engleman
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, Missouri 64108, USA
- Department of Pediatrics, University of Missouri-Kansas City, School of Medicine, Kansas City, Missouri 64110, USA
| | - Lei Zhang
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, Missouri 64108, USA
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City, School of Medicine, Kansas City, Missouri 64110, USA
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, Missouri 64108, USA
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri 64108, USA
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City, School of Medicine, Kansas City, Missouri 64110, USA
| | - Gabor Oroszi
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, Missouri 64108, USA
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City, School of Medicine, Kansas City, Missouri 64110, USA
| |
Collapse
|
10
|
Lansdon LA, Fleming EA, Viso FD, Sullivan BR, Saunders CJ. Second patient with GNB2-related neurodevelopmental disease: Further evidence for a gene-disease association. Eur J Med Genet 2021; 64:104243. [PMID: 33971351 DOI: 10.1016/j.ejmg.2021.104243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/28/2021] [Accepted: 05/02/2021] [Indexed: 11/30/2022]
Abstract
G-proteins are ubiquitously expressed heterotrimeric proteins consisting of α, β and γ subunits and mediate G-protein coupled receptor signalling cascades. The β subunit is encoded by one of five highly similar paralogs (GNB1-GNB5, accordingly). The developmental importance of G-proteins is highlighted by the clinical relevance of variants in genes such as GNB1, which cause severe neurodevelopmental disease (NDD). Recently the candidacy of GNB2 was raised in association with NDD in an individual with a de novo variant affecting a codon conserved across paralogs and recurrently mutated in GNB1-related disease, c.229G>A p.(Gly77Arg), in association with global developmental delay, intellectual disability and dysmorphic features. Here, we report a patient with strikingly similar facial features and NDD in association with a de novo GNB2 variant affecting the same codon, c.229G>T p.(Gly77Trp). In addition, this individual has epilepsy and overgrowth. Our report is the second to implicate a de novo GNB2 variant with a severe yet variable NDD.
Collapse
Affiliation(s)
- Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy-Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Emily A Fleming
- Division of Clinical Genetics, Children's Mercy-Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Florencia Del Viso
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy-Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Children's Mercy-Kansas City, 2401 Gillham Road, Kansas City, MO, USA; University of Missouri-Kansas City, School of Medicine, 2411 Holmes Street, Kansas City, MO, USA
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy-Kansas City, 2401 Gillham Road, Kansas City, MO, USA; University of Missouri-Kansas City, School of Medicine, 2411 Holmes Street, Kansas City, MO, USA.
| |
Collapse
|
11
|
Radio FC, Pang K, Ciolfi A, Levy MA, Hernández-García A, Pedace L, Pantaleoni F, Liu Z, de Boer E, Jackson A, Bruselles A, McConkey H, Stellacci E, Lo Cicero S, Motta M, Carrozzo R, Dentici ML, McWalter K, Desai M, Monaghan KG, Telegrafi A, Philippe C, Vitobello A, Au M, Grand K, Sanchez-Lara PA, Baez J, Lindstrom K, Kulch P, Sebastian J, Madan-Khetarpal S, Roadhouse C, MacKenzie JJ, Monteleone B, Saunders CJ, Jean Cuevas JK, Cross L, Zhou D, Hartley T, Sawyer SL, Monteiro FP, Secches TV, Kok F, Schultz-Rogers LE, Macke EL, Morava E, Klee EW, Kemppainen J, Iascone M, Selicorni A, Tenconi R, Amor DJ, Pais L, Gallacher L, Turnpenny PD, Stals K, Ellard S, Cabet S, Lesca G, Pascal J, Steindl K, Ravid S, Weiss K, Castle AMR, Carter MT, Kalsner L, de Vries BBA, van Bon BW, Wevers MR, Pfundt R, Stegmann APA, Kerr B, Kingston HM, Chandler KE, Sheehan W, Elias AF, Shinde DN, Towne MC, Robin NH, Goodloe D, Vanderver A, Sherbini O, Bluske K, Hagelstrom RT, Zanus C, Faletra F, Musante L, Kurtz-Nelson EC, Earl RK, Anderlid BM, Morin G, van Slegtenhorst M, Diderich KEM, Brooks AS, Gribnau J, Boers RG, Finestra TR, Carter LB, Rauch A, Gasparini P, Boycott KM, Barakat TS, Graham JM, Faivre L, Banka S, Wang T, Eichler EE, Priolo M, Dallapiccola B, Vissers LELM, Sadikovic B, Scott DA, Holder JL, Tartaglia M. SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females. Am J Hum Genet 2021; 108:502-516. [PMID: 33596411 DOI: 10.1016/j.ajhg.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/26/2021] [Indexed: 01/31/2023] Open
Abstract
Deletion 1p36 (del1p36) syndrome is the most common human disorder resulting from a terminal autosomal deletion. This condition is molecularly and clinically heterogeneous. Deletions involving two non-overlapping regions, known as the distal (telomeric) and proximal (centromeric) critical regions, are sufficient to cause the majority of the recurrent clinical features, although with different facial features and dysmorphisms. SPEN encodes a transcriptional repressor commonly deleted in proximal del1p36 syndrome and is located centromeric to the proximal 1p36 critical region. Here, we used clinical data from 34 individuals with truncating variants in SPEN to define a neurodevelopmental disorder presenting with features that overlap considerably with those of proximal del1p36 syndrome. The clinical profile of this disease includes developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI, especially in females. SPEN also emerges as a relevant gene for del1p36 syndrome by co-expression analyses. Finally, we show that haploinsufficiency of SPEN is associated with a distinctive DNA methylation episignature of the X chromosome in affected females, providing further evidence of a specific contribution of the protein to the epigenetic control of this chromosome, and a paradigm of an X chromosome-specific episignature that classifies syndromic traits. We conclude that SPEN is required for multiple developmental processes and SPEN haploinsufficiency is a major contributor to a disorder associated with deletions centromeric to the previously established 1p36 critical regions.
Collapse
Affiliation(s)
| | - Kaifang Pang
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea Ciolfi
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Andrés Hernández-García
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lucia Pedace
- Oncohaematology Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Zhandong Liu
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elke de Boer
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Adam Jackson
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Emilia Stellacci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Stefania Lo Cicero
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Marialetizia Motta
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Rosalba Carrozzo
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Maria Lisa Dentici
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | | | | | - Christophe Philippe
- Inserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France
| | - Antonio Vitobello
- Inserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France
| | - Margaret Au
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Joanne Baez
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | | | - Peggy Kulch
- Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - Jessica Sebastian
- Division of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Suneeta Madan-Khetarpal
- Division of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | | | | | - Berrin Monteleone
- Clinical genetics, NYU Langone Long Island School of Medicine, Mineola, NY 11501, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - July K Jean Cuevas
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Laura Cross
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Dihong Zhou
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Sarah L Sawyer
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | | | | | - Fernando Kok
- Mendelics Genomic Analysis, Campo Belo - São Paulo 04013-000, Brazil
| | | | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Eva Morava
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | - Romano Tenconi
- Dipartimento di Pediatria, Università di Padova, 35137 Padua, Italy
| | - David J Amor
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Lynn Pais
- Medical and Populations Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | | | - Karen Stals
- Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Sian Ellard
- Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Sara Cabet
- Department of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France
| | - Gaetan Lesca
- Department of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France
| | - Joset Pascal
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Sarit Ravid
- Pediatric Neurology Unit, Ruth Children's Hospital, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Israel Institute of Technology, Haifa 3109601, Israel
| | - Alison M R Castle
- Department of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Melissa T Carter
- Department of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Louisa Kalsner
- Connecticut Children's Medical Center, University of Connecticut School of Medicine, Farmington, CT 06032, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Marijke R Wevers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center+, 6229 HX Maastricht, the Netherlands
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Helen M Kingston
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Willow Sheehan
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA
| | - Abdallah F Elias
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA
| | | | | | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dana Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Omar Sherbini
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Krista Bluske
- Illumina Clinical Services Laboratory, San Diego, CA 92122, USA
| | | | - Caterina Zanus
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | | | - Rachel K Earl
- Department of Psychiatry & Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Gilles Morin
- CA de Génétique Clinique & Oncogénétique, CHU Amiens-Picardie, 80054 Amiens, France
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Teresa Robert Finestra
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Lauren B Carter
- Department of Pediatrics, Division of Medical Genetics, Levine Children's Hospital Atrium Health, Charlotte, NC 28203, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy; Department of Medicine, Surgery & Health Science, University of Trieste, 34143 Trieste, Italy
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Laurence Faivre
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD et Institut GIMI, 77908 Dijon, France; UMR 1231 GAD, Inserm - Université Bourgogne-Franche Comté, 77908 Dijon, France
| | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Manuela Priolo
- UOSD Genetica Medica del Grande Ospedale Metropolitano "Bianchi Melacrino Morelli" di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - 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
| | - Jimmy Lloyd Holder
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marco Tartaglia
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
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
| |
Collapse
|
14
|
Faundes V, Jennings MD, Crilly S, Legraie S, Withers SE, Cuvertino S, Davies SJ, Douglas AGL, Fry AE, Harrison V, Amiel J, Lehalle D, Newman WG, Newkirk P, Ranells J, Splitt M, Cross LA, Saunders CJ, Sullivan BR, Granadillo JL, Gordon CT, Kasher PR, Pavitt GD, Banka S. Impaired eIF5A function causes a Mendelian disorder that is partially rescued in model systems by spermidine. Nat Commun 2021; 12:833. [PMID: 33547280 PMCID: PMC7864902 DOI: 10.1038/s41467-021-21053-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
The structure of proline prevents it from adopting an optimal position for rapid protein synthesis. Poly-proline-tract (PPT) associated ribosomal stalling is resolved by highly conserved eIF5A, the only protein to contain the amino acid hypusine. We show that de novo heterozygous EIF5A variants cause a disorder characterized by variable combinations of developmental delay, microcephaly, micrognathia and dysmorphism. Yeast growth assays, polysome profiling, total/hypusinated eIF5A levels and PPT-reporters studies reveal that the variants impair eIF5A function, reduce eIF5A-ribosome interactions and impair the synthesis of PPT-containing proteins. Supplementation with 1 mM spermidine partially corrects the yeast growth defects, improves the polysome profiles and restores expression of PPT reporters. In zebrafish, knockdown eif5a partly recapitulates the human phenotype that can be rescued with 1 µM spermidine supplementation. In summary, we uncover the role of eIF5A in human development and disease, demonstrate the mechanistic complexity of EIF5A-related disorder and raise possibilities for its treatment.
Collapse
Affiliation(s)
- Víctor Faundes
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Martin D Jennings
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Siobhan Crilly
- Division of Neuroscience & Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sarah Legraie
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sarah E Withers
- Division of Neuroscience & Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sara Cuvertino
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sally J Davies
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Andrew G L Douglas
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Andrew E Fry
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Victoria Harrison
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Jeanne Amiel
- Department of Genetics, AP-HP, Hôpital Necker Enfants Malades, Paris, France
- 1Laboratory of Embryology and Genetics of Human Malformations, INSERM UMR 1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Daphné Lehalle
- Department of Genetics, AP-HP, Hôpital Necker Enfants Malades, Paris, France
| | - William G Newman
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Patricia Newkirk
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, FL, UK
| | - Judith Ranells
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, FL, UK
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle upon Tyne, UK
| | - Laura A Cross
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO, USA
- Department of Pediatrics, University of Missour-Kansas City, Kansas City, MO, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine Children's Mercy, Kansas City, MO, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO, USA
- Department of Pediatrics, University of Missour-Kansas City, Kansas City, MO, USA
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher T Gordon
- 1Laboratory of Embryology and Genetics of Human Malformations, INSERM UMR 1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Paul R Kasher
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
- Division of Neuroscience & Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
| | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK.
| |
Collapse
|
15
|
Lansdon LA, Saunders CJ. Genotype-phenotype correlation in GNB1-related neurodevelopmental disorder: Potential association of p.Leu95Pro with cleft palate. Am J Med Genet A 2021; 185:1341-1343. [PMID: 33427398 DOI: 10.1002/ajmg.a.62080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri, USA.,Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri, USA
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri, USA.,Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Jenkins J, Barnes A, Birnbaum B, Papagiannis J, Thiffault I, Saunders CJ. LZTR1-Related Hypertrophic Cardiomyopathy Without Typical Noonan Syndrome Features. Circ Genom Precis Med 2020; 13:e002690. [PMID: 32004086 DOI: 10.1161/circgen.119.002690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Janda Jenkins
- Department of Pediatrics (J.J., A.B., B.B., J.P., I.T., C.J.S.), Children's Mercy-Kansas City.,School of Medicine (J.J., A.B., B.B., J.P.), University of Missouri-Kansas City, Kansas City, MO
| | - Aliessa Barnes
- Department of Pediatrics (J.J., A.B., B.B., J.P., I.T., C.J.S.), Children's Mercy-Kansas City.,School of Medicine (J.J., A.B., B.B., J.P.), University of Missouri-Kansas City, Kansas City, MO
| | - Brian Birnbaum
- Department of Pediatrics (J.J., A.B., B.B., J.P., I.T., C.J.S.), Children's Mercy-Kansas City.,School of Medicine (J.J., A.B., B.B., J.P.), University of Missouri-Kansas City, Kansas City, MO
| | - John Papagiannis
- Department of Pediatrics (J.J., A.B., B.B., J.P., I.T., C.J.S.), Children's Mercy-Kansas City.,School of Medicine (J.J., A.B., B.B., J.P.), University of Missouri-Kansas City, Kansas City, MO
| | - Isabelle Thiffault
- Department of Pediatrics (J.J., A.B., B.B., J.P., I.T., C.J.S.), Children's Mercy-Kansas City.,Center for Pediatric Genomic Medicine (I.T., C.J.S.), Children's Mercy-Kansas City.,Department of Pathology and Laboratory Medicine (I.T., C.J.S.), Children's Mercy-Kansas City
| | - Carol J Saunders
- Department of Pediatrics (J.J., A.B., B.B., J.P., I.T., C.J.S.), Children's Mercy-Kansas City.,Center for Pediatric Genomic Medicine (I.T., C.J.S.), Children's Mercy-Kansas City.,Department of Pathology and Laboratory Medicine (I.T., C.J.S.), Children's Mercy-Kansas City
| |
Collapse
|
18
|
Zollino M, Zweier C, Van Balkom ID, Sweetser DA, Alaimo J, Bijlsma EK, Cody J, Elsea SH, Giurgea I, Macchiaiolo M, Smigiel R, Thibert RL, Benoist I, Clayton-Smith J, De Winter CF, Deckers S, Gandhi A, Huisman S, Kempink D, Kruisinga F, Lamacchia V, Marangi G, Menke L, Mulder P, Nordgren A, Renieri A, Routledge S, Saunders CJ, Stembalska A, Van Balkom H, Whalen S, Hennekam RC. Diagnosis and management in Pitt-Hopkins syndrome: First international consensus statement. Clin Genet 2019; 95:462-478. [PMID: 30677142 DOI: 10.1111/cge.13506] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [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: 11/19/2018] [Revised: 12/20/2018] [Accepted: 01/09/2019] [Indexed: 02/06/2023]
Abstract
Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder characterized by intellectual disability, specific facial features, and marked autonomic nervous system dysfunction, especially with disturbances of regulating respiration and intestinal mobility. It is caused by variants in the transcription factor TCF4. Heterogeneity in the clinical and molecular diagnostic criteria and care practices has prompted a group of international experts to establish guidelines for diagnostics and care. For issues, for which there was limited information available in international literature, we collaborated with national support groups and the participants of a syndrome specific international conference to obtain further information. Here, we discuss the resultant consensus, including the clinical definition of PTHS and a molecular diagnostic pathway. Recommendations for managing particular health problems such as dysregulated respiration are provided. We emphasize the need for integration of care for physical and behavioral issues. The recommendations as presented here will need to be evaluated for improvements to allow for continued optimization of diagnostics and care.
Collapse
Affiliation(s)
- Marcella Zollino
- Fondazione Policlinico Universitario A.Gemelli, IRCCS, UOC Genetica.,Università Cattolica Sacro Cuore, Istituto di Medicina Genomica, Roma, Italy
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ingrid D Van Balkom
- Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, The Netherlands.,Rob Giel Research Centre, Department of Psychiatry, University Medical Center Groningen, Groningen, The Netherlands
| | - David A Sweetser
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, Massachusetts
| | - Joseph Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jannine Cody
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Irina Giurgea
- Sorbonne Université, INSERM, UMR_S 933, Assistance Publique Hôpitaux de Paris, Département de Génétique Médicale, Hôpital Trousseau, Paris, France
| | - Marina Macchiaiolo
- Rare and Genetic Diseases Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - Robert Smigiel
- Department of Pediatrics, Division of Pediatrics and Rare Disorders, Wroclaw Medical University, Wroclaw, Poland
| | - Ronald L Thibert
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ingrid Benoist
- Dutch Pitt-Hopkins Syndrome Foundation, Vlaggeschip, Oosterhout, The Netherlands
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, St Mary's Hospital, and Division of Evolution and Genomic Sciences School of Biological Sciences, University of Manchester, Manchester, UK
| | - Channa F De Winter
- Organisation for Individuals with Intellectual Disabilities, Trajectum, Zwolle, The Netherlands
| | - Stijn Deckers
- Department of Pedagogical Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anusha Gandhi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Sylvia Huisman
- Department of Pediatrics, Academic Medical Centre, Amsterdam UMC, Amsterdam, The Netherlands
| | - Dagmar Kempink
- Department of Orthopedic Surgery, Sophia Children's Hospital, UMCR, Rotterdam, The Netherlands
| | - Frea Kruisinga
- Department of Pediatrics, Academic Medical Centre, Amsterdam UMC, Amsterdam, The Netherlands
| | | | - Giuseppe Marangi
- Fondazione Policlinico Universitario A.Gemelli, IRCCS, UOC Genetica.,Università Cattolica Sacro Cuore, Istituto di Medicina Genomica, Roma, Italy
| | - Leonie Menke
- Department of Pediatrics, Academic Medical Centre, Amsterdam UMC, Amsterdam, The Netherlands
| | - Paul Mulder
- Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, The Netherlands.,Rob Giel Research Centre, Department of Psychiatry, University Medical Center Groningen, Groningen, The Netherlands
| | - Ann Nordgren
- Karolinska Center for Rare Diseases, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | | | - Hans Van Balkom
- Behavioral Science Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sandra Whalen
- Sorbonne Université, INSERM, UMR_S 933, Assistance Publique Hôpitaux de Paris, Département de Génétique Médicale, Hôpital Trousseau, Paris, France
| | - Raoul C Hennekam
- Department of Pediatrics, Academic Medical Centre, Amsterdam UMC, Amsterdam, The Netherlands
| |
Collapse
|
19
|
Caylor RC, Grote L, Thiffault I, Farrow EG, Willig L, Soden S, Amudhavalli SM, Nopper AJ, Horii KA, Fleming E, Jenkins J, Welsh H, Ilyas M, Engleman K, Abdelmoity A, Saunders CJ. Incidental diagnosis of tuberous sclerosis complex by exome sequencing in three families with subclinical findings. Neurogenetics 2018; 19:205-213. [PMID: 29926239 DOI: 10.1007/s10048-018-0551-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 12/19/2022]
Abstract
Tuberous sclerosis complex (TSC) is an autosomal-dominant neurocutaneous disorder characterized by lesions and benign tumors in multiple organ systems including the brain, skin, heart, eyes, kidneys, and lungs. The phenotype is highly variable, although penetrance is reportedly complete. We report the molecular diagnosis of TSC in individuals exhibiting extreme intra-familial variability, including the incidental diagnosis of asymptomatic family members. Exome sequencing was performed in three families, with probands referred for epilepsy, autism, and absent speech (Family 1); epileptic spasms (Family 2); and connective tissue disorders (Family 3.) Pathogenic variants in TSC1 or TSC2 were identified in nine individuals, including relatives with limited or no medical concerns at the time of testing. Of the nine individuals reported here, six had post-diagnosis examinations and three met clinical diagnostic criteria for TSC. One did not meet clinical criteria for a possible or definite diagnosis of TSC, and two had only a possible clinical diagnosis following post-diagnosis workup. These individuals as well as their mothers demonstrated limited features that would not raise concern for TSC in the absence of molecular results. In addition, three individuals exhibited epilepsy with normal brain MRIs, and two without seizures or intellectual disability had MRI findings fulfilling major criteria for TSC highlighting the difficulty providers face when relying on clinical criteria to guide genetic testing. Given the importance of a timely TSC diagnosis for clinical management, such cases demonstrate a potential benefit for clinical criteria to include seizures and an unbiased molecular approach to genetic testing.
Collapse
Affiliation(s)
- R C Caylor
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - L Grote
- Division of Clinical Genetics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - I Thiffault
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals, 2420 Pershing Rd., Kansas City, MO, 64108, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
| | - E G Farrow
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals, 2420 Pershing Rd., Kansas City, MO, 64108, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
| | - L Willig
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals, 2420 Pershing Rd., Kansas City, MO, 64108, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
- Division of Nephrology, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - S Soden
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals, 2420 Pershing Rd., Kansas City, MO, 64108, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
| | - S M Amudhavalli
- Division of Clinical Genetics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
| | - A J Nopper
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
- Division of Dermatology, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - K A Horii
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
- Division of Dermatology, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - E Fleming
- Division of Clinical Genetics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - J Jenkins
- Division of Clinical Genetics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - H Welsh
- Division of Clinical Genetics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - M Ilyas
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
- Division of Neurology, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - K Engleman
- Division of Clinical Genetics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - A Abdelmoity
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
- Division of Neurology, Children's Mercy Hospitals, Kansas City, MO, 64108, USA
| | - C J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, 64108, USA.
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals, 2420 Pershing Rd., Kansas City, MO, 64108, USA.
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA.
| |
Collapse
|
20
|
Petrikin JE, Cakici JA, Clark MM, Willig LK, Sweeney NM, Farrow EG, Saunders CJ, Thiffault I, Miller NA, Zellmer L, Herd SM, Holmes AM, Batalov S, Veeraraghavan N, Smith LD, Dimmock DP, Leeder JS, Kingsmore SF. The NSIGHT1-randomized controlled trial: rapid whole-genome sequencing for accelerated etiologic diagnosis in critically ill infants. NPJ Genom Med 2018; 3:6. [PMID: 29449963 PMCID: PMC5807510 DOI: 10.1038/s41525-018-0045-8] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/02/2018] [Accepted: 01/12/2018] [Indexed: 12/31/2022] Open
Abstract
Genetic disorders are a leading cause of morbidity and mortality in infants in neonatal and pediatric intensive care units (NICU/PICU). While genomic sequencing is useful for genetic disease diagnosis, results are usually reported too late to guide inpatient management. We performed an investigator-initiated, partially blinded, pragmatic, randomized, controlled trial to test the hypothesis that rapid whole-genome sequencing (rWGS) increased the proportion of NICU/PICU infants receiving a genetic diagnosis within 28 days. The participants were families with infants aged <4 months in a regional NICU and PICU, with illnesses of unknown etiology. The intervention was trio rWGS. Enrollment from October 2014 to June 2016, and follow-up until November 2016. Of all, 26 female infants, 37 male infants, and 2 infants of undetermined sex were randomized to receive rWGS plus standard genetic tests (n = 32, cases) or standard genetic tests alone (n = 33, controls). The study was terminated early due to loss of equipoise: 73% (24) controls received genomic sequencing as standard tests, and 15% (five) controls underwent compassionate cross-over to receive rWGS. Nevertheless, intention to treat analysis showed the rate of genetic diagnosis within 28 days of enrollment (the primary end-point) to be higher in cases (31%, 10 of 32) than controls (3%, 1 of 33; difference, 28% [95% CI, 10-46%]; p = 0.003). Among infants enrolled in the first 25 days of life, the rate of neonatal diagnosis was higher in cases (32%, 7 of 22) than controls (0%, 0 of 23; difference, 32% [95% CI, 11-53%];p = 0.004). Median age at diagnosis (25 days [range 14-90] in cases vs. 130 days [range 37-451] in controls) and median time to diagnosis (13 days [range 1-84] in cases, vs. 107 days [range 21-429] in controls) were significantly less in cases than controls (p = 0.04). In conclusion, rWGS increased the proportion of NICU/PICU infants who received timely diagnoses of genetic diseases.
Collapse
Affiliation(s)
- Josh E. Petrikin
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- Department of Pediatrics, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
| | - Julie A. Cakici
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Michelle M. Clark
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Laurel K. Willig
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- Department of Pediatrics, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
| | - Nathaly M. Sweeney
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
- Department of Pediatrics, University of California, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Emily G. Farrow
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- Department of Pediatrics, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
| | - Carol J. Saunders
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
- Department of Pathology, Children’s Mercy, Kansas City, MO 64108 USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
- Department of Pathology, Children’s Mercy, Kansas City, MO 64108 USA
| | - Neil A. Miller
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
| | - Suzanne M. Herd
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
| | - Anne M. Holmes
- Department of Pediatrics, Children’s Mercy, Kansas City, MO 64108 USA
| | - Serge Batalov
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | | | - Laurie D. Smith
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - David P. Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - J. Steven Leeder
- Department of Pediatrics, Children’s Mercy, Kansas City, MO 64108 USA
- School of Medicine, University of Missouri, Kansas City, MO 64108 USA
| | | |
Collapse
|
21
|
Abstract
The goal of this study was to explore variation among informed consent documents for clinical whole exome sequencing (WES) in order to identify the level of consistency with the recommendations from the American College of Medical Genetics and Genomics (ACMG) and the Presidential Commission for the Study of Bioethical Issues (Bioethics Commission) regarding informed consent for clinical WES. Recommendations were organized into a framework of key points for analysis. Content analysis was conducted on a sample of informed consent documents for clinical WES downloaded from 18 laboratory websites. We observed considerable variability in the content of informed consent documents among the sample of 18 laboratories. The mean Flesch-Kincaid Grade Level, a measure of readability, of the consent forms was 10.8, above the recommended 8th grade level. For each of the individual ACMG and Bioethics Commission recommendations, the frequency of inclusion ranged from 11% to 100%. For the overall list of 18 consent items, inclusion ranged from 11 to 17 items (Mean = 13.44, Mode = 14). This analysis will be useful to laboratories that wish to create informed consent documents that comply with these recommendations. The consistent use of standardized informed consent process could improve communication between clinicians and patients and increase understanding of genetic testing.
Collapse
Affiliation(s)
- Sara A Fowler
- Department of Biomedical and Health Informatics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Mark A Hoffman
- Department of Biomedical and Health Informatics, University of Missouri-Kansas City, Kansas City, MO, USA. .,Children's Mercy Hospital, 2401 Gilham Road, Kansas City, MO, 64108, USA.
| |
Collapse
|
22
|
Gallo V, Dotta L, Giardino G, Cirillo E, Lougaris V, D'Assante R, Prandini A, Consolini R, Farrow EG, Thiffault I, Saunders CJ, Leonardi A, Plebani A, Badolato R, Pignata C. Diagnostics of Primary Immunodeficiencies through Next-Generation Sequencing. Front Immunol 2016; 7:466. [PMID: 27872624 PMCID: PMC5098274 DOI: 10.3389/fimmu.2016.00466] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/17/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Recently, a growing number of novel genetic defects underlying primary immunodeficiencies (PIDs) have been identified, increasing the number of PID up to more than 250 well-defined forms. Next-generation sequencing (NGS) technologies and proper filtering strategies greatly contributed to this rapid evolution, providing the possibility to rapidly and simultaneously analyze large numbers of genes or the whole exome. OBJECTIVE To evaluate the role of targeted NGS and whole exome sequencing (WES) in the diagnosis of a case series, characterized by complex or atypical clinical features suggesting a PID, difficult to diagnose using the current diagnostic procedures. METHODS We retrospectively analyzed genetic variants identified through targeted NGS or WES in 45 patients with complex PID of unknown etiology. RESULTS Forty-seven variants were identified using targeted NGS, while 5 were identified using WES. Newly identified genetic variants were classified into four groups: (I) variations associated with a well-defined PID, (II) variations associated with atypical features of a well-defined PID, (III) functionally relevant variations potentially involved in the immunological features, and (IV) non-diagnostic genotype, in whom the link with phenotype is missing. We reached a conclusive genetic diagnosis in 7/45 patients (~16%). Among them, four patients presented with a typical well-defined PID. In the remaining three cases, mutations were associated with unexpected clinical features, expanding the phenotypic spectrum of typical PIDs. In addition, we identified 31 variants in 10 patients with complex phenotype, individually not causative per se of the disorder. CONCLUSION NGS technologies represent a cost-effective and rapid first-line genetic approach for the evaluation of complex PIDs. WES, despite a moderate higher cost compared to targeted, is emerging as a valuable tool to reach in a timely manner, a PID diagnosis with a considerable potential to draw genotype-phenotype correlation. Nevertheless, a large fraction of patients still remains without a conclusive diagnosis. In these patients, the sum of non-diagnostic variants might be proven informative in future studies with larger cohorts of patients.
Collapse
Affiliation(s)
- Vera Gallo
- Department of Translational Medical Sciences, Federico II University , Naples , Italy
| | - Laura Dotta
- Department of Clinical and Experimental Medicine, "Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia , Brescia , Italy
| | - Giuliana Giardino
- Department of Translational Medical Sciences, Federico II University , Naples , Italy
| | - Emilia Cirillo
- Department of Translational Medical Sciences, Federico II University , Naples , Italy
| | - Vassilios Lougaris
- Department of Clinical and Experimental Medicine, "Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia , Brescia , Italy
| | - Roberta D'Assante
- Department of Translational Medical Sciences, Federico II University , Naples , Italy
| | - Alberto Prandini
- Department of Clinical and Experimental Medicine, "Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia , Brescia , Italy
| | - Rita Consolini
- Department of Clinical and Experimental Medicine, University of Pisa , Pisa , Italy
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital , Kansas City, MO , USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital , Kansas City, MO , USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital , Kansas City, MO , USA
| | - Antonio Leonardi
- Department of Molecular Medicine and Medical Biotechnology, Federico II University , Naples , Italy
| | - Alessandro Plebani
- Department of Clinical and Experimental Medicine, "Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia , Brescia , Italy
| | - Raffaele Badolato
- Department of Clinical and Experimental Medicine, "Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia , Brescia , Italy
| | - Claudio Pignata
- Department of Translational Medical Sciences, Federico II University , Naples , Italy
| |
Collapse
|
23
|
Flex E, Niceta M, Cecchetti S, Thiffault I, Au MG, Capuano A, Piermarini E, Ivanova AA, Francis JW, Chillemi G, Chandramouli B, Carpentieri G, Haaxma CA, Ciolfi A, Pizzi S, Douglas GV, Levine K, Sferra A, Dentici ML, Pfundt RR, Le Pichon JB, Farrow E, Baas F, Piemonte F, Dallapiccola B, Graham JM, Saunders CJ, Bertini E, Kahn RA, Koolen DA, Tartaglia M. Biallelic Mutations in TBCD, Encoding the Tubulin Folding Cofactor D, Perturb Microtubule Dynamics and Cause Early-Onset Encephalopathy. Am J Hum Genet 2016; 99:962-973. [PMID: 27666370 DOI: 10.1016/j.ajhg.2016.08.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/09/2016] [Indexed: 12/13/2022] Open
Abstract
Microtubules are dynamic cytoskeletal elements coordinating and supporting a variety of neuronal processes, including cell division, migration, polarity, intracellular trafficking, and signal transduction. Mutations in genes encoding tubulins and microtubule-associated proteins are known to cause neurodevelopmental and neurodegenerative disorders. Growing evidence suggests that altered microtubule dynamics may also underlie or contribute to neurodevelopmental disorders and neurodegeneration. We report that biallelic mutations in TBCD, encoding one of the five co-chaperones required for assembly and disassembly of the αβ-tubulin heterodimer, the structural unit of microtubules, cause a disease with neurodevelopmental and neurodegenerative features characterized by early-onset cortical atrophy, secondary hypomyelination, microcephaly, thin corpus callosum, developmental delay, intellectual disability, seizures, optic atrophy, and spastic quadriplegia. Molecular dynamics simulations predicted long-range and/or local structural perturbations associated with the disease-causing mutations. Biochemical analyses documented variably reduced levels of TBCD, indicating relative instability of mutant proteins, and defective β-tubulin binding in a subset of the tested mutants. Reduced or defective TBCD function resulted in decreased soluble α/β-tubulin levels and accelerated microtubule polymerization in fibroblasts from affected subjects, demonstrating an overall shift toward a more rapidly growing and stable microtubule population. These cells displayed an aberrant mitotic spindle with disorganized, tangle-shaped microtubules and reduced aster formation, which however did not alter appreciably the rate of cell proliferation. Our findings establish that defective TBCD function underlies a recognizable encephalopathy and drives accelerated microtubule polymerization and enhanced microtubule stability, underscoring an additional cause of altered microtubule dynamics with impact on neuronal function and survival in the developing brain.
Collapse
|
24
|
Thiffault I, Speca DJ, Austin DC, Cobb MM, Eum KS, Safina NP, Grote L, Farrow EG, Miller N, Soden S, Kingsmore SF, Trimmer JS, Saunders CJ, Sack JT. A novel epileptic encephalopathy mutation in KCNB1 disrupts Kv2.1 ion selectivity, expression, and localization. ACTA ACUST UNITED AC 2016; 146:399-410. [PMID: 26503721 PMCID: PMC4621747 DOI: 10.1085/jgp.201511444] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A missense mutation in the pore-forming α subunit of a delayed rectifier Kv channel is associated with epileptic encephalopathy, alters the cation selectivity of voltage-gated currents, and disrupts channel expression and localization. The epileptic encephalopathies are a group of highly heterogeneous genetic disorders. The majority of disease-causing mutations alter genes encoding voltage-gated ion channels, neurotransmitter receptors, or synaptic proteins. We have identified a novel de novo pathogenic K+ channel variant in an idiopathic epileptic encephalopathy family. Here, we report the effects of this mutation on channel function and heterologous expression in cell lines. We present a case report of infantile epileptic encephalopathy in a young girl, and trio-exome sequencing to determine the genetic etiology of her disorder. The patient was heterozygous for a de novo missense variant in the coding region of the KCNB1 gene, c.1133T>C. The variant encodes a V378A mutation in the α subunit of the Kv2.1 voltage-gated K+ channel, which is expressed at high levels in central neurons and is an important regulator of neuronal excitability. We found that expression of the V378A variant results in voltage-activated currents that are sensitive to the selective Kv2 channel blocker guangxitoxin-1E. These voltage-activated Kv2.1 V378A currents were nonselective among monovalent cations. Striking cell background–dependent differences in expression and subcellular localization of the V378A mutation were observed in heterologous cells. Further, coexpression of V378A subunits and wild-type Kv2.1 subunits reciprocally affects their respective trafficking characteristics. A recent study reported epileptic encephalopathy-linked missense variants that render Kv2.1 a tonically activated, nonselective cation channel that is not voltage activated. Our findings strengthen the correlation between mutations that result in loss of Kv2.1 ion selectivity and development of epileptic encephalopathy. However, the strong voltage sensitivity of currents from the V378A mutant indicates that the loss of voltage-sensitive gating seen in all other reported disease mutants is not required for an epileptic encephalopathy phenotype. In addition to electrophysiological differences, we suggest that defects in expression and subcellular localization of Kv2.1 V378A channels could contribute to the pathophysiology of this KCNB1 variant.
Collapse
Affiliation(s)
- Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108
| | - David J Speca
- Department of Neurobiology, Physiology and Behavior, Department of Physiology and Membrane Biology, and Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA 95616
| | - Daniel C Austin
- Department of Neurobiology, Physiology and Behavior, Department of Physiology and Membrane Biology, and Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA 95616
| | - Melanie M Cobb
- Department of Neurobiology, Physiology and Behavior, Department of Physiology and Membrane Biology, and Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA 95616
| | - Kenneth S Eum
- Department of Neurobiology, Physiology and Behavior, Department of Physiology and Membrane Biology, and Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA 95616
| | - Nicole P Safina
- Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108
| | - Lauren Grote
- Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108
| | - Neil Miller
- Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108
| | - Sarah Soden
- Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108 Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108 University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108 Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108 Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108 University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108
| | - James S Trimmer
- Department of Neurobiology, Physiology and Behavior, Department of Physiology and Membrane Biology, and Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA 95616 Department of Neurobiology, Physiology and Behavior, Department of Physiology and Membrane Biology, and Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA 95616
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108 Center for Pediatric Genomic Medicine, Department of Pathology and Laboratory Medicine, and Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108 University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108
| | - Jon T Sack
- Department of Neurobiology, Physiology and Behavior, Department of Physiology and Membrane Biology, and Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA 95616 Department of Neurobiology, Physiology and Behavior, Department of Physiology and Membrane Biology, and Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA 95616
| |
Collapse
|
25
|
Noll AC, Miller NA, Smith LD, Yoo B, Fiedler S, Cooley LD, Willig LK, Petrikin JE, Cakici J, Lesko J, Newton A, Detherage K, Thiffault I, Saunders CJ, Farrow EG, Kingsmore SF. Clinical detection of deletion structural variants in whole-genome sequences. NPJ Genom Med 2016; 1:16026. [PMID: 29263817 PMCID: PMC5685307 DOI: 10.1038/npjgenmed.2016.26] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 12/13/2022] Open
Abstract
Optimal management of acutely ill infants with monogenetic diseases requires rapid identification of causative haplotypes. Whole-genome sequencing (WGS) has been shown to identify pathogenic nucleotide variants in such infants. Deletion structural variants (DSVs, >50 nt) are implicated in many genetic diseases, and tools have been designed to identify DSVs using short-read WGS. Optimisation and integration of these tools into a WGS pipeline could improve diagnostic sensitivity and specificity of WGS. In addition, it may improve turnaround time when compared with current CNV assays, enhancing utility in acute settings. Here we describe DSV detection methods for use in WGS for rapid diagnosis in acutely ill infants: SKALD (Screening Konsensus and Annotation of Large Deletions) combines calls from two tools (Breakdancer and GenomeStrip) with calibrated filters and clinical interpretation rules. In four WGS runs, the average analytic precision (positive predictive value) of SKALD was 78%, and recall (sensitivity) was 27%, when compared with validated reference DSV calls. When retrospectively applied to a cohort of 36 families with acutely ill infants SKALD identified causative DSVs in two. The first was heterozygous deletion of exons 1–3 of MMP21 in trans with a heterozygous frame-shift deletion in two siblings with transposition of the great arteries and heterotaxy. In a newborn female with dysmorphic features, ventricular septal defect and persistent pulmonary hypertension, SKALD identified the breakpoints of a heterozygous, de novo 1p36.32p36.13 deletion. In summary, consensus DSV calling, implemented in an 8-h computational pipeline with parameterised filtering, has the potential to increase the diagnostic yield of WGS in acutely ill neonates and discover novel disease genes.
Collapse
Affiliation(s)
- Aaron C Noll
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Heartland Institute for Clinical and Translational Research, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Heartland Institute for Clinical and Translational Research, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Byunggil Yoo
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Stephanie Fiedler
- Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Linda D Cooley
- Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA.,Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Julie Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - John Lesko
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Angela Newton
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Kali Detherage
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA.,Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA.,Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Stephen F Kingsmore
- Heartland Institute for Clinical and Translational Research, University of Kansas Medical Center, Kansas City, KS, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| |
Collapse
|
26
|
Giardino G, Gallo V, Somma D, Farrow EG, Thiffault I, D'Assante R, Donofrio V, Paciolla M, Ursini MV, Leonardi A, Saunders CJ, Pignata C. Targeted next-generation sequencing revealed MYD88 deficiency in a child with chronic yersiniosis and granulomatous lymphadenitis. J Allergy Clin Immunol 2015; 137:1591-1595.e4. [PMID: 26632527 DOI: 10.1016/j.jaci.2015.09.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 09/07/2015] [Accepted: 09/16/2015] [Indexed: 10/22/2022]
Affiliation(s)
- Giuliana Giardino
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | - Vera Gallo
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | - Domenico Somma
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Naples, Italy
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pathology, Children's Mercy-Kansas City, Kansas City, Mo; School of Medicine, University of Missouri-Kansas City, Kansas City, Mo
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pathology, Children's Mercy-Kansas City, Kansas City, Mo; School of Medicine, University of Missouri-Kansas City, Kansas City, Mo
| | - Roberta D'Assante
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | | | | | | | - Antonio Leonardi
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Naples, Italy
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pathology, Children's Mercy-Kansas City, Kansas City, Mo; School of Medicine, University of Missouri-Kansas City, Kansas City, Mo
| | - Claudio Pignata
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy.
| |
Collapse
|
27
|
Saunders CJ, Moon SH, Liu X, Thiffault I, Coffman K, LePichon JB, Taboada E, Smith LD, Farrow EG, Miller N, Gibson M, Patterson M, Kingsmore SF, Gross RW. Loss of function variants in human PNPLA8 encoding calcium-independent phospholipase A2 γ recapitulate the mitochondriopathy of the homologous null mouse. Hum Mutat 2015; 36:301-6. [PMID: 25512002 DOI: 10.1002/humu.22743] [Citation(s) in RCA: 27] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/09/2014] [Indexed: 12/13/2022]
Abstract
Mitochondriopathies are a group of clinically heterogeneous genetic diseases caused by defects in mitochondrial metabolism, bioenergetic efficiency, and/or signaling functions. The large majority of proteins involved in mitochondrial function are encoded by nuclear genes, with many yet to be associated with human disease. We performed exome sequencing on a young girl with a suspected mitochondrial myopathy that manifested as progressive muscle weakness, hypotonia, seizures, poor weight gain, and lactic acidosis. She was compound heterozygous for two frameshift mutations, p.Asn112HisfsX29 and p.Leu659AlafsX4, in the PNPLA8 gene, which encodes mitochondrial calcium-independent phospholipase A2 γ (iPLA2 γ). Western blot analysis of affected muscle displayed the absence of PNPLA8 protein. iPLA2 s are critical mediators of a variety of cellular processes including growth, metabolism, and lipid second messenger generation, exerting their functions through catalyzing the cleavage of the acyl groups in glycerophospholipids. The clinical presentation, muscle histology and the mitochondrial ultrastructural abnormalities of this proband are highly reminiscent of Pnpla8 null mice. Although other iPLA2 -related diseases have been identified, namely, infantile neuroaxonal dystrophy and neutral lipid storage disease with myopathy, this is the first report of PNPLA8-related disease in a human. We suggest PNPLA8 join the increasing list of human genes involved in lipid metabolism associated with neuromuscular diseases due to mitochondrial dysfunction.
Collapse
Affiliation(s)
- Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals, Kansas City, Missouri
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Guimier A, Gabriel GC, Bajolle F, Tsang M, Liu H, Noll A, Schwartz M, El Malti R, Smith LD, Klena NT, Jimenez G, Miller NA, Oufadem M, Moreau de Bellaing A, Yagi H, Saunders CJ, Baker CN, Di Filippo S, Peterson KA, Thiffault I, Bole-Feysot C, Cooley LD, Farrow EG, Masson C, Schoen P, Deleuze JF, Nitschké P, Lyonnet S, de Pontual L, Murray SA, Bonnet D, Kingsmore SF, Amiel J, Bouvagnet P, Lo CW, Gordon CT. MMP21 is mutated in human heterotaxy and is required for normal left-right asymmetry in vertebrates. Nat Genet 2015; 47:1260-3. [PMID: 26437028 PMCID: PMC5620017 DOI: 10.1038/ng.3376] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/10/2015] [Indexed: 12/26/2022]
Abstract
Heterotaxy results from a failure to establish normal left-right asymmetry early in embryonic development. By whole-exome sequencing, whole-genome sequencing and high-throughput cohort resequencing, we identified recessive mutations in MMP21 (encoding matrix metallopeptidase 21) in nine index cases with heterotaxy. In addition, Mmp21-mutant mice and mmp21-morphant zebrafish displayed heterotaxy and abnormal cardiac looping, respectively, suggesting a new role for extracellular matrix remodeling in the establishment of laterality in vertebrates.
Collapse
Affiliation(s)
- Anne Guimier
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Fanny Bajolle
- Unité Médico-Chirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de Référence Malformations Cardiaques Congénitales Complexes (M3C), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Hui Liu
- Laboratoire Cardiogénétique, Hospices Civils de Lyon, Bron, France
- EA 4173, Université Lyon 1 and Hôpital Nord Ouest, Lyon, France
| | - Aaron Noll
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Molly Schwartz
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rajae El Malti
- Laboratoire Cardiogénétique, Hospices Civils de Lyon, Bron, France
- EA 4173, Université Lyon 1 and Hôpital Nord Ouest, Lyon, France
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Nikolai T Klena
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Gina Jimenez
- Laboratoire Cardiogénétique, Hospices Civils de Lyon, Bron, France
- EA 4173, Université Lyon 1 and Hôpital Nord Ouest, Lyon, France
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Myriam Oufadem
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Anne Moreau de Bellaing
- Laboratoire Cardiogénétique, Hospices Civils de Lyon, Bron, France
- EA 4173, Université Lyon 1 and Hôpital Nord Ouest, Lyon, France
| | - Hisato Yagi
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | | | - Sylvie Di Filippo
- Service de Cardiologie Pédiatrique, Hospices Civils de Lyon, Lyon, France
| | | | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Christine Bole-Feysot
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Linda D Cooley
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Cécile Masson
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Patric Schoen
- Department of Pediatric Cardiology and Congenital Heart Disease, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Jean-François Deleuze
- Centre National de Génotypage, Institut de Génomique, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Evry, France
| | - Patrick Nitschké
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
- Service de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Loic de Pontual
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Damien Bonnet
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
- Unité Médico-Chirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de Référence Malformations Cardiaques Congénitales Complexes (M3C), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
- Service de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Patrice Bouvagnet
- Laboratoire Cardiogénétique, Hospices Civils de Lyon, Bron, France
- EA 4173, Université Lyon 1 and Hôpital Nord Ouest, Lyon, France
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| |
Collapse
|
29
|
Miller NA, Farrow EG, Gibson M, Willig LK, Twist G, Yoo B, Marrs T, Corder S, Krivohlavek L, Walter A, Petrikin JE, Saunders CJ, Thiffault I, Soden SE, Smith LD, Dinwiddie DL, Herd S, Cakici JA, Catreux S, Ruehle M, Kingsmore SF. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Med 2015; 7:100. [PMID: 26419432 PMCID: PMC4588251 DOI: 10.1186/s13073-015-0221-8] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/10/2015] [Indexed: 12/14/2022] Open
Abstract
While the cost of whole genome sequencing (WGS) is approaching the realm of routine medical tests, it remains too tardy to help guide the management of many acute medical conditions. Rapid WGS is imperative in light of growing evidence of its utility in acute care, such as in diagnosis of genetic diseases in very ill infants, and genotype-guided choice of chemotherapy at cancer relapse. In such situations, delayed, empiric, or phenotype-based clinical decisions may meet with substantial morbidity or mortality. We previously described a rapid WGS method, STATseq, with a sensitivity of >96 % for nucleotide variants that allowed a provisional diagnosis of a genetic disease in 50 h. Here improvements in sequencing run time, read alignment, and variant calling are described that enable 26-h time to provisional molecular diagnosis with >99.5 % sensitivity and specificity of genotypes. STATseq appears to be an appropriate strategy for acutely ill patients with potentially actionable genetic diseases.
Collapse
Affiliation(s)
- Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Margaret Gibson
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Byunggil Yoo
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Tyler Marrs
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Shane Corder
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Lisa Krivohlavek
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Adam Walter
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA
| | - Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Darrell L Dinwiddie
- Deparment of Pediatrics, and Clinical Translational Science Center, University of New Mexico Health Science Center, Albuquerque, NM, 87131, USA
| | - Suzanne Herd
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Julie A Cakici
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Severine Catreux
- Edico Genome, Inc., 3344 North Torrey Pines Court, Plaza Level, La Jolla, CA, 92037, USA
| | - Mike Ruehle
- Edico Genome, Inc., 3344 North Torrey Pines Court, Plaza Level, La Jolla, CA, 92037, USA
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA. .,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA. .,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA. .,Rady Pediatric Genomics and Systems Medicine Institute, Rady Chlildren's Hospital, 3020 Children's Way, San Diego, CA, 92123, USA.
| |
Collapse
|
30
|
Soden SE, Saunders CJ, Willig LK, Farrow EG, Smith LD, Petrikin JE, LePichon JB, Miller NA, Thiffault I, Dinwiddie DL, Twist G, Noll A, Heese BA, Zellmer L, Atherton AM, Abdelmoity AT, Safina N, Nyp SS, Zuccarelli B, Larson IA, Modrcin A, Herd S, Creed M, Ye Z, Yuan X, Brodsky RA, Kingsmore SF. Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci Transl Med 2015; 6:265ra168. [PMID: 25473036 DOI: 10.1126/scitranslmed.3010076] [Citation(s) in RCA: 384] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neurodevelopmental disorders (NDDs) affect more than 3% of children and are attributable to single-gene mutations at more than 1000 loci. Traditional methods yield molecular diagnoses in less than one-half of children with NDD. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) can enable diagnosis of NDD, but their clinical and cost-effectiveness are unknown. One hundred families with 119 children affected by NDD received diagnostic WGS and/or WES of parent-child trios, wherein the sequencing approach was guided by acuity of illness. Forty-five percent received molecular diagnoses. An accelerated sequencing modality, rapid WGS, yielded diagnoses in 73% of families with acutely ill children (11 of 15). Forty percent of families with children with nonacute NDD, followed in ambulatory care clinics (34 of 85), received diagnoses: 33 by WES and 1 by staged WES then WGS. The cost of prior negative tests in the nonacute patients was $19,100 per family, suggesting sequencing to be cost-effective at up to $7640 per family. A change in clinical care or impression of the pathophysiology was reported in 49% of newly diagnosed families. If WES or WGS had been performed at symptom onset, genomic diagnoses may have been made 77 months earlier than occurred in this study. It is suggested that initial diagnostic evaluation of children with NDD should include trio WGS or WES, with extension of accelerated sequencing modalities to high-acuity patients.
Collapse
Affiliation(s)
- Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA.
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Jean-Baptiste LePichon
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Darrell L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA. Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Aaron Noll
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Bryce A Heese
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Andrea M Atherton
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Ahmed T Abdelmoity
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Nicole Safina
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Sarah S Nyp
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Britton Zuccarelli
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Ingrid A Larson
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Ann Modrcin
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Suzanne Herd
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Mitchell Creed
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Zhaohui Ye
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Xuan Yuan
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robert A Brodsky
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| |
Collapse
|
31
|
Affiliation(s)
- Jean-Baptiste LePichon
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri2School of Medicine, University of Missouri-Kansas City, Kansas City
| | - Carol J Saunders
- School of Medicine, University of Missouri-Kansas City, Kansas City3Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | - Sarah E Soden
- School of Medicine, University of Missouri-Kansas City, Kansas City3Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| |
Collapse
|
32
|
Saunders CJ, Moon SH, Liu X, Thiffault I, Coffman K, LePichon JB, Taboada E, Smith LD, Farrow EG, Miller N, Gibson M, Patterson M, Kingsmore SF, Gross RW. Loss of Function Variants in Human PNPLA8Encoding Calcium-Independent Phospholipase A 2γ Recapitulate the Mitochondriopathy of the Homologous Null Mouse. Hum Mutat 2015. [DOI: 10.1002/humu.22790] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Carol J. Saunders
- Center for Pediatric Genomic Medicine; Children's Mercy Hospitals; Kansas City Missouri
| | - Sung Ho Moon
- Division of Bioorganic Chemistry and Molecular Pharmacology, Departments of Internal Medicine and Developmental Biology; Washington University School of Medicine; St. Louis Missouri
| | - Xinping Liu
- Division of Bioorganic Chemistry and Molecular Pharmacology, Departments of Internal Medicine and Developmental Biology; Washington University School of Medicine; St. Louis Missouri
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine; Children's Mercy Hospitals; Kansas City Missouri
| | - Keith Coffman
- Division of Neurology, Department of Pediatrics; Children's Mercy Hospitals; Kansas City Missouri
| | - Jean-Baptiste LePichon
- Division of Neurology, Department of Pediatrics; Children's Mercy Hospitals; Kansas City Missouri
| | - Eugenio Taboada
- Department of Pathology and Laboratory Medicine; Children's Mercy Hospitals; Kansas City Missouri
| | - Laurie D. Smith
- Center for Pediatric Genomic Medicine; Children's Mercy Hospitals; Kansas City Missouri
| | - Emily G. Farrow
- Center for Pediatric Genomic Medicine; Children's Mercy Hospitals; Kansas City Missouri
| | - Neil Miller
- Center for Pediatric Genomic Medicine; Children's Mercy Hospitals; Kansas City Missouri
| | - Margaret Gibson
- Center for Pediatric Genomic Medicine; Children's Mercy Hospitals; Kansas City Missouri
| | - Melanie Patterson
- Center for Pediatric Genomic Medicine; Children's Mercy Hospitals; Kansas City Missouri
| | - Stephen F. Kingsmore
- Center for Pediatric Genomic Medicine; Children's Mercy Hospitals; Kansas City Missouri
| | - Richard W. Gross
- Division of Bioorganic Chemistry and Molecular Pharmacology, Departments of Internal Medicine and Developmental Biology; Washington University School of Medicine; St. Louis Missouri
| |
Collapse
|
33
|
Willig LK, Petrikin JE, Smith LD, Saunders CJ, Thiffault I, Miller NA, Soden SE, Cakici JA, Herd SM, Twist G, Noll A, Creed M, Alba PM, Carpenter SL, Clements MA, Fischer RT, Hays JA, Kilbride H, McDonough RJ, Rosterman JL, Tsai SL, Zellmer L, Farrow EG, Kingsmore SF. Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: a retrospective analysis of diagnostic and clinical findings. Lancet Respir Med 2015; 3:377-87. [PMID: 25937001 DOI: 10.1016/s2213-2600(15)00139-3] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 12/28/2022]
Abstract
BACKGROUND Genetic disorders and congenital anomalies are the leading causes of infant mortality. Diagnosis of most genetic diseases in neonatal and paediatric intensive care units (NICU and PICU) is not sufficiently timely to guide acute clinical management. We used rapid whole-genome sequencing (STATseq) in a level 4 NICU and PICU to assess the rate and types of molecular diagnoses, and the prevalence, types, and effect of diagnoses that are likely to change medical management in critically ill infants. METHODS We did a retrospective comparison of STATseq and standard genetic testing in a case series from the NICU and PICU of a large children's hospital between Nov 11, 2011, and Oct 1, 2014. The participants were families with an infant younger than 4 months with an acute illness of suspected genetic cause. The intervention was STATseq of trios (both parents and their affected infant). The main measures were the diagnostic rate, time to diagnosis, and rate of change in management after standard genetic testing and STATseq. FINDINGS 20 (57%) of 35 infants were diagnosed with a genetic disease by use of STATseq and three (9%) of 32 by use of standard genetic testing (p=0·0002). Median time to genome analysis was 5 days (range 3-153) and median time to STATseq report was 23 days (5-912). 13 (65%) of 20 STATseq diagnoses were associated with de-novo mutations. Acute clinical usefulness was noted in 13 (65%) of 20 infants with a STATseq diagnosis, four (20%) had diagnoses with strongly favourable effects on management, and six (30%) were started on palliative care. 120-day mortality was 57% (12 of 21) in infants with a genetic diagnosis. INTERPRETATION In selected acutely ill infants, STATseq had a high rate of diagnosis of genetic disorders. Most diagnoses altered the management of infants in the NICU or PICU. The very high infant mortality rate indicates a substantial need for rapid genomic diagnoses to be allied with a novel framework for precision medicine for infants in NICU and PICU who are diagnosed with genetic diseases to improve outcomes. FUNDING Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Human Genome Research Institute, and National Center for Advancing Translational Sciences.
Collapse
Affiliation(s)
- Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Julie A Cakici
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Suzanne M Herd
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Aaron Noll
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Mitchell Creed
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Patria M Alba
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Shannon L Carpenter
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Mark A Clements
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Ryan T Fischer
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - J Allyson Hays
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Howard Kilbride
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Ryan J McDonough
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Jamie L Rosterman
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Sarah L Tsai
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA.
| |
Collapse
|
34
|
Dinwiddie DL, Soden SE, Saunders CJ, Miller NA, Farrow EG, Smith LD, Kingsmore SF. De novo frameshift mutation in ASXL3 in a patient with global developmental delay, microcephaly, and craniofacial anomalies. BMC Med Genomics 2013; 6:32. [PMID: 24044690 PMCID: PMC3851682 DOI: 10.1186/1755-8794-6-32] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/11/2013] [Indexed: 12/23/2022] Open
Abstract
Background Currently, diagnosis of affected individuals with rare genetic disorders can be lengthy and costly, resulting in a diagnostic odyssey and in many patients a definitive molecular diagnosis is never achieved despite extensive clinical investigation. The recent advent and use of genomic medicine has resulted in a paradigm shift in the clinical molecular genetics of rare diseases and has provided insight into the causes of numerous rare genetic conditions. In particular, whole exome and genome sequencing of families has been particularly useful in discovering de novo germline mutations as the cause of both rare diseases and complex disorders. Case presentation We present a six year old, nonverbal African American female with microcephaly, autism, global developmental delay, and metopic craniosynostosis. Exome sequencing of the patient and her two parents revealed a heterozygous two base pair de novo deletion, c.1897_1898delCA, p.Gln633ValfsX13 in ASXL3, predicted to result in a frameshift at codon 633 with substitution of a valine for a glutamine and introduction of a premature stop codon. Conclusions We provide additional evidence that, truncating and frameshifting mutations in the ASXL3 gene are the cause of a newly recognized disorder characterized by severe global developmental delay, short stature, microcephaly, and craniofacial anomalies. Furthermore, we expand the knowledge about disease causing mutations and the genotype-phenotype relationships in ASXL3 and provide evidence that rare, nonsynonymous, damaging mutations are not associated with developmental delay or microcephaly.
Collapse
Affiliation(s)
- Darrell L Dinwiddie
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
| | | | | | | | | | | | | |
Collapse
|
35
|
Langley RJ, Tsalik EL, van Velkinburgh JC, Glickman SW, Rice BJ, Wang C, Chen B, Carin L, Suarez A, Mohney RP, Freeman DH, Wang M, You J, Wulff J, Thompson JW, Moseley MA, Reisinger S, Edmonds BT, Grinnell B, Nelson DR, Dinwiddie DL, Miller NA, Saunders CJ, Soden SS, Rogers AJ, Gazourian L, Fredenburgh LE, Massaro AF, Baron RM, Choi AMK, Corey GR, Ginsburg GS, Cairns CB, Otero RM, Fowler VG, Rivers EP, Woods CW, Kingsmore SF. An integrated clinico-metabolomic model improves prediction of death in sepsis. Sci Transl Med 2013; 5:195ra95. [PMID: 23884467 DOI: 10.1126/scitranslmed.3005893] [Citation(s) in RCA: 322] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sepsis is a common cause of death, but outcomes in individual patients are difficult to predict. Elucidating the molecular processes that differ between sepsis patients who survive and those who die may permit more appropriate treatments to be deployed. We examined the clinical features and the plasma metabolome and proteome of patients with and without community-acquired sepsis, upon their arrival at hospital emergency departments and 24 hours later. The metabolomes and proteomes of patients at hospital admittance who would ultimately die differed markedly from those of patients who would survive. The different profiles of proteins and metabolites clustered into the following groups: fatty acid transport and β-oxidation, gluconeogenesis, and the citric acid cycle. They differed consistently among several sets of patients, and diverged more as death approached. In contrast, the metabolomes and proteomes of surviving patients with mild sepsis did not differ from survivors with severe sepsis or septic shock. An algorithm derived from clinical features together with measurements of five metabolites predicted patient survival. This algorithm may help to guide the treatment of individual patients with sepsis.
Collapse
|
36
|
Dinwiddie DL, Kingsmore SF, Caracciolo S, Rossi G, Moratto D, Mazza C, Sabelli C, Bacchetta R, Passerini L, Magri C, Bell CJ, Miller NA, Hateley SL, Saunders CJ, Zhang L, Schroth GP, Barlati S, Badolato R. Combined DOCK8 and CLEC7A mutations causing immunodeficiency in 3 brothers with diarrhea, eczema, and infections. J Allergy Clin Immunol 2013; 131:594-7.e1-3. [PMID: 23374272 DOI: 10.1016/j.jaci.2012.10.062] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 10/29/2012] [Accepted: 10/31/2012] [Indexed: 11/25/2022]
|
37
|
Dinwiddie DL, Smith LD, Miller NA, Atherton AM, Farrow EG, Strenk ME, Soden SE, Saunders CJ, Kingsmore SF. Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome. Genomics 2013; 102:148-56. [PMID: 23631824 DOI: 10.1016/j.ygeno.2013.04.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [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: 03/12/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 01/22/2023]
Abstract
Mitochondrial diseases are notoriously difficult to diagnose due to extreme locus and allelic heterogeneity, with both nuclear and mitochondrial genomes potentially liable. Using exome sequencing we demonstrate the ability to rapidly and cost effectively evaluate both the nuclear and mitochondrial genomes to obtain a molecular diagnosis for four patients with three distinct mitochondrial disorders. One patient was found to have Leigh syndrome due to a mutation in MT-ATP6, two affected siblings were discovered to be compound heterozygous for mutations in the NDUFV1 gene, which causes mitochondrial complex I deficiency, and one patient was found to have coenzyme Q10 deficiency due to compound heterozygous mutations in COQ2. In all cases conventional diagnostic testing failed to identify a molecular diagnosis. We suggest that additional studies should be conducted to evaluate exome sequencing as a primary diagnostic test for mitochondrial diseases, including those due to mtDNA mutations.
Collapse
Affiliation(s)
- Darrell L Dinwiddie
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Saunders CJ, Li WY, Patel TD, Muday JA, Silver WL. Dissecting the role of TRPV1 in detecting multiple trigeminal irritants in three behavioral assays for sensory irritation. F1000Res 2013; 2:74. [PMID: 24358880 PMCID: PMC3814916 DOI: 10.12688/f1000research.2-74.v1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/04/2013] [Indexed: 01/11/2023] Open
Abstract
Polymodal neurons of the trigeminal nerve innervate the nasal cavity, nasopharynx, oral cavity and cornea. Trigeminal nociceptive fibers express a diverse collection of receptors and are stimulated by a wide variety of chemicals. However, the mechanism of stimulation is known only for relatively few of these compounds. Capsaicin, for example, activates transient receptor potential vanilloid 1 (TRPV1) channels. In the present study, wildtype (C57Bl/6J) and TRPV1 knockout mice were tested in three behavioral assays for irritation to determine if TRPV1 is necessary to detect trigeminal irritants in addition to capsaicin. In one assay mice were presented with a chemical via a cotton swab and their response scored on a 5 level scale. In another assay, a modified two bottle preference test, which avoids the confound of mixing irritants with the animal’s drinking water, was used to assess aversion. In the final assay, an air dilution olfactometer was used to administer volatile compounds to mice restrained in a double-chambered plethysmograph where respiratory reflexes were monitored. TRPV1 knockouts showed deficiencies in the detection of benzaldehyde, cyclohexanone and eugenol in at least one assay. However, cyclohexanone was the only substance tested that appears to act solely through TRPV1.
Collapse
Affiliation(s)
- C J Saunders
- Department of Biology, Wake Forest University, Winston-Salem, NC, 27109, USA ; Rocky Mountain Taste and Smell Center, Neuroscience Program, Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Winston Y Li
- Department of Biology, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Tulsi D Patel
- Department of Biology, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Jeffrey A Muday
- Department of Biology, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Wayne L Silver
- Department of Biology, Wake Forest University, Winston-Salem, NC, 27109, USA
| |
Collapse
|
39
|
Bass JA, Goldman J, Jackson MA, Gasior AC, Sharp SW, Drews AA, Saunders CJ, St Peter SD. Pediatric Crohn disease presenting as appendicitis: differentiating features from typical appendicitis. Eur J Pediatr Surg 2012; 22:274-8. [PMID: 22648194 DOI: 10.1055/s-0032-1313348] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
BACKGROUND The initial presentation of Crohn disease (CD) may mimic acute appendicitis, and preoperative clues may aid in recognizing patients at risk for CD. METHODS A retrospective case control study of patients presenting over 10 years compared control patients with appendicitis versus patients presenting with appendicitis who ultimately developed CD. We matched 10 patients of the same age, gender, and perforated versus nonperforated appendicitis status for each of the CD patients. Demographic, laboratory, and clinical data were compared. Additionally, appendectomy specimens of CD patients were genotyped for common NOD2 (nucleotide-binding oligomerization domain-containing protein 2) mutations. RESULTS Of 2718 patients treated for appendicitis, 8 subsequently developed CD. Compared to the matched controls, CD patients were found to have lower hemoglobin (10.4 + 1.0 vs. 13.3 + 0.2, p < 0.0001) and mean corpuscular volume (MCV) (72.5 + 3.4 vs. 84.1 + 0.5, p < 0.0001) values, and higher platelets values (444.8 + 42.2 vs. 275.6 + 8.0, p < 0.0001) at initial presentation. Anthropometric z-scores, length of stay, and antibiotic therapy duration did not significantly differ between groups. The NOD2 mutation frequency (25%) was consistent with the currently described CD population. CONCLUSIONS Preoperative findings of a low hemoglobin level and MCV count, and a high platelet count in a child presenting with appendicitis warrant further evaluation for CD, as prompt diagnosis allows for optimal treatment and quality of life for these patients.
Collapse
Affiliation(s)
- Julie A Bass
- Division of Gastroenterology, Children's Mercy Hospitals and Clinics, Kansas City, Missouri 64108, United States.
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Kingsmore SF, Dinwiddie DL, Miller NA, Soden SE, Saunders CJ. Adopting orphans: comprehensive genetic testing of Mendelian diseases of childhood by next-generation sequencing. Expert Rev Mol Diagn 2012; 11:855-68. [PMID: 22022947 DOI: 10.1586/erm.11.70] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Orphan diseases are individually uncommon but collectively contribute significantly to pediatric morbidity, mortality and healthcare costs. Current molecular testing for rare genetic disorders is often a lengthy and costly endeavor, and in many cases a molecular diagnosis is never achieved despite extensive testing. Diseases with locus heterogeneity or overlapping signs and symptoms are especially challenging owing to the number of potential targets. Consequently, there is immense need for scalable, economical, rapid, multiplexed diagnostic testing for rare Mendelian diseases. Recent advances in next-generation sequencing and bioinformatic technologies have the potential to change the standard of care for the diagnosis of rare genetic disorders. These advances will be reviewed in the setting of a recently developed test for 592 autosomal recessive and X-linked diseases.
Collapse
Affiliation(s)
- Stephen F Kingsmore
- Children's Mercy Hospital & Clinics, 2401 Gillham Road, Kansas City, MO 64108, USA.
| | | | | | | | | |
Collapse
|
41
|
Kingsmore SF, Lantos JD, Dinwiddie DL, Miller NA, Soden SE, Farrow EG, Saunders CJ. Next-generation community genetics for low- and middle-income countries. Genome Med 2012; 4:25. [PMID: 22458566 PMCID: PMC3446275 DOI: 10.1186/gm324] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A recent report by the World Health Organization calls for implementation of community genetics programs in low- and middle-income countries (LMICs). Their focus is prevention of congenital disorders and genetic diseases at the population level, in addition to providing genetics services, including diagnosis and counseling. The proposed strategies include both newborn screening and population screening for carrier detection, in addition to lowering the incidence of congenital disorders and genetic diseases through the removal of environmental factors. In this article, we consider the potential impact of such testing on global health and highlight the near-term relevance of next-generation sequencing (NGS) and bioinformatic approaches to their implementation. Key attributes of NGS for community genetics programs are homogeneous approach, high multiplexing of diseases and samples, as well as rapidly falling costs of new technologies. In the near future, we estimate that appropriate use of population-specific test panels could cost as little as $10 for 10 Mendelian disorders and could have a major impact on diseases that currently affect 2% of children worldwide. However, the successful deployment of this technological innovation in LMICs will require high value for human life, thoughtful implementation, and autonomy of individual decisions, supported by appropriate genetic counseling and community education.
Collapse
Affiliation(s)
- Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - John D Lantos
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - Darrell L Dinwiddie
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| |
Collapse
|
42
|
Gianakopoulos PJ, Zhang Y, Pencea N, Orlic-Milacic M, Mittal K, Windpassinger C, White SJ, Kroisel PM, Chow EWC, Saunders CJ, Minassian BA, Vincent JB. Mutations in MECP2 exon 1 in classical Rett patients disrupt MECP2_e1 transcription, but not transcription of MECP2_e2. Am J Med Genet B Neuropsychiatr Genet 2012; 159B:210-6. [PMID: 22213695 DOI: 10.1002/ajmg.b.32015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 12/05/2011] [Indexed: 11/07/2022]
Abstract
The overwhelming majority of Rett syndrome cases are caused by mutations in the gene MECP2. MECP2 has two isoforms, termed MECP2_e1 and MECP2_e2, which differ in their N-terminal amino acid sequences. A growing body of evidence has indicated that MECP2_e1 may be the etiologically relevant isoform in Rett Syndrome based on its expression profile in the brain and because, strikingly, no mutations have been discovered that affect MECP2_e2 exclusively. In this study we sought to characterize four classical Rett patients with mutations that putatively affect only the MECP2_e1 isoform. Our hypothesis was that the classical Rett phenotype seen here is the result of disrupted MECP2_e1 expression, but with MECP2_e2 expression unaltered. We used quantitative reverse transcriptase PCR to assay mRNA expression for each isoform independently, and used cytospinning methods to assay total MECP2 in peripheral blood lymphocytes (PBL). In the two Rett patients with identical 11 bp deletions within the coding portion of exon 1, MECP2_e2 levels were unaffected, whilst a significant reduction of MECP2_e1 levels was detected. In two Rett patients harboring mutations in the exon 1 start codon, MECP2_e1 and MECP2_e2 mRNA amounts were unaffected. In summary, we have shown that patients with exon 1 mutations transcribe normal levels of MECP2_e2 mRNA, and most PBL are positive for MeCP2 protein, despite them theoretically being unable to produce the MECP2_e1 isoform, and yet still exhibit the classical RTT phenotype. Altogether, our work further supports our hypothesis that MECP2_e1 is the predominant isoform involved in the neuropathology of Rett syndrome.
Collapse
Affiliation(s)
- Peter J Gianakopoulos
- Molecular Neuropsychiatry and Development Lab, Neurogenetics Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
Genomic medicine is rapidly evolving. Next-generation sequencing is changing the diagnostic paradigm by allowing genetic testing to be carried out more quickly, less expensively and with much higher resolution; pushing the envelope on existing moral norms and legal regulations. Early experience with implementation of next-generation sequencing to diagnose rare genetic conditions in symptomatic children suggests ways that genomic medicine might come to be used and some of the ethical issues that arise, impacting test design, patient selection, consent, sequencing analysis and communication of results. The ethical issues that arise from use of new technologies cannot be satisfactorily analyzed until they are understood and they cannot be understood until the technologies are deployed in the real world.
Collapse
Affiliation(s)
- Sarah E Soden
- University of Missouri, Children’s Mercy Hospital, Kansas City, MO, USA
| | - Emily G Farrow
- University of Missouri, Children’s Mercy Hospital, Kansas City, MO, USA
| | - Carol J Saunders
- University of Missouri, Children’s Mercy Hospital, Kansas City, MO, USA
| | - John D Lantos
- University of Missouri, Children’s Mercy Hospital, Kansas City, MO, USA
| |
Collapse
|
44
|
Abstract
Next-generation sequencing technologies have greatly lowered the cost of whole-genome sequencing (WGS) and related approaches. Thus, comprehensive sequencing for diagnostic purposes may clear this financial hurdle in the near future. The report by Bainbridge and colleagues in this issue of Science Translational Medicine illustrates the diagnostic power of WGS. In this Perspective, we discuss whether and how genome sequencing might become routine for clinical diagnosis.
Collapse
|
45
|
Guest EM, Neville KA, Hoyer JD, Safo MK, Garg U, Saunders CJ, Abdulmalik O, Zwick DL. Hb Lake Tapawingo [α46(CE4)Phe→Ser; HBA2:c.140T>C]: a new unstable α chain hemoglobin variant associated with low systemic arterial saturation. Hemoglobin 2011; 35:411-6. [PMID: 21797707 DOI: 10.3109/03630269.2011.598986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A new unstable α-globin variant was detected in a child with hypoxemia and anemia. The child's mother was found to carry the same mutation. The hemoglobin (Hb) variant co-eluted with Hb A(2) by cation exchange high performance liquid chromatography (HPLC) and appeared cathodal to Hb A and anodal to Hb F by isoelectric focusing. It represented less than 20% of the total Hb and was unstable by isopropanol testing. Gene sequencing identified a missense mutation on the α2 gene [HBA2:c.140T>C]. Oxygen dissociation and P(50) test results were normal.
Collapse
Affiliation(s)
- Erin M Guest
- Department of Pediatrics, Division of Hematology/Oncology, Children's Mercy Hospital and Clinics, Kansas City, Missouri 64108, USA.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Ivings MJ, Gant SE, Saunders CJ, Pocock DJ. Flammable gas cloud build up in a ventilated enclosure. J Hazard Mater 2010; 184:170-176. [PMID: 20855156 DOI: 10.1016/j.jhazmat.2010.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 08/05/2010] [Accepted: 08/07/2010] [Indexed: 05/29/2023]
Abstract
Ventilation is frequently used as a means for preventing the build up of flammable or toxic gases in enclosed spaces. The effectiveness of the ventilation often has to be considered as part of a safety case or risk assessment. In this paper methods for assessing ventilation effectiveness for hazardous area classification are examined. The analysis uses data produced from Computational Fluid Dynamics (CFD) simulations of low-pressure jet releases of flammable gas in a ventilated enclosure. The CFD model is validated against experimental measurements of gas releases in a ventilation-controlled test chamber. Good agreement is found between the model predictions and the experimental data. Analysis of the CFD results shows that the flammable gas cloud volume resulting from a leak is largely dependent on the mass release rate of flammable gas and the ventilation rate of the enclosure. The effectiveness of the ventilation for preventing the build up of flammable gas can therefore be assessed by considering the average gas concentration at the enclosure outlet(s). It is found that the ventilation rate of the enclosure provides a more useful measure of ventilation effectiveness than considering the enclosure air change rate.
Collapse
Affiliation(s)
- M J Ivings
- Health and Safety Laboratory, Harpur Hill, Buxton SK17 9JN, UK.
| | - S E Gant
- Health and Safety Laboratory, Harpur Hill, Buxton SK17 9JN, UK
| | - C J Saunders
- Health and Safety Laboratory, Harpur Hill, Buxton SK17 9JN, UK
| | - D J Pocock
- Health and Safety Laboratory, Harpur Hill, Buxton SK17 9JN, UK
| |
Collapse
|
47
|
Saunders CJ, Friez MJ, Patterson M, Nzabi M, Zhao W, Bi C. Allele drop-out in the MECP2 gene due to G-quadruplex and i-motif sequences when using polymerase chain reaction-based diagnosis for Rett syndrome. Genet Test Mol Biomarkers 2010; 14:241-7. [PMID: 20384458 DOI: 10.1089/gtmb.2009.0178] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although few examples are formally documented, all polymerase chain reaction-based testing is theoretically vulnerable to allele drop-out (ADO), the failure to amplify one of the two alleles present in a cell. In a clinical setting, this can lead to false positive or negative diagnosis. We investigated the mechanisms leading to ADO in the MECP2 gene in two unrelated female patients undergoing testing for Rett syndrome. Both the patients had two benign DNA variations, c.819G > T and c.1161C > T, that appeared homozygous due to ADO. Bioinformatics analyses indicate that this region of the MECP2 gene is rich in complex tertiary structures called G-quadruplex and i-motifs, the disruption of which by the c.819G > T and c.1161C > T variants leads to preferential amplification of the variant allele. Other examples of ADO likely occur, and consideration of disrupting G-quadruplex and i-motif structures should be given when this phenomenon is unexpected. We identify factors in both the polymerase chain reaction amplification and the sequencing steps that help overcome ADO.
Collapse
Affiliation(s)
- Carol J Saunders
- Department of Pathology and Laboratory Medicine, The Children's Mercy Hospitals and Clinics, Kansas City, Missouri 64108, USA.
| | | | | | | | | | | |
Collapse
|
48
|
Saunders CJ, Zhao W, Ardinger HH. ComprehensiveZEB2gene analysis for Mowat-Wilson syndrome in a North American cohort: A suggested approach to molecular diagnostics. Am J Med Genet A 2009; 149A:2527-31. [DOI: 10.1002/ajmg.a.33067] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
49
|
Abstract
Objective. To describe the incidence of injuries in a professional rugby team, and to identify any associations between injury rates and training volume.Methods. This retrospective, descriptive study included all injuries diagnosed as grade 1 and above in a South African Super 12 rugby team. Injury incidence and injury rates were calculated and compared with training volume and hours of match play.Results. Thirty-eight male rugby players were injured during the study period. The total number of annual injuries decreased from 50 (2002) to 38 (2004) (χ2=0.84, p=0.36). The number of new injuries showed a similar trend (χ2=2.81, p=0.09), while the number of recurring injuries increased over the 3-year period. There was a tendency for total in-season injury rates to decrease over the 3 years (χ2=2.89, p=0.09). The pre-season injury rate increased significantly over the 3 years (χ2=12.7, pConclusions. One has to be cognisant of the balance between performance improvement and injury risk when designing training programmes for elite rugby players. Although the reduction in training volume was associated with a slight reduction in the number of acute injuries and in-season injury rates over the three seasons, the performance of the team changed from 3rd to 7th (2002 and 2004, respectively). Further studies are required to determine the optimal training necessary to improve rugby performancewhile reducing injury rates.
Collapse
|
50
|
Zhang D, Saunders CJ, Zhao W, Davis M, Cunningham MT. The clonality of CD3+ CD10+ T cells in angioimmunoblastic T cell lymphoma, B cell lymphoma, and reactive lymphoid hyperplasia. Am J Hematol 2009; 84:606-8. [PMID: 19650143 DOI: 10.1002/ajh.21483] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
T cells coexpressing CD3 and CD10 are a characteristic feature of angioimmunoblastic T-cell lymphoma (AITL) [1]. However, they are not unique to AITL, as these cells are also present in B cell lymphoma and reactive lymphoid hyperplasia [2]. To determine the significance of CD3+ CD10+ T cells, we used flow cytometry with cell sorting and molecular biology techniques for T cell gene rearrangement to study T cells from patients with AITL, B cell lymphoma, and reactive lymph node hyperplasia. We found that CD3+ CD10+ T cells in B cell lymphoma and reactive lymphoid hyperplasia were polyclonal. In early stage of AITL, they were oligoclonal, and became monoclonal as AITL progressed. These findings illustrate the differences between early and late lymphoma and could be important for the diagnosis of AITL.
Collapse
|