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Liaqat K, Treat K, Mantcheva L, Nasir A, Weaver DD, Conboy E, Vetrini F. A case of MBTPS1-related disorder due to compound heterozygous variants in MBTPS1 gene: Genotype-phenotype expansion and the emergence of a novel syndrome. Am J Med Genet A 2024; 194:e63499. [PMID: 38135440 DOI: 10.1002/ajmg.a.63499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
MBTPS1 (NM_003791.4) encodes Site-1 protease, a serine protease that functions sequentially with Site-2 protease regulating cholesterol homeostasis and endoplasmic reticulum stress response. MBTPS1 pathogenic variants are associated with spondyloepiphyseal dysplasia, Kondo-Fu type (MIM:618392; cataract, alopecia, oral mucosal disorder, and psoriasis-like syndrome, and Silver-Russell-like syndrome). In this report, we describe a 14-year-old female with a complex medical history including white matter volume loss, early-onset cataracts, retrognathia, laryngomalacia, inguinal hernia, joint hypermobility, feeding dysfunction, and speech delay. Additionally, features of ectodermal dysplasia that she has include decreased sweating, heat intolerance, dysplastic nails, chronically dry skin, and abnormal hair growth issues. Exome sequencing analysis identified compound heterozygous variants in the MBTPS1 gene: c.2255G > T p.(Gly752Val) predicted to affect important function of the protein, which was inherited from the mother, and a splice site variant c.2831 + 5G > T, which was inherited from the father. The RNA-seq analysis of the splice variant showed skipping of exon 21, predicted to result in frameshifting p.(Ser901fs28*) leading to non-sense mediated decay. To our knowledge, only eight studies have been published that described the MBPTS1-related disorders. Interestingly, we observed the features of ectodermal dysplasia in our patient that further expands the phenotypic spectrum of MBTPS1 gene-related disorders.
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Affiliation(s)
- Khurram Liaqat
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kayla Treat
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Lili Mantcheva
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Abdul Nasir
- Department of Anesthesiology, Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - David D Weaver
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Erin Conboy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
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Liaqat K, Treat K, Wilson TE, Conboy E, Vetrini F. Further evidence of involvement of ITSN1 in autosomal dominant neurodevelopmental disorder. Clin Genet 2024; 105:455-456. [PMID: 38346866 DOI: 10.1111/cge.14497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 03/07/2024]
Abstract
A 5-year-old affected male had following phenotypes: autism, motor stereotypy, developmental regression, staring gaze, absent speech, and behavioral abnormality. The biochemical testing was normal and genetic testing identified a de novo pathogenic variant in ITSN1 gene in the proband. To our knowledge, this is the second report that elucidates the role of ITSN1 gene in an autosomal dominant neurodevelopmental disorder.
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Affiliation(s)
- Khurram Liaqat
- Department of Medical and Molecular Genetics, Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kayla Treat
- Department of Medical and Molecular Genetics, Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Theodore E Wilson
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Erin Conboy
- Department of Medical and Molecular Genetics, Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
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Bruns R, Liaqat K, Nasir A, Treat K, Murthy VS, Mantcheva L, Torres W, Conboy E, Vetrini F. Undiagnosed rare disease clinic identifies a novel UBE3A variant in two sisters with Angelman syndrome: The end of a diagnostic odyssey. Congenit Anom (Kyoto) 2024. [PMID: 38520260 DOI: 10.1111/cga.12566] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
Angelman syndrome (AS, MIM #105830) is a neurodevelopmental disorder characterized by severe intellectual disability, profound developmental delay, movement or balance problems, an excessively cheerful disposition, and seizures. AS results from inadequate expression of the maternal UBE3A gene (MIM #601623), which encodes an E3 ligase in the ubiquitin-proteasome pathway. Here we present the case of two sisters with features consistent with AS who had negative methylation analyses. An autism/intellectual disability expanded panel revealed a maternally inherited novel UBE3A (NM_001354506.2) variant c.2443C>T p.(Pro815Ser) in both patients that was initially classified as a variant of uncertain significance. The patients were enrolled in Indiana University's Undiagnosed Rare Disease Clinic (URDC) to further investigate the variant. Additional data, including deep phenotyping, familial segregation analysis, and in silico studies, suggest that the variant is likely pathogenic. 3D modeling studies based on the available crystal structure revealed that the Pro815Ser variant can introduce more flexibility into the protein and alter its enzymatic activity. Recent literature confirms the pathogenic nature of the variant. Reanalysis of the UBE3A variant has heightened existing knowledge of AS and has offered this family an end to their diagnostic odyssey.
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Affiliation(s)
- Rebecca Bruns
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Khurram Liaqat
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Abdul Nasir
- Department of Anesthesiology, Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kayla Treat
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Vinaya S Murthy
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
| | - Lili Mantcheva
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Wilfredo Torres
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
| | - Erin Conboy
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Francesco Vetrini
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
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Koop K, Yuan W, Tessadori F, Rodriguez-Polanco WR, Grubbs J, Zhang B, Osmond M, Graham G, Sawyer S, Conboy E, Vetrini F, Treat K, Płoski R, Pienkowski VM, Kłosowska A, Fieg E, Krier J, Mallebranche C, Alban Z, Aldinger KA, Ritter D, Macnamara E, Sullivan B, Herriges J, Alaimo JT, Helbig C, Ellis CA, van Eyk C, Gecz J, Farrugia D, Osei-Owusu I, Adès L, van den Boogaard MJ, Fuchs S, Bakker J, Duran K, Dawson ZD, Lindsey A, Huang H, Baldridge D, Silverman GA, Grant BD, Raizen D, van Haaften G, Pak SC, Rehmann H, Schedl T, van Hasselt P. Macrocephaly and developmental delay caused by missense variants in RAB5C. Hum Mol Genet 2023; 32:3063-3077. [PMID: 37552066 PMCID: PMC10586195 DOI: 10.1093/hmg/ddad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/06/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023] Open
Abstract
Rab GTPases are important regulators of intracellular vesicular trafficking. RAB5C is a member of the Rab GTPase family that plays an important role in the endocytic pathway, membrane protein recycling and signaling. Here we report on 12 individuals with nine different heterozygous de novo variants in RAB5C. All but one patient with missense variants (n = 9) exhibited macrocephaly, combined with mild-to-moderate developmental delay. Patients with loss of function variants (n = 2) had an apparently more severe clinical phenotype with refractory epilepsy and intellectual disability but a normal head circumference. Four missense variants were investigated experimentally. In vitro biochemical studies revealed that all four variants were damaging, resulting in increased nucleotide exchange rate, attenuated responsivity to guanine exchange factors and heterogeneous effects on interactions with effector proteins. Studies in C. elegans confirmed that all four variants were damaging in vivo and showed defects in endocytic pathway function. The variant heterozygotes displayed phenotypes that were not observed in null heterozygotes, with two shown to be through a dominant negative mechanism. Expression of the human RAB5C variants in zebrafish embryos resulted in defective development, further underscoring the damaging effects of the RAB5C variants. Our combined bioinformatic, in vitro and in vivo experimental studies and clinical data support the association of RAB5C missense variants with a neurodevelopmental disorder characterized by macrocephaly and mild-to-moderate developmental delay through disruption of the endocytic pathway.
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Affiliation(s)
- Klaas Koop
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, 3584 EA, The Netherlands
| | - Weimin Yuan
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Federico Tessadori
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, The Netherlands
| | - Wilmer R Rodriguez-Polanco
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jeremy Grubbs
- Department of Neurology and the Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bo Zhang
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Matt Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada
| | - Gail Graham
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada
| | - Sarah Sawyer
- Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, K1H 8L1, Canada
| | - Erin Conboy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kayla Treat
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Rafal Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, 02-106, Poland
| | - Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, 02-106, Poland
- Marseille Medical Genetics U1251, Aix Marseille University, Marseille, 13005, France
| | - Anna Kłosowska
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdańsk, Gdańsk, 80-210, Poland
| | - Elizabeth Fieg
- Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Joel Krier
- Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Coralie Mallebranche
- Unité d'Onco-Hémato-Immunologie pédiatrique, CHU d’Angers, Angers, 49933, France
| | - Ziegler Alban
- Service de génétique, CHU d’Angers, Angers, 49933, France
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, 98195, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Deborah Ritter
- Department of Pediatrics, Oncology Section, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ellen Macnamara
- Undiagnosed Diseases Program Translational Laboratory, NHGRI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bonnie Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, 64108, USA
| | - John Herriges
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, MO, 64108, USA
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, MO, 64108, USA
| | - Catherine Helbig
- The Epilepsy Neurogenetics Initiative, Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Colin A Ellis
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, 19104, USA
| | - Clare van Eyk
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5006, Australia
| | - Jozef Gecz
- Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5006, Australia
| | | | - Ikeoluwa Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lesley Adès
- Department of Clinical Genetics, The Children’s Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, 2145, Australia
| | - Marie-Jose van den Boogaard
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, 3584EA, The Netherlands
| | - Sabine Fuchs
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, 3584 EA, The Netherlands
| | - Jeroen Bakker
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, The Netherlands
| | - Karen Duran
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, The Netherlands
| | - Zachary D Dawson
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Anika Lindsey
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Huiyan Huang
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Dustin Baldridge
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Gary A Silverman
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Barth D Grant
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - David Raizen
- Department of Neurology and the Chronobiology and Sleep Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, 3584EA, The Netherlands
| | - Stephen C Pak
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Holger Rehmann
- Department of Energy and Biotechnology, Flensburg University of Applied Sciences, 24943, Flensburg, Germany
| | - Tim Schedl
- Departments of Pediatrics and Genetics, C. elegans Model Organism Screening Center, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Peter van Hasselt
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, 3584 EA, The Netherlands
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Gage H, Wetherill L, Anderson K, Conboy E, Haider K. Motivations and expectations of parents seeking genetic testing for their children with ocular genetic disease. Ophthalmic Genet 2023:1-8. [PMID: 37170870 DOI: 10.1080/13816810.2023.2209170] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
BACKGROUND To date, almost 600 genes have been associated with ocular genetic diseases. As these discoveries are made, clinical genetic testing continues to grow and become a more common element in the diagnostic workup of children with blindness and reduced vision. However, few studies have explored the motivations of parents of pediatric patients for pursuing genetic testing or the topics they would like to discuss during their visit. This study explored these gaps in the existing knowledge of clinical care for children with vision loss. MATERIALS AND METHODS We distributed a REDCap survey to parents of pediatric patients in the Indiana University Ocular Genetics Clinic and through the Foundation Fighting Blindness MyRetinaTracker database to examine factors that motivate families to undergo genetic testing, topics they are interested in discussing, and satisfaction with their current care. RESULTS Parents were primarily motivated by the opportunity to learn about their child's prognosis, formal diagnosis, and possible treatment options. Parents were most interested in discussing prognosis, adaptations for vision loss, and testing logistics. Parents reported satisfaction with the care received; however, less than half were very satisfied with their understanding of prognosis and the support resources provided. CONCLUSIONS Parents seem to be generally satisfied by the care from their ocular genetics team. However, families' desires are not being fully met, especially with information about prognosis and support resources. As the field of ocular genetics continues to grow, it is important we improve these offerings and optimize care for this patient population.
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Affiliation(s)
- Hannah Gage
- Department of Genetic Counseling, Baylor University Medical Center, Dallas, Texas, USA
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Katelynn Anderson
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Erin Conboy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kathryn Haider
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Rahim MQ, Rahrig A, Overholt K, Conboy E, Czader M, Saraf AJ. A familial SAMD9 variant present in pediatric myelodysplastic syndrome. Cold Spring Harb Mol Case Stud 2023; 9:mcs.a006256. [PMID: 37160314 DOI: 10.1101/mcs.a006256] [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: 11/14/2022] [Accepted: 03/01/2023] [Indexed: 05/11/2023] Open
Abstract
Myelodysplastic syndrome (MDS) is a rare pediatric diagnosis characterized by ineffective hematopoiesis with potential to evolve into acute myelogenous leukemia (AML). In this report, we describe a unique case of a 17-yr-old female with an aggressive course of MDS with excess blasts who was found to have monosomy 7 and a SAMD9 germline variant, which has not previously been associated with a MDS phenotype. This case of MDS was extremely rapidly progressing, showing resistance to chemotherapy and stem cell transplant, unfortunately resulting in patient death. It is imperative to further investigate this rare variant to aid in the future care of patients with this variant.
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Affiliation(s)
- Mahvish Q Rahim
- Pediatric Hematology Oncology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA;
- Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana, USA
| | - April Rahrig
- Pediatric Hematology Oncology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana, USA
| | - Kathleen Overholt
- Pediatric Hematology Oncology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana, USA
| | - Erin Conboy
- Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Magdalena Czader
- Department of Pathology and Laboratory Medicine/Indiana University Healthy Pathology Laboratory, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Amanda June Saraf
- Pediatric Hematology Oncology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana, USA
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Patel SH, Bakhsh S, Conboy E, Hajrasouliha AR. Case of IFT140-associated Mainzer Saldino Syndrome. Ophthalmic Genet 2023; 44:208-210. [PMID: 36063079 DOI: 10.1080/13816810.2022.2113545] [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: 10/14/2022]
Affiliation(s)
- Shivam H Patel
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Saaquib Bakhsh
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Erin Conboy
- Department of Medical and Molecular Genetics and Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Amir R Hajrasouliha
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, United States
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Doyle TA, Conboy E, Halverson CME. Diagnostic deserts: Community-level barriers to appropriate genetics services. Am J Med Genet A 2023; 191:296-298. [PMID: 36282041 DOI: 10.1002/ajmg.a.63016] [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] [Received: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 12/14/2022]
Affiliation(s)
- Tom A Doyle
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Erin Conboy
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Colin M E Halverson
- Indiana University School of Medicine, Indianapolis, Indiana, USA.,Charles Warren Fairbanks Center for Medical Ethics, Indianapolis, Indiana, USA
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Buchh M, Gillespie PJ, Treat K, Abreu MA, Schwantes-An THL, Helm BM, Fang F, Xuei X, Mantcheva L, Suhrie KR, Graham BH, Conboy E, Vetrini F. Characterization of a novel deep-intronic variant in DYNC2H1 identified by whole-exome sequencing in a patient with a lethal form of a short-rib thoracic dysplasia type III. Cold Spring Harb Mol Case Stud 2022; 8:a006254. [PMID: 36442996 PMCID: PMC9808550 DOI: 10.1101/mcs.a006254] [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: 10/21/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022] Open
Abstract
Biallelic pathogenic variants in DYNC2H1 are the cause of short-rib thoracic dysplasia type III with or without polydactyly (OMIM #613091), a skeletal ciliopathy characterized by thoracic hypoplasia due to short ribs. In this report, we review the case of a patient who was admitted to the Neonatal Intensive Care Unit (NICU) of Indiana University Health (IUH) for respiratory support after experiencing respiratory distress secondary to a small, narrow chest causing restrictive lung disease. Additional phenotypic features include postaxial polydactyly, short proximal long bones, and ambiguous genitalia were noted. Exome sequencing (ES) revealed a maternally inherited likely pathogenic variant c.10322C > T p.(Leu3448Pro) in the DYNC2H1 gene. However, there was no variant found on the paternal allele. Microarray analysis to detect deletion or duplication in DYNC2H1 was normal. Therefore, there was insufficient evidence to establish a molecular diagnosis. To further explore the data and perform additional investigations, the patient was subsequently enrolled in the Undiagnosed Rare Disease Clinic (URDC) at Indiana University School of Medicine (IUSM). The investigators at the URDC performed a reanalysis of the ES raw data, which revealed a paternally inherited DYNC2H1 deep-intronic variant c.10606-14A > G predicted to create a strong cryptic acceptor splice site. Additionally, the RNA sequencing of fibroblasts demonstrated partial intron retention predicted to cause a premature stop codon and nonsense-mediated mRNA decay (NMD). Droplet digital RT-PCR (RT-ddPCR) showed a drastic reduction by 74% of DYNCH2H1 mRNA levels. As a result, the intronic variant was subsequently reclassified as likely pathogenic resulting in a definitive clinical and genetic diagnosis for this patient. Reanalysis of ES and fibroblast mRNA experiments confirmed the pathogenicity of the splicing variants to supplement critical information not revealed in original ES or CMA reports. The NICU and URDC collaboration ended the diagnostic odyssey for this family; furthermore, its importance is emphasized by the possibility of prenatally diagnosing the mother's current pregnancy.
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Affiliation(s)
- Muqsit Buchh
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | | | - Kayla Treat
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Marco A Abreu
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Tae-Hwi Linus Schwantes-An
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Benjamin M Helm
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Fang Fang
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Lili Mantcheva
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Kristen R Suhrie
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Brett H Graham
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Erin Conboy
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Francesco Vetrini
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
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10
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Latshaw S, Conboy E, Overholt K, Kim M, Jin J. EARLY DETECTION OF X-LINKED MOESIN-ASSOCIATED IMMUNE DEFICIENCY ON NEWBORN SCREENING. Ann Allergy Asthma Immunol 2022. [DOI: 10.1016/j.anai.2022.08.879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Treat K, Jangam S, Yamamoto S, White K, Kanca O, Christensen C, Lynch S, Baptista J, Tsang MHY, Jay K, Chung BHY, Yuen LYP, Chui MMC, Bellen H, Wangler M, Conboy E, Vetrini F. eP410: De novo missense variants in DDX39B cause a novel syndrome characterized by neurodevelopmental delay, short stature and congenital hypotonia. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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12
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Luna C, Griffin C, Lah M, Conboy E, McPheron M, Graham B, Hainline B, Miller M. OP006: Is it time to move beyond acylcarnitine profiles? Lessons from the clinical application of a high-definition LC-MS/MS acylcarnitine method. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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13
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Walters J, Treat K, Conboy E, Vetrini F. eP271: Bi-allelic loss of function variant of the ACTG2 gene that proposes a potential novel mechanism for visceral myopathies. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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14
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Jacobs A, Burns C, Patel P, Treat K, Helm BM, Conboy E, Vetrini F. Reanalysis of a novel variant in the IGF1R gene in a family with variable pre-and postnatal growth retardation and dysmorphic features: benefits and feasibility of IUSM-URDC (Undiagnosed Rare Disease Clinic) program. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006170. [PMID: 35091507 PMCID: PMC8958911 DOI: 10.1101/mcs.a006170] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/27/2022] [Indexed: 11/24/2022] Open
Abstract
IGF1R-related disorders are associated with intrauterine growth restriction (IUGR), postnatal growth failure, short stature, microcephaly, developmental delay, and dysmorphic facial features. We report a patient who presented to medical genetics at 7 mo of age with a history of IUGR, poor feeding, mild developmental delays, microcephaly, and dysmorphic facial features. Whole-exome sequencing revealed a novel c.1464T > G p.(Cys488Trp) variant in the IGF1R gene, initially classified as a variation of uncertain significance (VUS). We enrolled the patient in the URDC (Undiagnosed Rare Disease Clinic) and performed additional studies including deep phenotyping and familial segregation analysis, which demonstrated that the patient's IGF1R VUS was present in phenotypically similar family members. Furthermore, biochemical testing revealed an elevated serum IGF-1 level consistent with abnormal IGF-1 receptor function. Workup resulted in the patient's variant being upgraded from a VUS to likely pathogenic. Our report expands the variant and phenotypic spectrum of IGF1R-related disorders and illustrates benefits and feasibility of reassessing a VUS beyond the initial molecular diagnosis by deep phenotyping, 3D modeling, additional biochemical testing, and familial segregation studies through the URDC, a multidisciplinary clinical program whose major goal is to end the diagnostic odyssey in patients with rare diseases.
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Affiliation(s)
- Annalise Jacobs
- Indiana University School of Medicine, Department of Pediatrics, Riley Hospital for Children, Indianapolis, IN
| | | | - Purva Patel
- Indiana University School of Medicine, Indianapolis, IN
| | - Kayla Treat
- Indiana University School of Medicine, Department of Medical and Human Genetics; Undiagnosed Rare Disease Clinic (URDC), Indianapolis, IN
| | | | - Erin Conboy
- Indiana University School of Medicine, Department of Medical and Human Genetics; Undiagnosed Rare Disease Clinic (URDC), Indianapolis, IN
| | - Francesco Vetrini
- Indiana University School of Medicine, Department of Medical and Human Genetics; Undiagnosed Rare Disease Clinic (URDC), Indianapolis, IN;
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15
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Barish S, Barakat TS, Michel BC, Mashtalir N, Phillips JB, Valencia AM, Ugur B, Wegner J, Scott TM, Bostwick B, Murdock DR, Dai H, Perenthaler E, Nikoncuk A, van Slegtenhorst M, Brooks AS, Keren B, Nava C, Mignot C, Douglas J, Rodan L, Nowak C, Ellard S, Stals K, Lynch SA, Faoucher M, Lesca G, Edery P, Engleman KL, Zhou D, Thiffault I, Herriges J, Gass J, Louie RJ, Stolerman E, Washington C, Vetrini F, Otsubo A, Pratt VM, Conboy E, Treat K, Shannon N, Camacho J, Wakeling E, Yuan B, Chen CA, Rosenfeld JA, Westerfield M, Wangler M, Yamamoto S, Kadoch C, Scott DA, Bellen HJ. BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms. Am J Hum Genet 2020; 107:1096-1112. [PMID: 33232675 PMCID: PMC7820627 DOI: 10.1016/j.ajhg.2020.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/03/2020] [Indexed: 12/30/2022] Open
Abstract
SWI/SNF-related intellectual disability disorders (SSRIDDs) are rare neurodevelopmental disorders characterized by developmental disability, coarse facial features, and fifth digit/nail hypoplasia that are caused by pathogenic variants in genes that encode for members of the SWI/SNF (or BAF) family of chromatin remodeling complexes. We have identified 12 individuals with rare variants (10 loss-of-function, 2 missense) in the BICRA (BRD4 interacting chromatin remodeling complex-associated protein) gene, also known as GLTSCR1, which encodes a subunit of the non-canonical BAF (ncBAF) complex. These individuals exhibited neurodevelopmental phenotypes that include developmental delay, intellectual disability, autism spectrum disorder, and behavioral abnormalities as well as dysmorphic features. Notably, the majority of individuals lack the fifth digit/nail hypoplasia phenotype, a hallmark of most SSRIDDs. To confirm the role of BICRA in the development of these phenotypes, we performed functional characterization of the zebrafish and Drosophila orthologs of BICRA. In zebrafish, a mutation of bicra that mimics one of the loss-of-function variants leads to craniofacial defects possibly akin to the dysmorphic facial features seen in individuals harboring putatively pathogenic BICRA variants. We further show that Bicra physically binds to other non-canonical ncBAF complex members, including the BRD9/7 ortholog, CG7154, and is the defining member of the ncBAF complex in flies. Like other SWI/SNF complex members, loss of Bicra function in flies acts as a dominant enhancer of position effect variegation but in a more context-specific manner. We conclude that haploinsufficiency of BICRA leads to a unique SSRIDD in humans whose phenotypes overlap with those previously reported.
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Affiliation(s)
- Scott Barish
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Brittany C Michel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nazar Mashtalir
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Alfredo M Valencia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology Program, Harvard University, Cambridge, MA 02138, USA
| | - Berrak Ugur
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeremy Wegner
- Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Tiana M Scott
- Department of Microbiology and Molecular Biology, College of Life Science, Brigham Young University, Provo, UT 84602, USA
| | - Brett Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David R Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Elena Perenthaler
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Anita Nikoncuk
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Boris Keren
- APHP Sorbonne Université, Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, 75006 Paris, France
| | - Caroline Nava
- APHP Sorbonne Université, Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, 75006 Paris, France
| | - Cyril Mignot
- APHP Sorbonne Université, Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, 75006 Paris, France
| | - Jessica Douglas
- Department of Pediatrics, Boston Children's at Waltham, Waltham, MA 02453, USA
| | - Lance Rodan
- Department of Pediatrics, Boston Children's at Waltham, Waltham, MA 02453, USA
| | - Catherine Nowak
- Department of Pediatrics, Boston Children's at Waltham, Waltham, MA 02453, USA
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK; Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter EX4 4PY, UK
| | - Sally Ann Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin D12 N512, Ireland
| | - Marie Faoucher
- Department of Medical Genetics, Lyon University Hospital, Université Claude bernard Lyon 1, Lyon 69100, France
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Université Claude bernard Lyon 1, Lyon 69100, France
| | - Patrick Edery
- Department of Medical Genetics, Lyon University Hospital, Université Claude bernard Lyon 1, Lyon 69100, France
| | - Kendra L Engleman
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Dihong Zhou
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - John Herriges
- Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Jennifer Gass
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Raymond J Louie
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Elliot Stolerman
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Camerun Washington
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Francesco Vetrini
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Aiko Otsubo
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Victoria M Pratt
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Erin Conboy
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Kayla Treat
- Department of Clinical Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Nora Shannon
- Regional Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK
| | - Jose Camacho
- Pediatric Genetics and Metabolism, Loma Linda University Children's Hospital, Loma Linda, CA 92354, USA
| | - Emma Wakeling
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Monte Westerfield
- Department of Biology, University of Oregon, Eugene, OR 97403, USA; Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Michael Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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16
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Pino G, Conboy E, Tortorelli S, Minnich S, Nickander K, Lacey J, Peck D, Studinski A, White A, Gavrilov D, Rinaldo P, Matern D, Oglesbee D, Giugliani R, Burin M, Raymond K. Multiplex testing for the screening of lysosomal storage disease in urine: Sulfatides and glycosaminoglycan profiles in 40 cases of sulfatiduria. Mol Genet Metab 2020; 129:106-110. [PMID: 31753749 DOI: 10.1016/j.ymgme.2019.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/30/2022]
Abstract
PURPOSE To describe an efficient and effective multiplex screening strategy for sulfatide degradation disorders and mucolipidosis type II/III (MLII/III) using 3 mL of urine. METHODS Glycosaminoglycans were analyzed by liquid chromatography-tandem mass spectrometry. Matrix assisted laser desorption/ionization-time of flight tandem mass spectrometry was used to identify free oligosaccharides and identify 22 ceramide trihexosides and 23 sulfatides, which are integrated by 670 calculated ratios. Collaborative Laboratory Integrated Reports (CLIR; https://clir.mayo.edu) was used for post-analytical interpretation of the complex metabolite profile and to aid in the differential diagnosis of abnormal results. RESULTS Multiplex analysis was performed on 25 sulfatiduria case samples and compiled with retrospective data from an additional 15 cases revealing unique patterns of biomarkers for each disorder of sulfatide degradation (MLD, MSD, and Saposin B deficiency) and for MLII/III, thus allowing the formulation of a novel algorithm for the biochemical diagnosis of these disorders. CONCLUSIONS Comprehensive and integrated urine screening could be very effective in the initial workup of patients suspected of having a lysosomal disorder as it covers disorders of sulfatide degradation and narrows down the differential diagnosis in patients with elevated glycosaminoglycans.
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Affiliation(s)
- Gisele Pino
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Erin Conboy
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Silvia Tortorelli
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sara Minnich
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kim Nickander
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jean Lacey
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dawn Peck
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - April Studinski
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Amy White
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dimitar Gavrilov
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Piero Rinaldo
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dietrich Matern
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Devin Oglesbee
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Roberto Giugliani
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maira Burin
- Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
| | - Kimiyo Raymond
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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17
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Cousin MA, Conboy E, Wang JS, Lenz D, Schwab TL, Williams M, Abraham RS, Barnett S, El-Youssef M, Graham RP, Gutierrez Sanchez LH, Hasadsri L, Hoffmann GF, Hull NC, Kopajtich R, Kovacs-Nagy R, Li JQ, Marx-Berger D, McLin V, McNiven MA, Mounajjed T, Prokisch H, Rymen D, Schulze RJ, Staufner C, Yang Y, Clark KJ, Lanpher BC, Klee EW. RINT1 Bi-allelic Variations Cause Infantile-Onset Recurrent Acute Liver Failure and Skeletal Abnormalities. Am J Hum Genet 2019; 105:108-121. [PMID: 31204009 DOI: 10.1016/j.ajhg.2019.05.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 05/13/2019] [Indexed: 01/12/2023] Open
Abstract
Pediatric acute liver failure (ALF) is life threatening with genetic, immunologic, and environmental etiologies. Approximately half of all cases remain unexplained. Recurrent ALF (RALF) in infants describes repeated episodes of severe liver injury with recovery of hepatic function between crises. We describe bi-allelic RINT1 alterations as the cause of a multisystem disorder including RALF and skeletal abnormalities. Three unrelated individuals with RALF onset ≤3 years of age have splice alterations at the same position (c.1333+1G>A or G>T) in trans with a missense (p.Ala368Thr or p.Leu370Pro) or in-frame deletion (p.Val618_Lys619del) in RINT1. ALF episodes are concomitant with fever/infection and not all individuals have complete normalization of liver function testing between episodes. Liver biopsies revealed nonspecific liver damage including fibrosis, steatosis, or mild increases in Kupffer cells. Skeletal imaging revealed abnormalities affecting the vertebrae and pelvis. Dermal fibroblasts showed splice-variant mediated skipping of exon 9 leading to an out-of-frame product and nonsense-mediated transcript decay. Fibroblasts also revealed decreased RINT1 protein, abnormal Golgi morphology, and impaired autophagic flux compared to control. RINT1 interacts with NBAS, recently implicated in RALF, and UVRAG, to facilitate Golgi-to-ER retrograde vesicle transport. During nutrient depletion or infection, Golgi-to-ER transport is suppressed and autophagy is promoted through UVRAG regulation by mTOR. Aberrant autophagy has been associated with the development of similar skeletal abnormalities and also with liver disease, suggesting that disruption of these RINT1 functions may explain the liver and skeletal findings. Clarifying the pathomechanism underlying this gene-disease relationship may inform therapeutic opportunities.
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18
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Oliver GR, Blackburn PR, Ellingson MS, Conboy E, Pinto E Vairo F, Webley M, Thorland E, Ferber M, Van Hul E, van der Werf IM, Wuyts W, Babovic-Vuksanovic D, Klee EW. RNA-Seq detects a SAMD12-EXT1 fusion transcript and leads to the discovery of an EXT1 deletion in a child with multiple osteochondromas. Mol Genet Genomic Med 2019; 7:e00560. [PMID: 30632316 PMCID: PMC6418362 DOI: 10.1002/mgg3.560] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/29/2018] [Accepted: 12/13/2018] [Indexed: 12/24/2022] Open
Abstract
Background We describe a patient presenting with pachygyria, epilepsy, developmental delay, short stature, failure to thrive, facial dysmorphisms, and multiple osteochondromas. Methods The patient underwent extensive genetic testing and analysis in an attempt to diagnose the cause of his condition. Clinical testing included metaphase karyotyping, array comparative genomic hybridization, direct sequencing and multiplex ligation‐dependent probe amplification and trio‐based exome sequencing. Subsequently, research‐based whole transcriptome sequencing was conducted to determine whether it might shed light on the undiagnosed phenotype. Results Clinical exome sequencing of patient and parent samples revealed a maternally inherited splice‐site variant in the doublecortin (DCX) gene that was classified as likely pathogenic and diagnostic of the patient's neurological phenotype. Clinical array comparative genome hybridization analysis revealed a 16p13.3 deletion that could not be linked to the patient phenotype based on affected genes. Further clinical testing to determine the cause of the patient's multiple osteochondromas was unrevealing despite extensive profiling of the most likely causative genes, EXT1 and EXT2, including mutation screening by direct sequence analysis and multiplex ligation‐dependent probe amplification. Whole transcriptome sequencing identified a SAMD12‐EXT1 fusion transcript that could have resulted from a chromosomal deletion, leading to the loss of EXT1 function. Re‐review of the clinical array comparative genomic hybridization results indicated a possible unreported mosaic deletion affecting the SAMD12 and EXT1 genes that corresponded precisely to the introns predicted to be affected by a fusion‐causing deletion. The existence of the mosaic deletion was subsequently confirmed clinically by an increased density copy number array and orthogonal methodologies Conclusions While mosaic mutations and deletions of EXT1 and EXT2 have been reported in the context of multiple osteochondromas, to our knowledge, this is the first time that transcriptomics technologies have been used to diagnose a patient via fusion transcript analysis in the congenital disease setting.
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Affiliation(s)
- Gavin R Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Patrick R Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Marissa S Ellingson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Erin Conboy
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Filippo Pinto E Vairo
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Matthew Webley
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Erik Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew Ferber
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Els Van Hul
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Ilse M van der Werf
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Wim Wuyts
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
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19
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Pinto E Vairo F, Conboy E, de Souza CFM, Jones A, Barnett SS, Klee EW, Lanpher BC. Diagnosis of Attenuated Mucopolysaccharidosis VI: Clinical, Biochemical, and Genetic Pitfalls. Pediatrics 2018; 142:peds.2018-0658. [PMID: 30470723 DOI: 10.1542/peds.2018-0658] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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] [Accepted: 08/02/2018] [Indexed: 11/24/2022] Open
Abstract
Mucopolysaccharidosis type VI (MPS VI) is a clinically heterogeneous lysosomal disease, which can be divided into 2 main categories on the basis of age of onset and severity of symptoms. The diagnosis of the attenuated form is often delayed given subtle facial features rather than the typical coarse facial features of the classic form. Here, we discuss the difficulties in establishing the diagnosis of MPS VI on the basis of the report of 4 individuals. The most common signs and symptoms in our series were bone abnormalities and hip pain as initial manifestations and cardiac changes detected after follow-up studies. On the basis of our cohort and others worldwide, awareness of attenuated forms of MPS VI should be increased particularly among general practitioners, pediatricians, rheumatologists, orthopedists, ophthalmologists, and cardiologists. Moreover, these health care providers should be aware of the technical aspects involved in the molecular and biochemical diagnosis process so that they are aware how diagnostic errors may occur.
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Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, and.,Departments of Health Sciences Research.,Clinical Genomics
| | | | | | | | - Sarah S Barnett
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; and
| | - Eric W Klee
- Center for Individualized Medicine, and.,Departments of Health Sciences Research.,Clinical Genomics.,Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; and
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Cheng H, Dharmadhikari AV, Varland S, Ma N, Domingo D, Kleyner R, Rope AF, Yoon M, Stray-Pedersen A, Posey JE, Crews SR, Eldomery MK, Akdemir ZC, Lewis AM, Sutton VR, Rosenfeld JA, Conboy E, Agre K, Xia F, Walkiewicz M, Longoni M, High FA, van Slegtenhorst MA, Mancini GMS, Finnila CR, van Haeringen A, den Hollander N, Ruivenkamp C, Naidu S, Mahida S, Palmer EE, Murray L, Lim D, Jayakar P, Parker MJ, Giusto S, Stracuzzi E, Romano C, Beighley JS, Bernier RA, Küry S, Nizon M, Corbett MA, Shaw M, Gardner A, Barnett C, Armstrong R, Kassahn KS, Van Dijck A, Vandeweyer G, Kleefstra T, Schieving J, Jongmans MJ, de Vries BBA, Pfundt R, Kerr B, Rojas SK, Boycott KM, Person R, Willaert R, Eichler EE, Kooy RF, Yang Y, Wu JC, Lupski JR, Arnesen T, Cooper GM, Chung WK, Gecz J, Stessman HAF, Meng L, Lyon GJ. Truncating Variants in NAA15 Are Associated with Variable Levels of Intellectual Disability, Autism Spectrum Disorder, and Congenital Anomalies. Am J Hum Genet 2018; 102:985-994. [PMID: 29656860 DOI: 10.1016/j.ajhg.2018.03.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/27/2018] [Indexed: 11/30/2022] Open
Abstract
N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.
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Affiliation(s)
| | | | - Sylvia Varland
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Ning Ma
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Deepti Domingo
- School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Robert Kleyner
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Alan F Rope
- Department of Medical Genetics, Kaiser Permanente Northwest, Portland, OR 97227, USA
| | - Margaret Yoon
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Asbjørg Stray-Pedersen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, and Institute of Clinical Medicine, University of Oslo, N-0318 Oslo, Norway
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah R Crews
- Department of Pharmacology, Creighton University Medical School, Omaha, NE, 68178, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX 77030, USA
| | - Vernon R Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erin Conboy
- Department of Clinical Genomics, Mayo Clinic, MN 55905, USA
| | - Katherine Agre
- Department of Clinical Genomics, Mayo Clinic, MN 55905, USA
| | - Fan Xia
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Magdalena Walkiewicz
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; The National Institute of Allergy and Infectious Disease, The National Institutes of Health, Bethesda, MD 20892, USA
| | - Mauro Longoni
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Frances A High
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Marjon A van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | | | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Nicolette den Hollander
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Sakkubai Naidu
- Kennedy Krieger Institute, 801 North Broadway Baltimore, MD 21205, USA
| | - Sonal Mahida
- Kennedy Krieger Institute, 801 North Broadway Baltimore, MD 21205, USA
| | - Elizabeth E Palmer
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW 2031, Australia
| | - Lucinda Murray
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Derek Lim
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Birmingham B15 2TG, UK
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL 33155, USA
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Stefania Giusto
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | - Emanuela Stracuzzi
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | - Corrado Romano
- Oasi Research Institute - Istituto di Ricovero e Cura a Carattere Scientifico, Troina 94018, Italy
| | | | - Raphael A Bernier
- Department of Psychiatry, University of Washington, Seattle WA, 98195, USA
| | - Sébastien Küry
- Department of Medical Genetics, Centre Hospitalier Universitaire, Nantes 44093, France
| | - Mathilde Nizon
- Department of Medical Genetics, Centre Hospitalier Universitaire, Nantes 44093, France
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Alison Gardner
- Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Christopher Barnett
- Paediatric and Reproductive Genetics, South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), Adelaide, SA 5006, Australia
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Clinical Genetics, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Karin S Kassahn
- Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, SA 5006, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Jolanda Schieving
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Marjolijn J Jongmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500HB, The Netherlands
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9PL, UK; Division of Evolution and Genomic Sciences School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Samantha K Rojas
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | | | | | - 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
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Yaping Yang
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center of Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway; Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Jozef Gecz
- School of Biological Sciences, Faculty of Genes and Evolution, the University of Adelaide, Adelaide, SA 5000, Australia; Adelaide Medical School and Robinson Research Institute, the University of Adelaide, Adelaide, SA 5000, Australia; Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Holly A F Stessman
- Department of Pharmacology, Creighton University Medical School, Omaha, NE, 68178, USA
| | - Linyan Meng
- Baylor Genetics, Houston, TX, 77021, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, 1Bungtown Road, Cold Spring Harbor Laboratory, NY 11724, USA.
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Vairo FP, Boczek NJ, Cousin MA, Kaiwar C, Blackburn PR, Conboy E, Lanpher BC, Gavrilova RH, Pichurin PN, Lazaridis KN, Babovic-Vuksanovic D, Klee EW. The prevalence of diseases caused by lysosome-related genes in a cohort of undiagnosed patients. Mol Genet Metab Rep 2017; 13:46-51. [PMID: 28831385 PMCID: PMC5554961 DOI: 10.1016/j.ymgmr.2017.08.001] [Citation(s) in RCA: 14] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/01/2017] [Indexed: 02/08/2023] Open
Abstract
Lysosomal diseases (LD) comprise a group of approximately 60 hereditary conditions caused by progressive accumulation of metabolites due to defects in lysosomal enzymes and degradation pathways, which lead to a wide range of clinical manifestations. The estimated combined incidence of LD is between 1 in 4000 to 1 in 13,000 live births, with recent data from pilot newborn screening studies showing even higher incidence. We aimed to determine the prevalence of the classical LD and other diseases caused by lysosome-related genes in our cohort of diagnostic odyssey patients. The Individualized Medicine Clinic at Mayo Clinic is increasingly utilizing whole exome sequencing (WES) to determine the genetic etiology of undiagnosed Mendelian disease. From September 2012 to April 2017, WES results from 350 patients with unexplained symptoms were reviewed. Disease-causing variants were identified in MYO6, CLN6, LRBA, KCTD7, and ARSB revealing a genetic diagnosis of a LD in 8 individuals from 5 families. Based on our findings, lysosome-related disorders may be collectively common, reaching up to 1.5% prevalence in a cohort of patients with undiagnosed diseases presenting to a genetics clinic.
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Affiliation(s)
- Filippo Pinto Vairo
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nicole J. Boczek
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Margot A. Cousin
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Patrick R. Blackburn
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Erin Conboy
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Brendan C. Lanpher
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H. Gavrilova
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N. Pichurin
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Konstantinos N. Lazaridis
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W. Klee
- Center for Individualized Medicine, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Biomedical Informatics, Mayo Clinic, Rochester, MN, USA
- Corresponding author at: 200 First Street SW, Rochester, MN, 55905, USA.200 First Street SWRochesterMN55905USA
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Conboy E, Dhamija R, Wang M, Xie J, Dyck PJ, Bridges AG, Spinner RJ, Clayton AC, Watson RE, Messiaen L, Babovic-Vuksanovic D. Paraspinal neurofibromas and hypertrophic neuropathy in Noonan syndrome with multiple lentigines. J Med Genet 2015; 53:123-6. [DOI: 10.1136/jmedgenet-2015-103177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/11/2015] [Indexed: 11/04/2022]
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Volk A, Conboy E, Wical B, Patterson M, Kirmani S. Whole-Exome Sequencing in the Clinic: Lessons from Six Consecutive Cases from the Clinician's Perspective. Mol Syndromol 2015; 6:23-31. [PMID: 25852444 DOI: 10.1159/000371598] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2014] [Indexed: 01/11/2023] Open
Abstract
Whole-exome sequencing (WES) is being used clinically to diagnose rare Mendelian disorders, especially when standard tests have failed. The diagnostic yield from WES is reported to be ∼15-30%; however, data regarding the clinical utility and interpretative challenges from the clinician's perspective are lacking. Here, we present a series of the first 6 unselected consecutive cases seen over a period of 6 months where WES was employed in clinical labs via trio-based testing (proband and parents). While we do not discount the value of WES in the clinical setting, our cases and experience illustrate the significant clinical challenges of WES, even when a diagnosis may be achieved.
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Affiliation(s)
- Amber Volk
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minn., USA
| | - Erin Conboy
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minn., USA
| | - Beverly Wical
- Department of Pediatric Neurology, Gillette Children's Hospital and Clinic, St. Paul, Minn., USA
| | - Marc Patterson
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minn., USA ; Department of Medical Genetics, Mayo Clinic, Rochester, Minn., USA ; Division of Child and Adolescent Neurology, Mayo Clinic, Rochester, Minn., USA
| | - Salman Kirmani
- Department of Medical Genetics, Mayo Clinic, Rochester, Minn., USA
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Rangachari V, Moore BD, Reed DK, Sonoda LK, Bridges AW, Conboy E, Hartigan D, Rosenberry TL. Amyloid-beta(1-42) rapidly forms protofibrils and oligomers by distinct pathways in low concentrations of sodium dodecylsulfate. Biochemistry 2007; 46:12451-62. [PMID: 17910477 DOI: 10.1021/bi701213s] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease (AD) is characterized by large numbers of senile plaques in the brain that consist of fibrillar aggregates of 40- and 42-residue amyloid-beta (Abeta) peptides. However, the degree of dementia in AD correlates better with the concentration of soluble Abeta species assayed biochemically than with histologically determined plaque counts, and several investigators now propose that soluble aggregates of Abeta are the neurotoxic agents that cause memory deficits and neuronal loss. These endogenous aggregates are minor components in brain extracts from AD patients and transgenic mice that express human Abeta, but several species have been detected by gel electrophoresis in sodium dodecylsulfate (SDS) and isolated by size exclusion chromatography (SEC). Endogenous Abeta aggregation is stimulated at cellular interfaces rich in lipid rafts, and anionic micelles that promote Abeta aggregation in vitro may be good models of these interfaces. We previously found that micelles formed in dilute SDS (2 mM) promote Abeta(1-40) fiber formation by supporting peptide interaction on the surface of a single micelle complex. In contrast, here we report that monomeric Abeta(1-42) undergoes an immediate conversion to a predominant beta-structured conformation in 2 mM SDS which does not proceed to amyloid fibrils. The conformational change is instead rapidly followed by the near quantitative conversion of the 4 kDa monomer SDS gel band to 8-14 kDa bands consistent with dimers through tetramers. Removal of SDS by dialysis gave a shift in the predominant SDS gel bands to 30-60 kDa. While these oligomers resemble the endogenous aggregates, they are less stable. In particular, they do not elute as discrete species on SEC, and they are completed disaggregated by boiling in 1% SDS. It appears that endogenous oligomeric Abeta aggregates are stabilized by undefined processes that have not yet been incorporated into in vitro Abeta aggregation procedures.
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Affiliation(s)
- Vijayaraghavan Rangachari
- Department of Neuroscience, Mayo Clinic College of Medicine, 4500 San Pablo Road, Jacksonville, Florida 32224, USA
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Yood RA, Harrold LR, Fish L, Cernieux J, Emani S, Conboy E, Gurwitz JH. Prevention of glucocorticoid-induced osteoporosis: experience in a managed care setting. ACTA ACUST UNITED AC 2001; 161:1322-7. [PMID: 11371261 DOI: 10.1001/archinte.161.10.1322] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
BACKGROUND Treatment with glucocorticoids is the leading cause of drug-induced osteoporosis. Currently available guidelines indicate that patients receiving long-term glucocorticoid therapy should receive measures to prevent osteoporosis. OBJECTIVES To examine whether patients receiving long-term glucocorticoid therapy in a managed care setting received preventive therapy or prescribed medications for osteoporosis and to identify patient and provider characteristics associated with treatment. SUBJECTS AND METHODS A cohort of 224 health plan enrollees 20 years and older who were dispensed at least 1 oral glucocorticoid prescription per quarter during the period October 1997 through September 1998 was identified from administrative data. Medical charts and administrative data were reviewed to determine use of preventive therapy and prescribed medications for osteoporosis. RESULTS Of the 224 patients, 62% had at least 1 documented intervention aimed at osteoporosis prevention (counseling about calcium or vitamin D or weight-bearing exercise; prescription for estrogen, calcitonin, or bisphosphonate; or a bone mineral density study). Women were more likely than men to receive intervention (76% vs 44%; prevalence odds ratio, 4.41; 95% confidence interval, 2.17-9.10). Patients receiving a mean daily prednisone dose of 10 mg or more or 5 to less than 10 mg were no more likely to receive intervention than those receiving 5 mg or less prednisone daily. Sixty-two (90%) of 69 patients who were prescribed glucocorticoid therapy by rheumatologists had at least 1 intervention documented compared with 29 (48%) of 60 for internists, 26 (55%) of 47 for pulmonologists, and 22 (46%) of 48 for all other physicians. In a multiple logistic regression model, including patient age, sex, mean daily glucocorticoid dose, and physician specialty, women and patients prescribed glucocorticoids by a rheumatologist were significantly more likely to receive intervention aimed at osteoporosis prevention. CONCLUSIONS A substantial proportion of patients receiving long-term glucocorticoid therapy do not receive preventive therapy for osteoporosis. Efforts should be made to reduce barriers to such treatment and increase the proportion of patients given preventive therapy.
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Affiliation(s)
- R A Yood
- Division of Rheumatology, Fallon Clinic, Meyers Primary Care Institute, Fallon Healthcare Systems, 135 Gold Star Blvd, Worcester, MA 01606, USA
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Hidlebaugh D, O'Mara P, Conboy E. Clinical and financial analyses of laparoscopically assisted vaginal hysterectomy versus abdominal hysterectomy. J Am Assoc Gynecol Laparosc 1994; 1:357-61. [PMID: 9138877 DOI: 10.1016/s1074-3804(05)80801-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
STUDY OBJECTIVE To perform clinical and financial analyses of laparoscopically assisted vaginal hysterectomy (LAVH) and total abdominal hysterectomy (TAH). DESIGN During the 16 months between August 1991 and December 1992, 34 women who underwent LAVH were compared with 60 women having TAH during 1990. Indications, surgical outcomes, complications, time to return to work, and hospital charges for each group were analyzed. SETTING A multispecialty group practice. PATIENTS The LAVH group included the first 34 cases by the senior author and were the only such procedures at this hospital. The TAH group included all patients having this procedure for benign conditions from the same group practice for 1990. Interventions. Either LAVH or TAH. MEASUREMENTS AND MAIN RESULTS The most common primary indication in both groups was fibroids. Only one LAVH failed and was converted to a TAH. Postoperative complications were significantly greater for TAH than for LAVH (45% vs 9%). The length of stay and time to return to work were significantly less after LAVH. Total hospital charges increased for LAVH over TAH ($7623 vs $4550) despite a significantly shorter length of stay after LAVH. CONCLUSIONS Although LAVH has a significantly lower complication rate than TAH, it is more costly to perform. This higher cost, despite a shorter hospital stay, is attributed to high operating room charges. Employers and patients benefit from early return to work with LAVH.
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Affiliation(s)
- D Hidlebaugh
- Fallon Fertility Center, 100 Central Street, Worcester, MA 01608, USA
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Hidlebaugh D, O'Mara P, Conboy E. Salpingo-oophorectomy: clinical and financial analyses of laparoscopic and open techniques. J Am Assoc Gynecol Laparosc 1994; 1:223-7. [PMID: 9050491 DOI: 10.1016/s1074-3804(05)81014-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To analyze clinical results and financial costs of salpingo-oophorectomy performed by laparoscopy versus laparotomy. STUDY DESIGN Comparison of laparoscopic salpingo-oophorectomy with procedures performed by laparotomy. SETTING St. Vincent's Hospital and Fallon Clinic in Worcester, Massachusetts. PATIENTS Twenty women in both groups. INTERVENTIONS Salpingo-oophorectomies performed by laparoscopy and laparotomy. MEASUREMENTS AND MAIN RESULTS Women undergoing laparotomy had a 25% rate of postoperative complications compared with 0% of those having laparoscopy. The duration of the procedures and hospital charges were similar for both groups. Length of hospital stay and time to return to work were significantly less after laparoscopy than laparotomy. CONCLUSIONS Laparoscopic salpingo-oophorectomy was associated with significantly fewer complications than the operations performed by laparotomy. Although women in the laparoscopy group had a shorter hospital stay, their higher charges were attributed to costly disposable instruments. Patients benefit from early return to work and other activities after laparoscopy.
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Affiliation(s)
- D Hidlebaugh
- Fallon Fertility Center, 100 Central Street, Worcester, MA 01608, USA
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