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Deignan JL, De Castro M, Horner VL, Johnston T, Macaya D, Maleszewski JJ, Reddi HV, Tayeh MK. Points to consider in the practice of postmortem genetic testing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100017. [PMID: 36799919 DOI: 10.1016/j.gim.2023.100017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 02/18/2023] Open
Affiliation(s)
- Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA Health, Los Angeles, CA
| | - Mauricio De Castro
- DHA Genetics Reference Laboratory, Air Force Medical Genetics Center, Keesler Air Force Base, Biloxi, MS; Division of Medical Genetics, Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS
| | - Vanessa L Horner
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI; Wisconsin State Laboratory of Hygiene, University of Wisconsin, Madison, WI
| | | | | | | | - Honey V Reddi
- Department of Pathology & Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Marwan K Tayeh
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
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Tayeh MK, Chen M, Fullerton SM, Gonzales PR, Huang SJ, Massingham LJ, O'Daniel JM, Stewart DR, Stiles AR, Evans BJ. The designated record set for clinical genetic and genomic testing: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100342. [PMID: 36547466 DOI: 10.1016/j.gim.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Margaret Chen
- Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI; GeneDx, Gaithersburg, MD
| | - Stephanie M Fullerton
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA
| | - Patrick R Gonzales
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Lenexa, KS
| | - Samuel J Huang
- Division of Medical Genetics, Marshfield Clinic, Marshfield, WI
| | - Lauren J Massingham
- Division of Medical Genetics, Department of Pediatrics, Hasbro Children's Hospital, Providence, RI; The Warren Alpert School of Medicine at Brown University, Providence, RI
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Ashlee R Stiles
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Barbara J Evans
- Levin College of Law, University of Florida, Gainesville, FL; Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL
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- American College of Medical Genetics and Genomics, Bethesda, MD
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Tayeh MK, DeVaul J, LeSueur K, Yang C, Bedoyan JK, Thomas P, Hannibal MC, Innis JW. Novel multilocus imprinting disturbances in a child with expressive language delay and intellectual disability. Am J Med Genet A 2022; 188:2209-2216. [PMID: 35365979 PMCID: PMC9321834 DOI: 10.1002/ajmg.a.62752] [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: 12/10/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022]
Abstract
Multilocus imprinting disturbances (MLID) have been associated with up to 12% of patients with Beckwith‐Wiedemann syndrome, Silver‐Russell syndrome, and pseudohypoparathyroidism type 1B (PHP1B). Single‐gene defects affecting components of the subcortical maternal complex (SCMC) have been reported in cases with multilocus hypomethylation defects. We present a patient with speech and language impairment with mild Angelman syndrome (AS) features who demonstrates maternal hypomethylation at 15q11.2 (SNRPN) as well as 11p15.5 (KCNQ1OT1) imprinted loci, but normal methylation at 6q24.2 (PLAGL1), 7p12.1 (GRB10), 7q32.2 (MEST), 11p15.5 (H19), 14q32.2 (MEG3), 19q13.43 (PEG3), and 20q13.32 (GNAS and GNAS‐AS1). The proband also has no copy number nor sequence variants within the AS imprinting center or in UBE3A. Maternal targeted next generation sequencing did not identify any pathogenic variants in ZPF57, NLRP2, NLRP5, NLRP7, KHDC3L, PADI6, TLE6, OOEP, UHRF1 or ZAR1. The presence of very delayed, yet functional speech, behavioral difficulties, EEG abnormalities but without clinical seizures, and normocephaly are consistent with the 15q11.2 hypomethylation defect observed in this patient. To our knowledge, this is the first report of MLID in a patient with mild, likely mosaic, Angelman syndrome.
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Affiliation(s)
- Marwan K Tayeh
- Department of Medical and Molecular Genetics, Division of Indiana, University Genetics Testing Laboratories, Indiana University, Indianapolis, Indiana, USA
| | - Janean DeVaul
- Department of Pediatrics, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Kristin LeSueur
- Department of Pediatrics, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Chen Yang
- Department of Pediatrics, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jirair K Bedoyan
- Department of Pediatrics, Division of Genetic and Genomic Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Peedikayil Thomas
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Mark C Hannibal
- Department of Pediatrics, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeffrey W Innis
- Department of Pediatrics, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
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4
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Tayeh MK, Gaedigk A, Goetz MP, Klein TE, Lyon E, McMillin GA, Rentas S, Shinawi M, Pratt VM, Scott SA. Clinical pharmacogenomic testing and reporting: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:759-768. [PMID: 35177334 DOI: 10.1016/j.gim.2021.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/14/2022] Open
Abstract
Pharmacogenomic testing interrogates germline sequence variants implicated in interindividual drug response variability to infer a drug response phenotype and to guide medication management for certain drugs. Specifically, discrete aspects of pharmacokinetics, such as drug metabolism, and pharmacodynamics, as well as drug sensitivity, can be predicted by genes that code for proteins involved in these pathways. Pharmacogenomics is unique and differs from inherited disease genetics because the drug response phenotype can be drug-dependent and is often unrecognized until an unexpected drug reaction occurs or a patient fails to respond to a medication. Genes and variants with sufficiently high levels of evidence and consensus may be included in a clinical pharmacogenomic test; however, result interpretation and phenotype prediction can be challenging for some genes and medications. This document provides a resource for laboratories to develop and implement clinical pharmacogenomic testing by summarizing publicly available resources and detailing best practices for pharmacogenomic nomenclature, testing, result interpretation, and reporting.
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Affiliation(s)
- Marwan K Tayeh
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO; Department of Pediatrics, UMKC School of Medicine, University of Missouri-Kansas City, Kansas City, MO
| | - Matthew P Goetz
- Department of Pharmacology and Oncology, Mayo Clinic, Rochester, MN
| | - Teri E Klein
- Department of Biomedical Data Science and Department of Medicine, Stanford University, Stanford, CA
| | - Elaine Lyon
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | - Stefan Rentas
- Department of Pathology, Duke University School of Medicine, Durham, NC
| | - Marwan Shinawi
- Division of Genetics & Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, CA; Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, CA
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Akinci B, Subauste A, Ajluni N, Esfandiari NH, Meral R, Neidert AH, Eraslan A, Hench R, Rus D, Mckenna B, Hussain HK, Chenevert TL, Tayeh MK, Rupani AR, Innis JW, Mantzoros CS, Conjeevaram HS, Burant CL, Oral EA. Metreleptin therapy for nonalcoholic steatohepatitis: Open-label therapy interventions in two different clinical settings. Med 2021; 2:814-835. [DOI: 10.1016/j.medj.2021.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Eldin AJ, Akinci B, da Rocha AM, Meral R, Simsir IY, Adiyaman SC, Ozpelit E, Bhave N, Gen R, Yurekli B, Kutbay NO, Siklar Z, Neidert AH, Hench R, Tayeh MK, Innis JW, Jalife J, Oral H, Oral EA. Cardiac phenotype in familial partial lipodystrophy. Clin Endocrinol (Oxf) 2021; 94:1043-1053. [PMID: 33502018 PMCID: PMC9003538 DOI: 10.1111/cen.14426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVES LMNA variants have been previously associated with cardiac abnormalities independent of lipodystrophy. We aimed to assess cardiac impact of familial partial lipodystrophy (FPLD) to understand the role of laminopathy in cardiac manifestations. STUDY DESIGN Retrospective cohort study. METHODS Clinical data from 122 patients (age range: 13-77, 101 females) with FPLD were analysed. Mature human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from a patient with an LMNA variant were studied as proof-of-concept for future studies. RESULTS Subjects with LMNA variants had a higher prevalence of overall cardiac events than others. The likelihood of having an arrhythmia was significantly higher in patients with LMNA variants (OR: 3.77, 95% CI: 1.45-9.83). These patients were at higher risk for atrial fibrillation or flutter (OR: 5.78, 95% CI: 1.04-32.16). The time to the first arrhythmia was significantly shorter in the LMNA group, with a higher HR of 3.52 (95% CI: 1.34-9.27). Non-codon 482 LMNA variants were more likely to be associated with cardiac events (vs. 482 LMNA: OR: 4.74, 95% CI: 1.41-15.98 for arrhythmia; OR: 17.67, 95% CI: 2.45-127.68 for atrial fibrillation or flutter; OR: 5.71, 95% CI: 1.37-23.76 for conduction disease). LMNA mutant hiPSC-CMs showed a higher frequency of spontaneous activity and shorter action potential duration. Functional syncytia of hiPSC-CMs displayed several rhythm alterations such as early afterdepolarizations, spontaneous quiescence and spontaneous tachyarrhythmia, and significantly slower recovery in chronotropic changes induced by isoproterenol exposure. CONCLUSIONS Our results highlight the need for vigilant cardiac monitoring in FPLD, especially in patients with LMNA variants who have an increased risk of developing cardiac arrhythmias. In addition, hiPSC-CMs can be studied to understand the basic mechanisms for the arrhythmias in patients with lipodystrophy to understand the impact of specific mutations.
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Affiliation(s)
- Abdelwahab Jalal Eldin
- Division of Metabolism, Endocrinology and Diabetes (MEND), Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Baris Akinci
- Division of Metabolism, Endocrinology and Diabetes (MEND), Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Division of Endocrinology, Department of Internal Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Andre Monteiro da Rocha
- Center for Arrhythmia Research, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Rasimcan Meral
- Division of Metabolism, Endocrinology and Diabetes (MEND), Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Ilgin Yildirim Simsir
- Division of Endocrinology, Department of Internal Medicine, Ege University, Izmir, Turkey
| | - Suleyman Cem Adiyaman
- Division of Endocrinology, Department of Internal Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Ebru Ozpelit
- Division of Cardiology, Department of Internal Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Nicole Bhave
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Ramazan Gen
- Division of Endocrinology, Department of Internal Medicine, Mersin University, Mersin, Turkey
| | - Banu Yurekli
- Division of Endocrinology, Department of Internal Medicine, Ege University, Izmir, Turkey
| | - Nilufer Ozdemir Kutbay
- Division of Endocrinology, Department of Internal Medicine, Celal Bayar University, Manisa, Turkey
| | - Zeynep Siklar
- Division of Endocrinology, Department of Pediatrics, Ankara University, Ankara, Turkey
| | - Adam H. Neidert
- Division of Metabolism, Endocrinology and Diabetes (MEND), Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Rita Hench
- Division of Metabolism, Endocrinology and Diabetes (MEND), Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Marwan K. Tayeh
- Departments of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey W. Innis
- Departments of Pediatrics, University of Michigan, Ann Arbor, MI, USA
- Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jose Jalife
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Cardiac Arrhythmia Section, Centro Nacional de Investigaciones Cardiovasculares (CNIC) Carlos III, Madrid, Spain
| | - Hakan Oral
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Elif A. Oral
- Division of Metabolism, Endocrinology and Diabetes (MEND), Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
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Noto FK, Sangodkar J, Adedeji BT, Moody S, McClain CB, Tong M, Ostertag E, Crawford J, Gao X, Hurst L, O’Connor CM, Hanson EN, Izadmehr S, Tohmé R, Narla J, LeSueur K, Bhattacharya K, Rupani A, Tayeh MK, Innis JW, Galsky MD, Evers BM, DiFeo A, Narla G, Jamling TY. The SRG rat, a Sprague-Dawley Rag2/Il2rg double-knockout validated for human tumor oncology studies. PLoS One 2020; 15:e0240169. [PMID: 33027304 PMCID: PMC7540894 DOI: 10.1371/journal.pone.0240169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
We have created the immunodeficient SRG rat, a Sprague-Dawley Rag2/Il2rg double knockout that lacks mature B cells, T cells, and circulating NK cells. This model has been tested and validated for use in oncology (SRG OncoRat®). The SRG rat demonstrates efficient tumor take rates and growth kinetics with different human cancer cell lines and PDXs. Although multiple immunodeficient rodent strains are available, some important human cancer cell lines exhibit poor tumor growth and high variability in those models. The VCaP prostate cancer model is one such cell line that engrafts unreliably and grows irregularly in existing models but displays over 90% engraftment rate in the SRG rat with uniform growth kinetics. Since rats can support much larger tumors than mice, the SRG rat is an attractive host for PDX establishment. Surgically resected NSCLC tissue from nine patients were implanted in SRG rats, seven of which engrafted and grew for an overall success rate of 78%. These developed into a large tumor volume, over 20,000 mm3 in the first passage, which would provide an ample source of tissue for characterization and/or subsequent passage into NSG mice for drug efficacy studies. Molecular characterization and histological analyses were performed for three PDX lines and showed high concordance between passages 1, 2 and 3 (P1, P2, P3), and the original patient sample. Our data suggest the SRG OncoRat is a valuable tool for establishing PDX banks and thus serves as an alternative to current PDX mouse models hindered by low engraftment rates, slow tumor growth kinetics, and multiple passages to develop adequate tissue banks.
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Affiliation(s)
- Fallon K. Noto
- Hera BioLabs Inc., Lexington, Kentucky, United States of America
- * E-mail:
| | - Jaya Sangodkar
- Division of Genetic Medicine, Department of Medicine, The University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Sam Moody
- Hera BioLabs Inc., Lexington, Kentucky, United States of America
| | | | - Ming Tong
- Poseida Therapeutics Inc., San Diego, California, United States of America
| | - Eric Ostertag
- Poseida Therapeutics Inc., San Diego, California, United States of America
| | - Jack Crawford
- Hera BioLabs Inc., Lexington, Kentucky, United States of America
| | - Xiaohua Gao
- Division of Genetic Medicine, Department of Medicine, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lauren Hurst
- Division of Genetic Medicine, Department of Medicine, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Caitlin M. O’Connor
- Division of Genetic Medicine, Department of Medicine, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Erika N. Hanson
- Division of Genetic Medicine, Department of Medicine, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sudeh Izadmehr
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Rita Tohmé
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
- Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jyothsna Narla
- Regional Medical Center, San Jose, California, United States of America
| | - Kristin LeSueur
- Department of Pediatrics, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kajari Bhattacharya
- Department of Pediatrics, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Amit Rupani
- Department of Pediatrics, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Marwan K. Tayeh
- Department of Pediatrics, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jeffrey W. Innis
- Department of Pediatrics, The University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, The University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Matthew D. Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - B. Mark Evers
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Analisa DiFeo
- Department of Obstetrics and Gynecology, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Goutham Narla
- Hera BioLabs Inc., Lexington, Kentucky, United States of America
- Division of Genetic Medicine, Department of Medicine, The University of Michigan, Ann Arbor, Michigan, United States of America
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Riggs ER, Nelson T, Merz A, Ackley T, Bunke B, Collins CD, Collinson MN, Fan YS, Goodenberger ML, Golden DM, Haglund-Hazy L, Krgovic D, Lamb AN, Lewis Z, Li G, Liu Y, Meck J, Neufeld-Kaiser W, Runke CK, Sanmann JN, Stavropoulos DJ, Strong E, Su M, Tayeh MK, Kokalj Vokac N, Thorland EC, Andersen E, Martin CL. Copy number variant discrepancy resolution using the ClinGen dosage sensitivity map results in updated clinical interpretations in ClinVar. Hum Mutat 2019; 39:1650-1659. [PMID: 30095202 DOI: 10.1002/humu.23610] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/16/2018] [Accepted: 08/03/2018] [Indexed: 11/07/2022]
Abstract
Conflict resolution in genomic variant interpretation is a critical step toward improving patient care. Evaluating interpretation discrepancies in copy number variants (CNVs) typically involves assessing overlapping genomic content with focus on genes/regions that may be subject to dosage sensitivity (haploinsufficiency (HI) and/or triplosensitivity (TS)). CNVs containing dosage sensitive genes/regions are generally interpreted as "likely pathogenic" (LP) or "pathogenic" (P), and CNVs involving the same known dosage sensitive gene(s) should receive the same clinical interpretation. We compared the Clinical Genome Resource (ClinGen) Dosage Map, a publicly available resource documenting known HI and TS genes/regions, against germline, clinical CNV interpretations within the ClinVar database. We identified 251 CNVs overlapping known dosage sensitive genes/regions but not classified as LP or P; these were sent back to their original submitting laboratories for re-evaluation. Of 246 CNVs re-evaluated, an updated clinical classification was warranted in 157 cases (63.8%); no change was made to the current classification in 79 cases (32.1%); and 10 cases (4.1%) resulted in other types of updates to ClinVar records. This effort will add curated interpretation data into the public domain and allow laboratories to focus attention on more complex discrepancies.
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Affiliation(s)
- Erin R Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Tristan Nelson
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Andrew Merz
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Todd Ackley
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | | | | | - Morag N Collinson
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, Wiltshire, UK
| | - Yao-Shan Fan
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - McKinsey L Goodenberger
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Denae M Golden
- Human Genetics Laboratory, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Linda Haglund-Hazy
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | - Danijela Krgovic
- University Medical Centre Maribor, Laboratory of Medical Genetics, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Allen N Lamb
- ARUP Laboratories, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
| | - Zoe Lewis
- ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Yajuan Liu
- Clinical Cytogenomics Laboratory, Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Whitney Neufeld-Kaiser
- Clinical Cytogenomics Laboratory, Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Cassandra K Runke
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jennifer N Sanmann
- Human Genetics Laboratory, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Emma Strong
- Genome Diagnostics, The Hospital for Sick Children, University of Toronto, Canada
| | - Meng Su
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - Marwan K Tayeh
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | - Nadja Kokalj Vokac
- University Medical Centre Maribor, Laboratory of Medical Genetics, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Erica Andersen
- ARUP Laboratories, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
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9
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Sahinoz M, Khairi S, Cuttitta A, Brady GF, Rupani A, Meral R, Tayeh MK, Thomas P, Riebschleger M, Camelo-Piragua S, Innis JW, Bishr Omary M, Michele DE, Oral EA. Potential association of LMNA-associated generalized lipodystrophy with juvenile dermatomyositis. Clin Diabetes Endocrinol 2018; 4:6. [PMID: 29610677 PMCID: PMC5870259 DOI: 10.1186/s40842-018-0058-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/20/2018] [Indexed: 11/10/2022] Open
Abstract
Background Juvenile dermatomyositis (JDM) is an auto-immune muscle disease which presents with skin manifestations and muscle weakness. At least 10% of the patients with JDM present with acquired lipodystrophy. Laminopathies are caused by mutations in the lamin genes and cover a wide spectrum of diseases including muscular dystrophies and lipodystrophy. The p.T10I LMNA variant is associated with a phenotype of generalized lipodystrophy that has also been called atypical progeroid syndrome. Case presentation A previously healthy female presented with bilateral proximal lower extremity muscle weakness at age 4. She was diagnosed with JDM based on her clinical presentation, laboratory tests and magnetic resonance imaging (MRI). She had subcutaneous fat loss which started in her extremities and progressed to her whole body. At age 7, she had diabetes, hypertriglyceridemia, low leptin levels and low body fat on dual energy X-ray absorptiometry (DEXA) scan, and was diagnosed with acquired generalized lipodystrophy (AGL). Whole exome sequencing (WES) revealed a heterozygous c.29C > T; p.T10I missense pathogenic variant in LMNA, which encodes lamins A and C. Muscle biopsy confirmed JDM rather than muscular dystrophy, showing perifascicular atrophy and perivascular mononuclear cell infiltration. Immunofluroscence of skin fibroblasts confirmed nuclear atypia and fragmentation. Conclusions This is a unique case with p.T10I LMNA variant displaying concurrent JDM and AGL. This co-occurrence raises the intriguing possibility that LMNA, and possibly p.T10I, may have a pathogenic role in not only the occurrence of generalized lipodystrophy, but also juvenile dermatomyositis. Careful phenotypic characterization of additional patients with laminopathies as well as individuals with JDM is warranted.
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Affiliation(s)
- Melis Sahinoz
- 1Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Shafaq Khairi
- 2Metabolism Endocrinology and Diabetes Division, Department of Internal Medicine, University of Michigan and Brehm Center for Diabetes, 1000 Wall Street, Room 5313, Ann Arbor, MI MI48105 USA
| | - Ashley Cuttitta
- 3Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI USA
| | - Graham F Brady
- 4Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI USA
| | - Amit Rupani
- 5Division of Genetics, Metabolism & Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI USA
| | - Rasimcan Meral
- 2Metabolism Endocrinology and Diabetes Division, Department of Internal Medicine, University of Michigan and Brehm Center for Diabetes, 1000 Wall Street, Room 5313, Ann Arbor, MI MI48105 USA
| | - Marwan K Tayeh
- 5Division of Genetics, Metabolism & Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI USA
| | - Peedikayil Thomas
- 5Division of Genetics, Metabolism & Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI USA
| | - Meredith Riebschleger
- 6Division of Pediatric Rheumatology, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI USA
| | | | - Jeffrey W Innis
- 5Division of Genetics, Metabolism & Genomic Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI USA.,8Department of Human Genetics, University of Michigan, Ann Arbor, MI USA
| | - M Bishr Omary
- 3Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI USA
| | - Daniel E Michele
- 3Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI USA
| | - Elif A Oral
- 2Metabolism Endocrinology and Diabetes Division, Department of Internal Medicine, University of Michigan and Brehm Center for Diabetes, 1000 Wall Street, Room 5313, Ann Arbor, MI MI48105 USA
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10
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Hussain I, Patni N, Ueda M, Sorkina E, Valerio CM, Cochran E, Brown RJ, Peeden J, Tikhonovich Y, Tiulpakov A, Stender SRS, Klouda E, Tayeh MK, Innis JW, Meyer A, Lal P, Godoy-Matos AF, Teles MG, Adams-Huet B, Rader DJ, Hegele RA, Oral EA, Garg A. A Novel Generalized Lipodystrophy-Associated Progeroid Syndrome Due to Recurrent Heterozygous LMNA p.T10I Mutation. J Clin Endocrinol Metab 2018; 103:1005-1014. [PMID: 29267953 PMCID: PMC6283411 DOI: 10.1210/jc.2017-02078] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/12/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Lamin A/C (LMNA) gene mutations cause a heterogeneous group of progeroid disorders, including Hutchinson-Gilford progeria syndrome, mandibuloacral dysplasia, and atypical progeroid syndrome (APS). Five of the 31 previously reported patients with APS harbored a recurrent de novo heterozygous LMNA p.T10I mutation. All five had generalized lipodystrophy, as well as similar metabolic and clinical features, suggesting a distinct progeroid syndrome. METHODS We report nine new patients and follow-up of two previously reported patients with the heterozygous LMNA p.T10I mutation and compare their clinical and metabolic features with other patients with APS. RESULTS Compared with other patients with APS, those with the heterozygous LMNA p.T10I mutation were younger in age but had increased prevalence of generalized lipodystrophy, diabetes mellitus, acanthosis nigricans, hypertriglyceridemia, and hepatomegaly, together with higher fasting serum insulin and triglyceride levels and lower serum leptin and high-density lipoprotein cholesterol levels. Prominent clinical features included mottled skin pigmentation, joint contractures, and cardiomyopathy resulting in cardiac transplants in three patients at ages 13, 33, and 47 years. Seven patients received metreleptin therapy for 0.5 to 16 years with all, except one noncompliant patient, showing marked improvement in metabolic complications. CONCLUSIONS Patients with the heterozygous LMNA p.T10I mutation have distinct clinical features and significantly worse metabolic complications compared with other patients with APS as well as patients with Hutchinson-Gilford progeria syndrome. We propose that they be recognized as having generalized lipodystrophy-associated progeroid syndrome. Patients with generalized lipodystrophy-associated progeroid syndrome should undergo careful multisystem assessment at onset and yearly metabolic and cardiac evaluation, as hyperglycemia, hypertriglyceridemia, hepatic steatosis, and cardiomyopathy are the major contributors to morbidity and mortality.
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Affiliation(s)
- Iram Hussain
- Division of Endocrinology, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas
| | - Nivedita Patni
- Division of Pediatric Endocrinology, Department of Pediatrics, Center for Human Nutrition, UT Southwestern Medical Center, Dallas, Texas
| | - Masako Ueda
- Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ekaterina Sorkina
- Endocrinology Research Centre, Moscow, Russia
- Laboratory of Molecular Endocrinology, Medical Scientific Educational Centre, Lomonosov Moscow State University, Moscow, Russia
| | - Cynthia M Valerio
- Division of Metabology, State Institute of Diabetes and Endocrinology, Rio de Janeiro, Brazil
| | - Elaine Cochran
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Rebecca J Brown
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Joseph Peeden
- East Tennessee Children’s Hospital, University of Tennessee Department of Medicine, Knoxville, Tennessee
| | | | | | - Sarah R S Stender
- Department of Pediatrics, University of California San Francisco–Fresno, Fresno, California
| | | | - Marwan K Tayeh
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Division of Genetics, Metabolism and Genomic Medicine and Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey W Innis
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan
| | - Anders Meyer
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Priti Lal
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amelio F Godoy-Matos
- Division of Metabology, State Institute of Diabetes and Endocrinology, Rio de Janeiro, Brazil
| | - Milena G Teles
- Monogenic Diabetes Group, Genetic Endocrinology Unit (LIM25), Hospital das Clinicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Beverley Adams-Huet
- Department of Clinical Sciences, Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Daniel J Rader
- Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robert A Hegele
- Department of Medicine, Western University, London, Ontario, Canada
| | - Elif A Oral
- Metabolism, Endocrinology and Diabetes Division, Department of Internal of Medicine, Brehm Center for Diabetes, University of Michigan, Ann Arbor, Michigan
| | - Abhimanyu Garg
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine, Center for Human Nutrition, UT Southwestern Medical Center, Dallas, Texas
- Correspondence and Reprint Requests: Abhimanyu Garg, MD, Division of Nutrition and Metabolic Diseases, Department of Internal Medicine and the Center for Human Nutrition, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8537. E-mail:
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11
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Ajluni N, Meral R, Neidert AH, Brady GF, Buras E, McKenna B, DiPaola F, Chenevert TL, Horowitz JF, Buggs-Saxton C, Rupani AR, Thomas PE, Tayeh MK, Innis JW, Omary MB, Conjeevaram H, Oral EA. Spectrum of disease associated with partial lipodystrophy: lessons from a trial cohort. Clin Endocrinol (Oxf) 2017; 86:698-707. [PMID: 28199729 PMCID: PMC5395301 DOI: 10.1111/cen.13311] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/18/2017] [Accepted: 02/10/2017] [Indexed: 12/29/2022]
Abstract
CONTEXT Partial lipodystrophy (PL) is associated with metabolic co-morbidities but may go undiagnosed as the disease spectrum is not fully described. OBJECTIVE The objective of the study was to define disease spectrum in PL using genetic, clinical (historical, morphometric) and laboratory characteristics. DESIGN Cross-sectional evaluation. PARTICIPANTS Twenty-three patients (22 with familial, one acquired, 78·3% female, aged 12-64 years) with PL and non-alcoholic fatty liver disease (NAFLD). MEASUREMENTS Genetic, clinical and laboratory characteristics, body composition indices, liver fat content by magnetic resonance imaging (MRI), histopathological and immunofluorescence examinations of liver biopsies. RESULTS Seven patients displayed heterozygous pathogenic variants in LMNA. Two related patients had a heterozygous, likely pathogenic novel variant of POLD1 (NM002691·3: c.3199 G>A; p.E1067K). Most patients had high ratios (>1·5) of percentage fat trunk to percentage fat legs (FMR) when compared to reference normals. Liver fat quantified using MR Dixon method was high (11·3 ± 6·3%) and correlated positively with haemoglobin A1c and triglycerides while leg fat by dual-energy X-ray absorptiometry (DEXA) correlated negatively with triglycerides. In addition to known metabolic comorbidities; chronic pain (78·3%), hypertension (56·5%) and mood disorders (52·2%) were highly prevalent. Mean NAFLD Activity Score (NAS) was 5 ± 1 and 78·3% had fibrosis. LMNA-immunofluorescence staining from select patients (including one with the novel POLD1 variant) showed a high degree of nuclear atypia and disorganization. CONCLUSIONS Partial lipodystrophy is a complex multi-system disorder. Metabolic parameters correlate negatively with extremity fat and positively with liver fat. DEXA-based FMR may prove useful as a diagnostic tool. Nuclear disorganization and atypia may be a common biomarker even in the absence of pathogenic variants in LMNA.
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Affiliation(s)
- Nevin Ajluni
- Brehm Center for Diabetes Research and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Rasimcan Meral
- Brehm Center for Diabetes Research and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Adam H. Neidert
- Brehm Center for Diabetes Research and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Graham F. Brady
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Eric Buras
- Brehm Center for Diabetes Research and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Barbara McKenna
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Frank DiPaola
- Division of Pediatric Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Colleen Buggs-Saxton
- Pediatric Endocrinology, Children’s Hospital of Michigan, Wayne School of Medicine, Detroit, MI, USA
| | - Amit R. Rupani
- Departments of Pediatrics and Communicable Diseases and Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Peedikayil E. Thomas
- Departments of Pediatrics and Communicable Diseases and Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Marwan K. Tayeh
- Departments of Pediatrics and Communicable Diseases and Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey W. Innis
- Departments of Pediatrics and Communicable Diseases and Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - M. Bishr Omary
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Hari Conjeevaram
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Elif A. Oral
- Brehm Center for Diabetes Research and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
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12
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Tayeh MK, Rocco T, Ackley T, Ernst L, Glover T, Innis JW. Nine de novo duplications affecting both maternal and paternal chromosomes and an inherited 15q11.2 deletion, in a patient with developmental delay. Clin Case Rep 2015; 3:396-401. [PMID: 26185636 PMCID: PMC4498850 DOI: 10.1002/ccr3.241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 10/31/2014] [Revised: 12/05/2014] [Accepted: 02/20/2015] [Indexed: 11/09/2022] Open
Abstract
A patient with developmental delay and nine, de novo, tandem duplications affecting eight different chromosomes that arose on both maternal and paternal chromosomes indicating a vulnerable zygotic or early postzygotic period of development for these errors, potentially affected by genetic and nongenetic factors.
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Affiliation(s)
- Marwan K Tayeh
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan Ann Arbor, Michigan
| | - Tracy Rocco
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan Ann Arbor, Michigan
| | - Todd Ackley
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan Ann Arbor, Michigan
| | - Leslie Ernst
- Department of Pathology, University of Michigan Ann Arbor, Michigan
| | - Thomas Glover
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan Ann Arbor, Michigan ; Department of Pathology, University of Michigan Ann Arbor, Michigan ; Department of Human Genetics, University of Michigan Ann Arbor, Michigan
| | - Jeffrey W Innis
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan Ann Arbor, Michigan ; Department of Human Genetics, University of Michigan Ann Arbor, Michigan
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13
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Tayeh MK, Yen HJ, Beck JS, Searby CC, Westfall TA, Griesbach H, Sheffield VC, Slusarski DC. Genetic interaction between Bardet-Biedl syndrome genes and implications for limb patterning. Hum Mol Genet 2008; 17:1956-67. [PMID: 18381349 DOI: 10.1093/hmg/ddn093] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a pleiotropic, genetically heterogeneous disorder characterized by obesity, retinopathy, polydactyly, cognitive impairment, renal and cardiac anomalies, as well as hypertension and diabetes. Multiple genes are known to independently cause BBS. These genes do not appear to code for the same functional category of proteins; yet, mutation of each results in a similar phenotype. Gene knockdown of different BBS genes in zebrafish shows strikingly overlapping phenotypes including defective melanosome transport and disruption of the ciliated Kupffer's vesicle. Here, we demonstrate that individual knockdown of bbs1 and bbs3 results in the same prototypical phenotypes as reported previously for other BBS genes. We utilize the zebrafish system to comprehensively determine whether simultaneous pair-wise knockdown of BBS genes reveals genetic interactions between BBS genes. Using this approach, we demonstrate eight genetic interactions between a subset of BBS genes. The synergistic relationships between distinct combinations are not due to functional redundancy but indicate specific interactions within a multi-subunit BBS complex. In addition, we utilize the zebrafish model system to investigate limb development. Human polydactyly is a cardinal feature of BBS not reproduced in BBS-mouse models. We evaluated zebrafish fin bud patterning and observed altered Sonic hedgehog (shh) expression and subsequent changes to fin skeletal elements. The SHH fin bud phenotype was also used to confirm specific genetic interactions between BBS genes. This study reveals an in vivo requirement for BBS function in limb bud patterning. Our results provide important new insights into the mechanism and biological significance of BBS.
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Affiliation(s)
- Marwan K Tayeh
- Department of Pediatrics, Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242, USA
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14
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Ferguson PJ, Chen S, Tayeh MK, Ochoa L, Leal SM, Pelet A, Munnich A, Lyonnet S, Majeed HA, El-Shanti H. Homozygous mutations in LPIN2 are responsible for the syndrome of chronic recurrent multifocal osteomyelitis and congenital dyserythropoietic anaemia (Majeed syndrome). J Med Genet 2006; 42:551-7. [PMID: 15994876 PMCID: PMC1736104 DOI: 10.1136/jmg.2005.030759] [Citation(s) in RCA: 266] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Majeed syndrome is an autosomal recessive, autoinflammatory disorder characterised by chronic recurrent multifocal osteomyelitis and congenital dyserythropoietic anaemia. The objectives of this study were to map, identify, and characterise the Majeed syndrome causal gene and to speculate on its function and role in skin and bone inflammation. METHODS Six individuals with Majeed syndrome from two unrelated families were identified for this study. Homozygosity mapping and parametric linkage analysis were employed for the localisation of the gene responsible for Majeed syndrome. Direct sequencing was utilised for the identification of mutations within the genes contained in the region of linkage. Expression studies and in silico characterisation of the identified causal gene and its protein were carried out. RESULTS The phenotype of Majeed syndrome includes inflammation of the bone and skin, recurrent fevers, and dyserythropoietic anaemia. The clinical picture of the six affected individuals is briefly reviewed. The gene was mapped to a 5.5 cM interval (1.8 Mb) on chromosome 18p. Examination of genes in this interval led to the identification of homozygous mutations in LPIN2 in affected individuals from the two families. LPIN2 was found to be expressed in almost all tissues. The function of LPIN2 and its role in inflammation remains unknown. CONCLUSIONS We conclude that homozygous mutations in LPIN2 result in Majeed syndrome. Understanding the aberrant immune response in this condition will shed light on the aetiology of other inflammatory disorders of multifactorial aetiology including isolated chronic recurrent multifocal osteomyelitis, Sweet syndrome, and psoriasis.
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Affiliation(s)
- P J Ferguson
- Department of Pediatrics, Division of Hematology/Oncology/Rheumatology, University of Iowa, Iowa City, IA, USA
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15
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Chiang AP, Beck JS, Yen HJ, Tayeh MK, Scheetz TE, Swiderski RE, Nishimura DY, Braun TA, Kim KYA, Huang J, Elbedour K, Carmi R, Slusarski DC, Casavant TL, Stone EM, Sheffield VC. Homozygosity mapping with SNP arrays identifies TRIM32, an E3 ubiquitin ligase, as a Bardet-Biedl syndrome gene (BBS11). Proc Natl Acad Sci U S A 2006; 103:6287-92. [PMID: 16606853 PMCID: PMC1458870 DOI: 10.1073/pnas.0600158103] [Citation(s) in RCA: 295] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The identification of mutations in genes that cause human diseases has largely been accomplished through the use of positional cloning, which relies on linkage mapping. In studies of rare diseases, the resolution of linkage mapping is limited by the number of available meioses and informative marker density. One recent advance is the development of high-density SNP microarrays for genotyping. The SNP arrays overcome low marker informativity by using a large number of markers to achieve greater coverage at finer resolution. We used SNP microarray genotyping for homozygosity mapping in a small consanguineous Israeli Bedouin family with autosomal recessive Bardet-Biedl syndrome (BBS; obesity, pigmentary retinopathy, polydactyly, hypogonadism, renal and cardiac abnormalities, and cognitive impairment) in which previous linkage studies using short tandem repeat polymorphisms failed to identify a disease locus. SNP genotyping revealed a homozygous candidate region. Mutation analysis in the region of homozygosity identified a conserved homozygous missense mutation in the TRIM32 gene, a gene coding for an E3 ubiquitin ligase. Functional analysis of this gene in zebrafish and expression correlation analyses among other BBS genes in an expression quantitative trait loci data set demonstrate that TRIM32 is a BBS gene. This study shows the value of high-density SNP genotyping for homozygosity mapping and the use of expression correlation data for evaluation of candidate genes and identifies the proteasome degradation pathway as a pathway involved in BBS.
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Affiliation(s)
- Annie P. Chiang
- Departments of *Electrical Engineering
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | - John S. Beck
- Pediatrics
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | - Hsan-Jan Yen
- Pediatrics
- Biological Sciences, and
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | - Marwan K. Tayeh
- Pediatrics
- Biological Sciences, and
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | | | | | | | | | - Kwang-Youn A. Kim
- **Biostatistics
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | | | - Khalil Elbedour
- Genetic Institute, Soroka Medical Center, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Rivka Carmi
- Genetic Institute, Soroka Medical Center, Ben Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | | | - Thomas L. Casavant
- Departments of *Electrical Engineering
- Ophthalmology
- Biomedical Engineering
| | - Edwin M. Stone
- Ophthalmology
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
| | - Val C. Sheffield
- Pediatrics
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242; and
- To whom correspondence should be addressed. E-mail:
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16
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Yen HJ, Tayeh MK, Mullins RF, Stone EM, Sheffield VC, Slusarski DC. Bardet-Biedl syndrome genes are important in retrograde intracellular trafficking and Kupffer's vesicle cilia function. Hum Mol Genet 2006; 15:667-77. [PMID: 16399798 DOI: 10.1093/hmg/ddi468] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.3] [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] [Indexed: 11/14/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is characterized by obesity, retinopathy, polydactyly, cognitive impairment, renal and cardiac anomalies as well as hypertension and diabetes. The nine known BBS genes do not appear to belong to the same functional category; yet mutation of these genes results in a nearly identical pleiotropic phenotype. Although the precise functions of the BBS proteins have yet to be determined, current data support a role in cilia function and intraflagellar transport. To gain insight into the biological processes controlled by BBS genes, we embarked on studies of six BBS orthologues from zebrafish. Knockdown of zebrafish bbs2, bbs4, bbs5, bbs6, bbs7 or bbs8 results in disruption of Kupffer's vesicle (KV), a ciliated organ thought to play a role in left-right patterning. KV defects are due to a progressive loss of cilia within the vesicle and result in subsequent alterations to organ laterality. We also note a specific defect altering retrograde melanosome transport. These studies are the first to comprehensively compare the diverse group of BBS genes in parallel and demonstrate a common role in intracellular trafficking, indicating that BBS proteins are involved in general organelle trafficking.
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Affiliation(s)
- Hsan-Jan Yen
- Howard Hughes Medical Institute, University of Iowa, Iowa City, IA 52242, USA
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17
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Al-Alami JR, Tanner SM, Tayeh MK, de la Chapelle A, El-Shanti H. Homozygous AMN mutation in hereditary selective intestinal malabsorption of vitamin B12 in Jordan. Saudi Med J 2005; 26:1061-4. [PMID: 16047053] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
OBJECTIVE Juvenile megaloblastic anemia is a rare and often hereditary disorder of cobalamin absorption, transport or intracellular metabolism. Several syndromes present with megaloblastic anemia such as congenital megaloblastic anemia due to intrinsic factor defect and juvenile megaloblastic anemia with proteinuria due to defects in the cubilin or the amnionless protein. METHODS We identified a large kindred with juvenile megaloblastic anemia. Four genes, GIF, CUBN, TCN1, and TCN2, was previously excluded from being responsible for the syndrome of this family who was discovered in Irbid, Jordan, during the year 1999. At that time, the amnionless (AMN) gene was not yet known to implicate in megaloblastic anemia. In this study, we screened the AMN for mutations in the Ohio State University, Iowa, United States of America. In addition, follow-up testing was carried out in the University of Iowa in 2004. RESULTS We identified a homozygous splice site mutation in the patients. This mutation was previously detected in families from Turkey and Tunisia. It is suspected to be a founder mutation of Middle Eastern origin. CONCLUSION Molecular testing for this specific mutation in cases of Middle Eastern origin is a valuable tool for presymptomatic diagnosis, carrier identification and perhaps prenatal diagnosis.
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Affiliation(s)
- Jamil R Al-Alami
- Department of Biochemistry and Medical Laboratory Science, Jordan University of Science and Technology, Irbid, Jordan
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18
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Fath MA, Mullins RF, Searby C, Nishimura DY, Wei J, Rahmouni K, Davis RE, Tayeh MK, Andrews M, Yang B, Sigmund CD, Stone EM, Sheffield VC. Mkks-null mice have a phenotype resembling Bardet-Biedl syndrome. Hum Mol Genet 2005; 14:1109-18. [PMID: 15772095 DOI: 10.1093/hmg/ddi123] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.1] [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] [Indexed: 01/18/2023] Open
Abstract
McKusick-Kaufman syndrome (MKS) is an autosomal recessive disorder characterized by post-axial polydactyly, congenital heart defects and hydrometrocolpos, a congenital structural abnormality of female genitalia. Mutations in the MKKS gene have also been shown to cause some cases of Bardet-Biedl syndrome (BBS) which is characterized by obesity, pigmentary retinopathy, polydactyly, renal abnormalities and hypogenitalism with secondary features of hypertension and diabetes. Although there is overlap in clinical features between MKS and BBS, MKS patients are not obese and do not develop retinopathy or have learning disabilities. To further explore the pathophysiology of BBS and the related disorder MKS, we have developed an Mkks(-/-) mouse model. This model shows that the absence of Mkks leads to retinal degeneration through apoptosis, failure of spermatozoa flagella formation, elevated blood pressure and obesity. The obesity is associated with hyperphagia and decreased activity. In addition, neurological screening reveals deficits in olfaction and social dominance. The mice do not have polydactyly or vaginal abnormalities. The phenotype of the Mkks(-/-) mice closely resembles the phenotype of other mouse models of BBS (Bbs2(-/-) and Bbs4(-/-)). These observations suggest that the complete absence of MKKS leads to BBS while the MKS phenotype is likely to be due to specific mutations.
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Affiliation(s)
- Melissa A Fath
- Department of Pediatrics, Division of Medcal Genetics, University of Iowa, Iowa City, IA 52242, USA
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19
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Al-Alami JR, Tayeh MK, Najib DA, Abu-Rubaiha ZA, Majeed HA, Al-Khateeb MS, El-Shanti HI. Familial Mediterranean fever mutation frequencies and carrier rates among a mixed Arabic population. Saudi Med J 2003; 24:1055-9. [PMID: 14578967] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
OBJECTIVE Familial Mediterranean Fever (FMF) is an autoinflammatory periodic disorder characterized by febrile and painful attacks due to inflammation involving the serosal membranes. The gene implicated in this disorder, MEFV, has been cloned and mutations in its coding regions have been identified. We aimed at identifying the frequency of MEFV mutations and carrier frequency in a mixed Arabic population. METHODS We identified 29 probands from 29 unrelated sibships segregating the disorder and representing the affected individual cohort. We screened 200 anonymous deoxyribonucleic acid (DNA) samples, representing a healthy adult cohort, for the mutations found to be common in the affected individual cohort. We also, screened anonymous DNA samples from 4 Arabic countries, namely, Egypt (231), Syria (225), Iraq (176) and the Kingdom of Saudi Arabia (107) thus enlarging our healthy adult cohort. The study was carried out between 1999 and 2002 at Jordan University of Science and Technology, Irbid and the University of Jordan, Amman, Jordan. RESULTS Out of the 58 alleles of the 29 probands, only 31 mutations were identified and M694V and V726A are the most common. The mutation E148Q was the most common among the healthy adult cohort, but was not present in affected individuals. The collective mutant allele frequency "q" was 0.101. The expected carrier rate was 18.1% (one in 5.5) while the observed carrier rate was 18.4% (one in 5.4). CONCLUSION E148Q has reduced penetrance and thus, a proportion of the individuals genetically affected with FMF remain asymptomatic. M694I and M680I are more prevalent in the affected individuals cohort, which points to their higher penetrance. The overall carrier rate is one in 5, but the selective heterozygote advantage could not be demonstrated in this study due to the relatively small sample size.
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Affiliation(s)
- Jamil R Al-Alami
- Department of Biochemistry, School of Medicine, Jordan University of Science and Technology, Irbid, Jordan
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Al-Alami JR, Tayeh MK, Al-Sheyyab MY, El-Shanti HI. Linkage analysis of a large inbred family with congenital megaloblastic anemia. Saudi Med J 2002; 23:1251-6. [PMID: 12436132] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
OBJECTIVE Megaloblastic anemia during infancy and early childhood often reflects a hereditary disorder of cobalamin's absorption, transport, or intracellular metabolism. There are 3 well defined autosomal recessive syndromes manifesting with megaloblastic anemia due to defects in cobalamin absorption or transport, namely congenital pernicious anemia, Imerslund-Grasbeck syndrome and Transcobalamin II deficiency. The genes responsible for the 3 disorders are gene intrinsic factor (GIF), MGA1 and TCN2, as well as the gene for Transcobalamin I, TCN1 are mapped or cloned, or both. METHODS We describe the clinical picture of 7 patients from 3 sibships, belong to one large inbred family who presented with megaloblastic anemia during infancy. The mode of inheritance follows an autosomal recessive pattern and the syndrome was completely reversed by parentral vitamin B12 therapy. The ascertainment of the family was carried out in 1998 in the Princess Rhama Children's Hospital, which is affiliated with Jordan University of Science and Technology, Jordan. We performed linkage analysis in this family for genes or regions involved in the above mentioned disorders. RESULTS The genes implicated in the etiology of the previously mentioned disorders were excluded from being responsible for the disorder in this family. CONCLUSION The exclusion of the involvement of GIF, MGA1, TCN1 and TCN2 in this family suggests that another gene and its product, involved in cobalamin absorption or transport, remains to be identified. A genome-wide search of the gene implicated in this family may give some insight on that gene, and its function.
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Affiliation(s)
- Jamil R Al-Alami
- Department of Biochemistry, Jordan University of Science and Technology, Irbid, Jordan
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