101
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Telegrafi A, Webb BD, Robbins SM, Speck-Martins CE, FitzPatrick D, Fleming L, Redett R, Dufke A, Houge G, van Harssel JJT, Verloes A, Robles A, Manoli I, Engle EC, Jabs EW, Valle D, Carey J, Hoover-Fong JE, Sobreira NLM. Identification of STAC3 variants in non-Native American families with overlapping features of Carey-Fineman-Ziter syndrome and Moebius syndrome. Am J Med Genet A 2017; 173:2763-2771. [PMID: 28777491 DOI: 10.1002/ajmg.a.38375] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/26/2017] [Accepted: 07/01/2017] [Indexed: 11/07/2022]
Abstract
Horstick et al. (2013) previously reported a homozygous p.Trp284Ser variant in STAC3 as the cause of Native American myopathy (NAM) in 5 Lumbee Native American families with congenital hypotonia and weakness, cleft palate, short stature, ptosis, kyphoscoliosis, talipes deformities, and susceptibility to malignant hyperthermia (MH). Here we present two non-Native American families, who were found to have STAC3 pathogenic variants. The first proband and her affected older sister are from a consanguineous Qatari family with a suspected clinical diagnosis of Carey-Fineman-Ziter syndrome (CFZS) based on features of hypotonia, myopathic facies with generalized weakness, ptosis, normal extraocular movements, cleft palate, growth delay, and kyphoscoliosis. We identified the homozygous c.851G>C;p.Trp284Ser variant in STAC3 in both sisters. The second proband and his affected sister are from a non-consanguineous, Puerto Rican family who was evaluated for a possible diagnosis of Moebius syndrome (MBS). His features included facial and generalized weakness, minimal limitation of horizontal gaze, cleft palate, and hypotonia, and he has a history of MH. The siblings were identified to be compound heterozygous for STAC3 variants c.851G>C;p.Trp284Ser and c.763_766delCTCT;p.Leu255IlefsX58. Given the phenotypic overlap of individuals with CFZS, MBS, and NAM, we screened STAC3 in 12 individuals diagnosed with CFZS and in 50 individuals diagnosed with MBS or a congenital facial weakness disorder. We did not identify any rare coding variants in STAC3. NAM should be considered in patients presenting with facial and generalized weakness, normal or mildly abnormal extraocular movement, hypotonia, cleft palate, and scoliosis, particularly if there is a history of MH.
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Affiliation(s)
| | - Bryn D Webb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sarah M Robbins
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - David FitzPatrick
- Human Genetics Unit, Medical and Developmental Genetics, University of Edinburgh Western General Hospital, Edinburgh, United Kingdom
| | - Leah Fleming
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Richard Redett
- Department of Plastic & Reconstructive Surgery, Johns Hopkins Hospital University School of Medicine, Baltimore, Maryland
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Jeske J T van Harssel
- Department of Clinical Genetics, University Medical Center, University of Utrecht, Utrecht, The Netherlands
| | - Alain Verloes
- Department of Genetics-Hospital Robert DEBRE, Paris, France
| | - Angela Robles
- Dr. Angela Robles Pediatrics Private Practice, San Sebastian, Puerto Rico
| | - Irini Manoli
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts.,Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts.,Howard Hughes Medical Institution, Chevy Chase, Maryland
| | | | - Ethylin W Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John Carey
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Julie E Hoover-Fong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Greenberg Center for Skeletal Dysplasias, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nara L M Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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De Novo Truncating Mutations in the Last and Penultimate Exons of PPM1D Cause an Intellectual Disability Syndrome. Am J Hum Genet 2017; 100:650-658. [PMID: 28343630 DOI: 10.1016/j.ajhg.2017.02.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/03/2017] [Indexed: 12/30/2022] Open
Abstract
Intellectual disability (ID) is a highly heterogeneous disorder involving at least 600 genes, yet a genetic diagnosis remains elusive in ∼35%-40% of individuals with moderate to severe ID. Recent meta-analyses statistically analyzing de novo mutations in >7,000 individuals with neurodevelopmental disorders highlighted mutations in PPM1D as a possible cause of ID. PPM1D is a type 2C phosphatase that functions as a negative regulator of cellular stress-response pathways by mediating a feedback loop of p38-p53 signaling, thereby contributing to growth inhibition and suppression of stress-induced apoptosis. We identified 14 individuals with mild to severe ID and/or developmental delay and de novo truncating PPM1D mutations. Additionally, deep phenotyping revealed overlapping behavioral problems (ASD, ADHD, and anxiety disorders), hypotonia, broad-based gait, facial dysmorphisms, and periods of fever and vomiting. PPM1D is expressed during fetal brain development and in the adult brain. All mutations were located in the last or penultimate exon, suggesting escape from nonsense-mediated mRNA decay. Both PPM1D expression analysis and cDNA sequencing in EBV LCLs of individuals support the presence of a stable truncated transcript, consistent with this hypothesis. Exposure of cells derived from individuals with PPM1D truncating mutations to ionizing radiation resulted in normal p53 activation, suggesting that p53 signaling is unaffected. However, a cell-growth disadvantage was observed, suggesting a possible effect on the stress-response pathway. Thus, we show that de novo truncating PPM1D mutations in the last and penultimate exons cause syndromic ID, which provides additional insight into the role of cell-cycle checkpoint genes in neurodevelopmental disorders.
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103
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Eldomery MK, Coban-Akdemir Z, Harel T, Rosenfeld JA, Gambin T, Stray-Pedersen A, Küry S, Mercier S, Lessel D, Denecke J, Wiszniewski W, Penney S, Liu P, Bi W, Lalani SR, Schaaf CP, Wangler MF, Bacino CA, Lewis RA, Potocki L, Graham BH, Belmont JW, Scaglia F, Orange JS, Jhangiani SN, Chiang T, Doddapaneni H, Hu J, Muzny DM, Xia F, Beaudet AL, Boerwinkle E, Eng CM, Plon SE, Sutton VR, Gibbs RA, Posey JE, Yang Y, Lupski JR. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med 2017; 9:26. [PMID: 28327206 PMCID: PMC5361813 DOI: 10.1186/s13073-017-0412-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/08/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. RESULTS Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). CONCLUSION An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.
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Affiliation(s)
- Mohammad K. Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Present Address: Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 350 W. 11th Street, Indianapolis, IN 46202 USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tamar Harel
- 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
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Women and Children’s Division, Oslo University Hospital, 0424 Oslo, Norway
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
- Atlantic Gene Therapies, UMR1089, Nantes, France
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard Alan Lewis
- 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
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Brett H. Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Jordan S. Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital Center for Human Immuno-Biology, Houston, TX USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX 7703 USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX 77030-3498 USA
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Osborn DPS, Pond HL, Mazaheri N, Dejardin J, Munn CJ, Mushref K, Cauley ES, Moroni I, Pasanisi MB, Sellars EA, Hill RS, Partlow JN, Willaert RK, Bharj J, Malamiri RA, Galehdari H, Shariati G, Maroofian R, Mora M, Swan LE, Voit T, Conti FJ, Jamshidi Y, Manzini MC. Mutations in INPP5K Cause a Form of Congenital Muscular Dystrophy Overlapping Marinesco-Sjögren Syndrome and Dystroglycanopathy. Am J Hum Genet 2017; 100:537-545. [PMID: 28190459 PMCID: PMC5339112 DOI: 10.1016/j.ajhg.2017.01.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/05/2017] [Indexed: 02/01/2023] Open
Abstract
Congenital muscular dystrophies display a wide phenotypic and genetic heterogeneity. The combination of clinical, biochemical, and molecular genetic findings must be considered to obtain the precise diagnosis and provide appropriate genetic counselling. Here we report five individuals from four families presenting with variable clinical features including muscular dystrophy with a reduction in dystroglycan glycosylation, short stature, intellectual disability, and cataracts, overlapping both the dystroglycanopathies and Marinesco-Sjögren syndrome. Whole-exome sequencing revealed homozygous missense and compound heterozygous mutations in INPP5K in the affected members of each family. INPP5K encodes the inositol polyphosphate-5-phosphatase K, also known as SKIP (skeletal muscle and kidney enriched inositol phosphatase), which is highly expressed in the brain and muscle. INPP5K localizes to both the endoplasmic reticulum and to actin ruffles in the cytoplasm. It has been shown to regulate myoblast differentiation and has also been implicated in protein processing through its interaction with the ER chaperone HSPA5/BiP. We show that morpholino-mediated inpp5k loss of function in the zebrafish results in shortened body axis, microphthalmia with disorganized lens, microcephaly, reduced touch-evoked motility, and highly disorganized myofibers. Altogether these data demonstrate that mutations in INPP5K cause a congenital muscular dystrophy syndrome with short stature, cataracts, and intellectual disability.
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Affiliation(s)
- Daniel P S Osborn
- Cardiovascular and Cell Sciences Institute, St George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Heather L Pond
- Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Science, Washington, DC 20037, USA
| | - Neda Mazaheri
- Department of Genetics, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran; Narges Medical Genetics and Prenatal Diagnosis Laboratory, East Mihan Ave., Kianpars, Ahvaz 6155689467, Iran
| | - Jeremy Dejardin
- Cardiovascular and Cell Sciences Institute, St George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Christopher J Munn
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Khaloob Mushref
- Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Science, Washington, DC 20037, USA
| | - Edmund S Cauley
- Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Science, Washington, DC 20037, USA
| | - Isabella Moroni
- Pediatric Neurology Unit, Fondazione IRCCS Istituto Neurologico C. Besta, 20133 Milan, Italy
| | - Maria Barbara Pasanisi
- Pediatric Neurology Unit, Fondazione IRCCS Istituto Neurologico C. Besta, 20133 Milan, Italy; Division of Neuromuscular Diseases and Neuroimmunology, Fondazione IRCCS Istituto Neurologico C. Besta, 20126 Milan, Italy
| | - Elizabeth A Sellars
- Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR 72202, USA
| | - R Sean Hill
- Program in Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jennifer N Partlow
- Program in Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Jaipreet Bharj
- Cardiovascular and Cell Sciences Institute, St George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Reza Azizi Malamiri
- Department of Paediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6163764648, Iran
| | - Hamid Galehdari
- Department of Genetics, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran; Narges Medical Genetics and Prenatal Diagnosis Laboratory, East Mihan Ave., Kianpars, Ahvaz 6155689467, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, East Mihan Ave., Kianpars, Ahvaz 6155689467, Iran; Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur, University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Reza Maroofian
- Cardiovascular and Cell Sciences Institute, St George's University of London, Cranmer Terrace, London SW17 0RE, UK; University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter EX1 2LU, UK
| | - Marina Mora
- Division of Neuromuscular Diseases and Neuroimmunology, Fondazione IRCCS Istituto Neurologico C. Besta, 20126 Milan, Italy
| | - Laura E Swan
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Thomas Voit
- NIHR GOSH Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Francesco J Conti
- NIHR GOSH Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Yalda Jamshidi
- Cardiovascular and Cell Sciences Institute, St George's University of London, Cranmer Terrace, London SW17 0RE, UK.
| | - M Chiara Manzini
- Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Science, Washington, DC 20037, USA.
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Whole-exome sequencing identifies novel variants in PNPT1 causing oxidative phosphorylation defects and severe multisystem disease. Eur J Hum Genet 2016; 25:79-84. [PMID: 27759031 DOI: 10.1038/ejhg.2016.128] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 08/10/2016] [Accepted: 08/23/2016] [Indexed: 11/08/2022] Open
Abstract
Recent advances in next-generation sequencing strategies have led to the discovery of many novel disease genes. We describe here a non-consanguineous family with two affected boys presenting with early onset of severe axonal neuropathy, optic atrophy, intellectual disability, auditory neuropathy and chronic respiratory and gut disturbances. Whole-exome sequencing (WES) was performed on all family members and we identified compound heterozygous variants (c.[760C>A];[1528G>C];p.[(Gln254Lys);(Ala510Pro)] in the polyribonucleotide nucleotidyltransferase 1 (PNPT1) gene in both affected individuals. PNPT1 encodes the polynucleotide phosphorylase (PNPase) protein, which is involved in the transport of small RNAs into the mitochondria. These RNAs are involved in the mitochondrial translation machinery, responsible for the synthesis of mitochondrially encoded subunits of the oxidative phosphorylation (OXPHOS) complexes. Both PNPT1 variants are within highly conserved regions and predicted to be damaging. These variants resulted in quaternary defects in the PNPase protein and a clear reduction in protein and mRNA expression of PNPT1 in patient fibroblasts compared with control cells. Protein analysis of the OXPHOS complexes showed a significant reduction in complex I (CI), complex III (CIII) and complex IV (CIV). Enzyme activity of CI and CIV was clearly reduced in patient fibroblasts compared with controls along with a 33% reduction in total mitochondrial protein synthesis. In vitro rescue experiments, using exogenous expression of wild-type PNPT1 in patient fibroblasts, ameliorated the deficiencies in the OXPHOS complex protein expression, supporting the likely pathogenicity of these variants and the importance of WES in efficiently identifying rare genetic disease genes.
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106
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Abou Tayoun AN, Krock B, Spinner NB. Sequencing-based diagnostics for pediatric genetic diseases: progress and potential. Expert Rev Mol Diagn 2016; 16:987-99. [PMID: 27388938 DOI: 10.1080/14737159.2016.1209411] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION The last two decades have witnessed revolutionary changes in clinical diagnostics, fueled by the Human Genome Project and advances in high throughput, Next Generation Sequencing (NGS). We review the current state of sequencing-based pediatric diagnostics, associated challenges, and future prospects. AREAS COVERED We present an overview of genetic disease in children, review the technical aspects of Next Generation Sequencing and the strategies to make molecular diagnoses for children with genetic disease. We discuss the challenges of genomic sequencing including incomplete current knowledge of variants, lack of data about certain genomic regions, mosaicism, and the presence of regions with high homology. Expert commentary: NGS has been a transformative technology and the gap between the research and clinical communities has never been so narrow. Therapeutic interventions are emerging based on genomic findings and the applications of NGS are progressing to prenatal genetics, epigenomics and transcriptomics.
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Affiliation(s)
- Ahmad N Abou Tayoun
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Bryan Krock
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Nancy B Spinner
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
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Moreno CA, Metze K, Lomazi EA, Bertola DR, Barbosa RHA, Cosentino V, Sobreira N, Cavalcanti DP. Visceral myopathy: Clinical and molecular survey of a cohort of seven new patients and state of the art of overlapping phenotypes. Am J Med Genet A 2016; 170:2965-2974. [PMID: 27481187 DOI: 10.1002/ajmg.a.37857] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 06/13/2016] [Indexed: 12/14/2022]
Abstract
Visceral motility dysfunction is a key feature of genetic disorders such as megacystis-microcolon-intestinal hypoperistalsis syndrome (MMIHS, MIM moved from 249210 to 155310), chronic intestinal pseudo-obstruction (CIPO, MIM609629), and multisystemic smooth muscle dysfunction syndrome (MSMDS, MIM613834). The genetic bases of these conditions recently begun to be clarified with the identification of pathogenic variants in ACTG2, ACTA2, and MYH11 in individuals with visceral motility dysfunction. The MMIHS was associated with the heterozygous variant in ACTG2 and homozygous variant in MYH11, while the heterozygous variant in ACTA2 was observed in patients with MSMDS. In this study, we describe the clinical data as well as the molecular investigation of seven individuals with visceral myopathy phenotypes. Five patients presented with MMIHS, including two siblings from consanguineous parents, one had CIPO, and the other had MSMDS. In three individuals with MMIHS and in one with CIPO we identified heterozygous variant in ACTG2, one being a novel variant (c.584C>T-p.Thr195Ile). In the individual with MSMDS we identified a heterozygous variant in ACTA2. We performed the whole-exome sequencing in one sibling with MMIHS and her parents; however, the pathogenic variant responsible for her phenotype could not be identified. These results reinforce the clinical and genetic heterogeneity of the visceral myopathies. Although many cases of MMIHS are associated with ACTG2 variants, we suggest that other genes, besides MYH11, could cause the MMIHS with autosomal recessive pattern. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Carolina Araujo Moreno
- Faculty of Medical Sciences, Departmentof Medical Genetics, State University of Campinas, Campinas, Brazil
| | - Konradin Metze
- Faculty of Medical Sciences, Department of Pathology, State University of Campinas, Campinas, Brazil
| | - Elizete Aparecida Lomazi
- Faculty of Medical Sciences, Department of Pediatrics, State University of Campinas, Campinas, Brazil
| | - Débora Romeo Bertola
- Genetic Unit, Faculty of Medicine, Children's Institute, University of São Paulo, São Paulo, Brazil
| | | | - Viviana Cosentino
- CEMIC (Center for Medical Education and Clinical Research), Buenos Aires, Argentina
| | - Nara Sobreira
- Department of Pediatrics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Denise Pontes Cavalcanti
- Faculty of Medical Sciences, Departmentof Medical Genetics, State University of Campinas, Campinas, Brazil.
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108
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Charng WL, Karaca E, Coban Akdemir Z, Gambin T, Atik MM, Gu S, Posey JE, Jhangiani SN, Muzny DM, Doddapaneni H, Hu J, Boerwinkle E, Gibbs RA, Rosenfeld JA, Cui H, Xia F, Manickam K, Yang Y, Faqeih EA, Al Asmari A, Saleh MAM, El-Hattab AW, Lupski JR. Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate. BMC Med Genomics 2016; 9:42. [PMID: 27435318 PMCID: PMC4950750 DOI: 10.1186/s12920-016-0208-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neurodevelopment is orchestrated by a wide range of genes, and the genetic causes of neurodevelopmental disorders are thus heterogeneous. We applied whole exome sequencing (WES) for molecular diagnosis and in silico analysis to identify novel disease gene candidates in a cohort from Saudi Arabia with primarily Mendelian neurologic diseases. METHODS We performed WES in 31 mostly consanguineous Arab families and analyzed both single nucleotide and copy number variants (CNVs) from WES data. Interaction/expression network and pathway analyses, as well as paralog studies were utilized to investigate potential pathogenicity and disease association of novel candidate genes. Additional cases for candidate genes were identified through the clinical WES database at Baylor Miraca Genetics Laboratories and GeneMatcher. RESULTS We found known pathogenic or novel variants in known disease genes with phenotypic expansion in 6 families, disease-associated CNVs in 2 families, and 12 novel disease gene candidates in 11 families, including KIF5B, GRM7, FOXP4, MLLT1, and KDM2B. Overall, a potential molecular diagnosis was provided by variants in known disease genes in 17 families (54.8 %) and by novel candidate disease genes in an additional 11 families, making the potential molecular diagnostic rate ~90 %. CONCLUSIONS Molecular diagnostic rate from WES is improved by exome-predicted CNVs. Novel candidate disease gene discovery is facilitated by paralog studies and through the use of informatics tools and available databases to identify additional evidence for pathogenicity. TRIAL REGISTRATION Not applicable.
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Affiliation(s)
- Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Mehmed M Atik
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Harsha Doddapaneni
- The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jianhong Hu
- The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Richard A Gibbs
- The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA.,Human Genome Sequencing Center, 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.,Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX, 77030, USA
| | - Hong Cui
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX, 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX, 77030, USA
| | - Kandamurugu Manickam
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Exome Laboratory, Baylor Miraca Genetics Laboratories, Houston, TX, 77030, USA
| | - Eissa A Faqeih
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Ali Al Asmari
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed A M Saleh
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,The Baylor-Hopkins Center for Mendelian Genomics, Houston, TX, 77030, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA.
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109
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Sobreira NL, Valle D. Lessons learned from the search for genes responsible for rare Mendelian disorders. Mol Genet Genomic Med 2016; 4:371-5. [PMID: 27468413 PMCID: PMC4947856 DOI: 10.1002/mgg3.233] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Nara L Sobreira
- McKusick-Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMaryland 21205; Department of PediatricsJohns Hopkins University School of MedicineBaltimoreMaryland 21205
| | - David Valle
- McKusick-Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMaryland 21205; Department of PediatricsJohns Hopkins University School of MedicineBaltimoreMaryland 21205
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110
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Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C, Brudno M. The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles. Hum Mutat 2016; 36:922-7. [PMID: 26255989 DOI: 10.1002/humu.22850] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/24/2015] [Indexed: 01/28/2023]
Abstract
Despite the increasing prevalence of clinical sequencing, the difficulty of identifying additional affected families is a key obstacle to solving many rare diseases. There may only be a handful of similar patients worldwide, and their data may be stored in diverse clinical and research databases. Computational methods are necessary to enable finding similar patients across the growing number of patient repositories and registries. We present the Matchmaker Exchange Application Programming Interface (MME API), a protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms. The initial version of the API has been successfully implemented by three members of the Matchmaker Exchange and was immediately able to reproduce previously identified matches and generate several new leads currently being validated. The API is available at https://github.com/ga4gh/mme-apis.
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Affiliation(s)
- Orion J Buske
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Lijia Huang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chris Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Michael Brudno
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
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111
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Warman Chardon J, Beaulieu C, Hartley T, Boycott KM, Dyment DA. Axons to Exons: the Molecular Diagnosis of Rare Neurological Diseases by Next-Generation Sequencing. Curr Neurol Neurosci Rep 2016; 15:64. [PMID: 26289954 DOI: 10.1007/s11910-015-0584-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Neurological disorders secondary to single gene mutations are an extremely heterogeneous group of diseases, individually rare, and often associated with progressive and severe disability. Given the degree of both clinical and genetic heterogeneity, next-generation sequencing (NGS) has become an important diagnostic tool. Multi-gene panel testing based on NGS is now prominently used, while whole-exome sequencing and whole-genome sequencing are emerging to facilitate the molecular diagnosis for many genetic neurological diseases. Although single-gene testing remains an important first tier test for disorders with clear phenotype-genotype correlation, NGS provides an expanding unbiased approach to identify rare mutations in genes known to be associated with genetically heterogeneous diseases, and those not initially considered by the clinician due to rarity or atypical clinical presentation. Given the decreasing costs and relatively rapid time to results, NGS-based assessment is quickly becoming a standard-of-care test for patients with genetic neurological diseases.
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Affiliation(s)
- Jodi Warman Chardon
- Division of Neurology, The Ottawa Hospital, 1053 Carling Avenue, Ottawa, ON, K1Y 4E9, Canada
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112
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A Syndromic Intellectual Disability Disorder Caused by Variants in TELO2, a Gene Encoding a Component of the TTT Complex. Am J Hum Genet 2016; 98:909-918. [PMID: 27132593 DOI: 10.1016/j.ajhg.2016.03.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/15/2016] [Indexed: 01/10/2023] Open
Abstract
The proteins encoded by TELO2, TTI1, and TTI2 interact to form the TTT complex, a co-chaperone for maturation of the phosphatidylinositol 3-kinase-related protein kinases (PIKKs). Here we report six affected individuals from four families with intellectual disability (ID) and neurological and other congenital abnormalities associated with compound heterozygous variants in TELO2. Although their fibroblasts showed reduced steady-state levels of TELO2 and the other components of the TTT complex, PIKK functions were normal in cellular assays. Our results suggest that these TELO2 missense variants result in loss of function, perturb TTT complex stability, and cause an autosomal-recessive syndromic form of ID.
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113
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Chacón-Camacho OF, Sobreira N, You J, Piña-Aguilar RE, Villegas-Ruiz V, Zenteno JC. Exome sequencing identifies a de novo frameshift mutation in the imprinted gene ZDBF2 in a sporadic patient with Nasopalpebral Lipoma-coloboma syndrome. Am J Med Genet A 2016; 170:1934-7. [PMID: 27139419 DOI: 10.1002/ajmg.a.37683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 04/06/2016] [Indexed: 11/07/2022]
Abstract
Nasopalpebral lipoma-coloboma syndrome (NPLCS, OMIM%167730) is an uncommon malformation entity with autosomal dominant inheritance characterized by the combination of nasopalpebral lipoma, colobomas in upper and lower eyelids, telecanthus, and maxillary hypoplasia. To date, no genetic defects have been associated with familial or sporadic NPLCS cases and the etiology of the disease remains unknown. In this work, the results of whole exome sequencing in a sporadic NPLCS patient are presented. Exome sequencing identified a de novo heterozygous frameshift dinucleotide insertion c.6245_6246 insTT (p.His2082fs*67) in ZDBF2 (zinc finger, DBF-type containing 2), a gene located at 2q33.3. This variant was absent in parental DNA, in a set of 300 ethnically matched controls, and in public exome variant databases. This is the first genetic variant identified in a NPLCS patient and evidence supporting the pathogenicity of the identified mutation is discussed. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Oscar F Chacón-Camacho
- Department of Genetics-Research Unit, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Nara Sobreira
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jing You
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Raul E Piña-Aguilar
- Division of Genomic Medicine, National Medical Center "20 de Noviembre", ISSSTE, Mexico City, Mexico
| | - Vanessa Villegas-Ruiz
- Department of Genetics-Research Unit, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Juan C Zenteno
- Department of Genetics-Research Unit, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
- Faculty of Medicine, Department of Biochemistry, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
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114
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Li R, Sobreira N, Witmer PD, Pratz KW, Braunstein EM. Two novel germline DDX41 mutations in a family with inherited myelodysplasia/acute myeloid leukemia. Haematologica 2016; 101:e228-31. [PMID: 26944477 DOI: 10.3324/haematol.2015.139790] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Ruijuan Li
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Hematology/Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, China
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - P Dane Witmer
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Keith W Pratz
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Evan M Braunstein
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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115
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Olgiati S, Quadri M, Bonifati V. Genetics of movement disorders in the next-generation sequencing era. Mov Disord 2016; 31:458-70. [DOI: 10.1002/mds.26521] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/29/2015] [Indexed: 12/15/2022] Open
Affiliation(s)
- Simone Olgiati
- Department of Clinical Genetics; Erasmus MC; Rotterdam The Netherlands
| | - Marialuisa Quadri
- Department of Clinical Genetics; Erasmus MC; Rotterdam The Netherlands
| | - Vincenzo Bonifati
- Department of Clinical Genetics; Erasmus MC; Rotterdam The Netherlands
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116
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Shaheen R, Patel N, Shamseldin H, Alzahrani F, Al-Yamany R, ALMoisheer A, Ewida N, Anazi S, Alnemer M, Elsheikh M, Alfaleh K, Alshammari M, Alhashem A, Alangari AA, Salih MA, Kircher M, Daza RM, Ibrahim N, Wakil SM, Alaqeel A, Altowaijri I, Shendure J, Al-Habib A, Faqieh E, Alkuraya FS. Accelerating matchmaking of novel dysmorphology syndromes through clinical and genomic characterization of a large cohort. Genet Med 2015; 18:686-95. [PMID: 26633546 DOI: 10.1038/gim.2015.147] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/03/2015] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Dysmorphology syndromes are among the most common referrals to clinical genetics specialists. Inability to match the dysmorphology pattern to a known syndrome can pose a major diagnostic challenge. With an aim to accelerate the establishment of new syndromes and their genetic etiology, we describe our experience with multiplex consanguineous families that appeared to represent novel autosomal recessive dysmorphology syndromes at the time of evaluation. METHODS Combined autozygome/exome analysis of multiplex consanguineous families with apparently novel dysmorphology syndromes. RESULTS Consistent with the apparent novelty of the phenotypes, our analysis revealed a strong candidate variant in genes that were novel at the time of the analysis in the majority of cases, and 10 of these genes are published here for the first time as novel candidates (CDK9, NEK9, ZNF668, TTC28, MBL2, CADPS, CACNA1H, HYAL2, CTU2, and C3ORF17). A significant minority of the phenotypes (6/31, 19%), however, were caused by genes known to cause Mendelian phenotypes, thus expanding the phenotypic spectrum of the diseases linked to these genes. The conspicuous inheritance pattern and the highly specific phenotypes appear to have contributed to the high yield (90%) of plausible molecular diagnoses in our study cohort. CONCLUSION Reporting detailed clinical and genomic analysis of a large series of apparently novel dysmorphology syndromes will likely lead to a trend to accelerate the establishment of novel syndromes and their underlying genes through open exchange of data for the benefit of patients, their families, health-care providers, and the research community.Genet Med 18 7, 686-695.
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Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ruah Al-Yamany
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Agaadir ALMoisheer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shamsa Anazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maha Alnemer
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Elsheikh
- Department of Obstetrics and Gynecology, Suliman AlHabib Hospital, Riyadh, Saudi Arabia
| | - Khaled Alfaleh
- Department of Obstetrics and Gynecology, Suliman AlHabib Hospital, Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Muneera Alshammari
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Abdullah A Alangari
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Salma M Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ahmed Alaqeel
- Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ikhlas Altowaijri
- Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Amro Al-Habib
- Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Eissa Faqieh
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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117
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Srour M, Hamdan F, McKnight D, Davis E, Mandel H, Schwartzentruber J, Martin B, Patry L, Nassif C, Dionne-Laporte A, Ospina L, Lemyre E, Massicotte C, Laframboise R, Maranda B, Labuda D, Décarie JC, Rypens F, Goldsher D, Fallet-Bianco C, Soucy JF, Laberge AM, Maftei C, Boycott K, Brais B, Boucher RM, Rouleau G, Katsanis N, Majewski J, Elpeleg O, Kukolich M, Shalev S, Michaud J, Michaud JL. Joubert Syndrome in French Canadians and Identification of Mutations in CEP104. Am J Hum Genet 2015; 97:744-53. [PMID: 26477546 DOI: 10.1016/j.ajhg.2015.09.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/22/2015] [Indexed: 10/22/2022] Open
Abstract
Joubert syndrome (JBTS) is a primarily autosomal-recessive disorder characterized by a distinctive mid-hindbrain and cerebellar malformation, oculomotor apraxia, irregular breathing, developmental delay, and ataxia. JBTS is a genetically heterogeneous ciliopathy. We sought to characterize the genetic landscape associated with JBTS in the French Canadian (FC) population. We studied 43 FC JBTS subjects from 35 families by combining targeted and exome sequencing. We identified pathogenic (n = 32 families) or possibly pathogenic (n = 2 families) variants in genes previously associated with JBTS in all of these subjects, except for one. In the latter case, we found a homozygous splice-site mutation (c.735+2T>C) in CEP104. Interestingly, we identified two additional non-FC JBTS subjects with mutations in CEP104; one of these subjects harbors a maternally inherited nonsense mutation (c.496C>T [p.Arg166*]) and a de novo splice-site mutation (c.2572-2A>G), whereas the other bears a homozygous frameshift mutation (c.1328_1329insT [p.Tyr444fs*3]) in CEP104. Previous studies have shown that CEP104 moves from the mother centriole to the tip of the primary cilium during ciliogenesis. Knockdown of CEP104 in retinal pigment epithelial (RPE1) cells resulted in severe defects in ciliogenesis. These observations suggest that CEP104 acts early during cilia formation by regulating the conversion of the mother centriole into the cilia basal body. We conclude that disruption of CEP104 causes JBTS. Our study also reveals that the cause of JBTS has been elucidated in the great majority of our FC subjects (33/35 [94%] families), even though JBTS shows substantial locus and allelic heterogeneity in this population.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jacques L Michaud
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, Université de Montréal, Montreal, QC H3T 1J4, Canada; Department of Neurosciences, Université de Montréal, Montreal, QC H3T 1J4, Canada.
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118
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Lawler M, Siu LL, Rehm HL, Chanock SJ, Alterovitz G, Burn J, Calvo F, Lacombe D, Teh BT, North KN, Sawyers CL. All the World's a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health. Cancer Discov 2015; 5:1133-6. [PMID: 26526696 DOI: 10.1158/2159-8290.cd-15-0821] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The recent explosion of genetic and clinical data generated from tumor genome analysis presents an unparalleled opportunity to enhance our understanding of cancer, but this opportunity is compromised by the reluctance of many in the scientific community to share datasets and the lack of interoperability between different data platforms. The Global Alliance for Genomics and Health is addressing these barriers and challenges through a cooperative framework that encourages "team science" and responsible data sharing, complemented by the development of a series of application program interfaces that link different data platforms, thus breaking down traditional silos and liberating the data to enable new discoveries and ultimately benefit patients.
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Affiliation(s)
- Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom.
| | | | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Washington, DC
| | | | - John Burn
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Fabien Calvo
- Cancer Core Europe and Institute Gustave Roussy Cancer Campus, Grand Paris, Villejuif, France
| | - Denis Lacombe
- European Organisation for the Research and Treatment of Cancer, Brussels, Belgium
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119
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Faden M, AlZahrani F, Mendoza-Londono R, Dupuis L, Hartley T, Kannu P, Raiman J, Howard A, Qin W, Tetreault M, Xi J, Al-Thamer I, Maas R, Boycott K, Alkuraya F, Alkuraya FS. Identification of a Recognizable Progressive Skeletal Dysplasia Caused by RSPRY1 Mutations. Am J Hum Genet 2015; 97:608-15. [PMID: 26365341 DOI: 10.1016/j.ajhg.2015.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/10/2015] [Indexed: 02/02/2023] Open
Abstract
Skeletal dysplasias are highly variable Mendelian phenotypes. Molecular diagnosis of skeletal dysplasias is complicated by their extreme clinical and genetic heterogeneity. We describe a clinically recognizable autosomal-recessive disorder in four affected siblings from a consanguineous Saudi family, comprising progressive spondyloepimetaphyseal dysplasia, short stature, facial dysmorphism, short fourth metatarsals, and intellectual disability. Combined autozygome/exome analysis identified a homozygous frameshift mutation in RSPRY1 with resulting nonsense-mediated decay. Using a gene-centric "matchmaking" system, we were able to identify a Peruvian simplex case subject whose phenotype is strikingly similar to the original Saudi family and whose exome sequencing had revealed a likely pathogenic homozygous missense variant in the same gene. RSPRY1 encodes a hypothetical RING and SPRY domain-containing protein of unknown physiological function. However, we detect strong RSPRY1 protein localization in murine embryonic osteoblasts and periosteal cells during primary endochondral ossification, consistent with a role in bone development. This study highlights the role of gene-centric matchmaking tools to establish causal links to genes, especially for rare or previously undescribed clinical entities.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Fowzan S Alkuraya
- Department of Genetics, King Faisal and Research Center, Riyadh 11211, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.
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120
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Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat 2015; 36:915-21. [PMID: 26295439 PMCID: PMC4610002 DOI: 10.1002/humu.22858] [Citation(s) in RCA: 351] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022]
Abstract
There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. Three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.
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Affiliation(s)
- Anthony A. Philippakis
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cardiology, Brigham & Women's Hospital,
Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Danielle R. Azzariti
- Laboratory for Molecular Medicine, Partners Personalized
Medicine, Boston, MA USA
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico, Barcelona,
Spain
| | | | - Catherine A. Brownstein
- Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and the Manton Center for
Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Genetics and Genome Biology Program, The Hospital for Sick
Children, Toronto, Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | - Han G. Brunner
- Radboud University Medical Center,Department of Human
Genetics, PO Box 9101, 6500HB Nijmegen, The Netherlands
- Maastricht University Medical Center, Department of Clinical
Genetics,PO Box 5800, 6202AZ Maastricht, The Netherlands
| | - Orion J. Buske
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Genetics and Genome Biology Program, The Hospital for Sick
Children, Toronto, Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | - Stephanie O.M. Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill
University, Canada
| | - Johan T. den Dunnen
- Human and Clinical Genetics, Leiden University Medical Center,
Leiden, Nederland
| | - Helen V. Firth
- East Anglian Medical Genetics Service, Box 134, Cambridge
University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ,
UK
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Tx 77030, U.S.A
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | - Melissa A. Haendel
- Department of Medical Informatics and Clinical Epidemiology,
Oregon Health & Science University, Portland, OR, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University, Baltimore, MD, USA
| | - Ingrid A. Holm
- Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and the Manton Center for
Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Lijia Huang
- The Children's Hospital of Eastern Ontario Research Institute,
Ottawa, ON, Canada
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Ben Hutton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Joel B. Krier
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA 02115, USA
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | - Justin Paschall
- European Molecular Biology Laboratory - European
Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD,
UK
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, 1156 High Street, Santa
Cruz, CA, USA
| | - Peter N. Robinson
- Institute for Medical Genetics and Human Genetics,
Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin,
Germany
- Institute for Bioinformatics, Department of Mathematics and
Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin Brandenburg Center for Regenerative Therapies, 13353
Berlin, Germany
| | | | - Nara L. Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University, Baltimore, MD, USA
| | - Ganesh J. Swaminathan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Peter E. Taschner
- Department of Medical Informatics and Clinical Epidemiology,
Oregon Health & Science University, Portland, OR, USA
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA 02115, USA
| | | | | | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics
and John P. Hussman Institute for Human Genomics, University of Miami Miller School of
Medicine, Miami, FL, USA
| | - Kym M. Boycott
- Department of Genetics, Children's Hospital of Eastern
Ontario, Ottawa, Ontario, Canada
| | - Heidi L. Rehm
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Laboratory for Molecular Medicine, Partners Personalized
Medicine, Boston, MA USA
- Department of Pathology, Brigham & Women's Hospital, Boston,
MA, USA
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121
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Ben-Salem S, Sobreira N, Akawi NA, Al-Shamsi AM, John A, Pramathan T, Valle D, Ali BR, Al-Gazali L. Gonadal mosaicism in ARID1B gene causes intellectual disability and dysmorphic features in three siblings. Am J Med Genet A 2015; 170A:156-61. [PMID: 26395437 PMCID: PMC5448135 DOI: 10.1002/ajmg.a.37405] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/03/2015] [Indexed: 02/05/2023]
Abstract
The gene encoding the AT-rich interaction domain-containing protein 1B (ARID1B) has recently been shown to be one of the most frequently mutated genes in patients with intellectual disability (ID). The phenotypic spectrums associated with variants in this gene vary widely ranging for mild to severe non-specific ID to Coffin-Siris syndrome. In this study, we evaluated three children from a consanguineous Emirati family affected with ID and dysmorphic features. Genomic DNA from all affected siblings was analyzed using CGH array and whole-exome sequencing (WES). Based on a recessive mode of inheritance, homozygous or compound heterozygous variants shared among all three affected children could not be identified. However, further analysis revealed a heterozygous variant (c.4318C>T; p.Q1440*) in the three affected children in an autosomal dominant ID causing gene, ARID1B. This variant was absent in peripheral blood samples obtained from both parents and unaffected siblings. Therefore, we propose that the most likely explanation for this situation is that one of the parents is a gonadal mosaic for the variant. To the best of our knowledge, this is the first report of a gonadal mosaicism inheritance of an ARID1B variant leading to familial ID recurrence.
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Affiliation(s)
- Salma Ben-Salem
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Nara Sobreira
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nadia A Akawi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Aisha M Al-Shamsi
- Department of Paediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Anne John
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Thachillath Pramathan
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - David Valle
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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122
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Sawyer SL, Hartley T, Dyment DA, Beaulieu CL, Schwartzentruber J, Smith A, Bedford HM, Bernard G, Bernier FP, Brais B, Bulman DE, Warman Chardon J, Chitayat D, Deladoëy J, Fernandez BA, Frosk P, Geraghty MT, Gerull B, Gibson W, Gow RM, Graham GE, Green JS, Heon E, Horvath G, Innes AM, Jabado N, Kim RH, Koenekoop RK, Khan A, Lehmann OJ, Mendoza-Londono R, Michaud JL, Nikkel SM, Penney LS, Polychronakos C, Richer J, Rouleau GA, Samuels ME, Siu VM, Suchowersky O, Tarnopolsky MA, Yoon G, Zahir FR, Majewski J, Boycott KM. Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care. Clin Genet 2015; 89:275-84. [PMID: 26283276 PMCID: PMC5053223 DOI: 10.1111/cge.12654] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/14/2015] [Accepted: 08/14/2015] [Indexed: 12/17/2022]
Abstract
An accurate diagnosis is an integral component of patient care for children with rare genetic disease. Recent advances in sequencing, in particular whole‐exome sequencing (WES), are identifying the genetic basis of disease for 25–40% of patients. The diagnostic rate is probably influenced by when in the diagnostic process WES is used. The Finding Of Rare Disease GEnes (FORGE) Canada project was a nation‐wide effort to identify mutations for childhood‐onset disorders using WES. Most children enrolled in the FORGE project were toward the end of the diagnostic odyssey. The two primary outcomes of FORGE were novel gene discovery and the identification of mutations in genes known to cause disease. In the latter instance, WES identified mutations in known disease genes for 105 of 362 families studied (29%), thereby informing the impact of WES in the setting of the diagnostic odyssey. Our analysis of this dataset showed that these known disease genes were not identified prior to WES enrollment for two key reasons: genetic heterogeneity associated with a clinical diagnosis and atypical presentation of known, clinically recognized diseases. What is becoming increasingly clear is that WES will be paradigm altering for patients and families with rare genetic diseases.
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Affiliation(s)
- S L Sawyer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - T Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - C L Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | - A Smith
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - H M Bedford
- Genetics Program, North York General Hospital, Toronto, Canada
| | - G Bernard
- Departments of Pediatrics, Neurology and Neurosurgery, Division of Pediatric Neurology, Montréal Children's Hospital, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - F P Bernier
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - B Brais
- Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | - D Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - J Deladoëy
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - B A Fernandez
- Disciplines of Genetics and Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - P Frosk
- Departments of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada
| | - M T Geraghty
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - B Gerull
- Cardiac Sciences and Medical Genetics, University of Calgary, Calgary, Canada
| | - W Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - R M Gow
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - G E Graham
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J S Green
- Disciplines of Genetics and Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - E Heon
- Department of Ophthalmology and Vision Sciences, Program of Genetics and Genomic Biology, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - G Horvath
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - A M Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - N Jabado
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - R H Kim
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada.,Department of Medicine, University of Toronto, Toronto, Canada
| | - R K Koenekoop
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Canada
| | - A Khan
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - O J Lehmann
- Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, Canada
| | - R Mendoza-Londono
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - J L Michaud
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - S M Nikkel
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - L S Penney
- Medical Genetics, IWK Health Centre, Halifax, Canada
| | - C Polychronakos
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - J Richer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - G A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - M E Samuels
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - V M Siu
- Division of Medical Genetics, Department of Pediatrics, University of Western Ontario, London, Canada
| | - O Suchowersky
- Departments of Medicine, Medical Genetics, and Pediatrics, University of Alberta, Edmonton, Canada
| | - M A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - G Yoon
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - F R Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | | | - J Majewski
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
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123
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Mutations in SPATA5 Are Associated with Microcephaly, Intellectual Disability, Seizures, and Hearing Loss. Am J Hum Genet 2015; 97:457-64. [PMID: 26299366 DOI: 10.1016/j.ajhg.2015.07.014] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/20/2015] [Indexed: 12/30/2022] Open
Abstract
Using whole-exome sequencing, we have identified in ten families 14 individuals with microcephaly, developmental delay, intellectual disability, hypotonia, spasticity, seizures, sensorineural hearing loss, cortical visual impairment, and rare autosomal-recessive predicted pathogenic variants in spermatogenesis-associated protein 5 (SPATA5). SPATA5 encodes a ubiquitously expressed member of the ATPase associated with diverse activities (AAA) protein family and is involved in mitochondrial morphogenesis during early spermatogenesis. It might also play a role in post-translational modification during cell differentiation in neuronal development. Mutations in SPATA5 might affect brain development and function, resulting in microcephaly, developmental delay, and intellectual disability.
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124
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Lambertson KF, Damiani SA, Might M, Shelton R, Terry SF. Participant-driven matchmaking in the genomic era. Hum Mutat 2015; 36:965-73. [PMID: 26252162 DOI: 10.1002/humu.22852] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/15/2015] [Indexed: 01/16/2023]
Abstract
Whole-genome and whole-exome sequencing are increasingly useful diagnostic tools for novel monogenic conditions. In order to confirm diagnoses made using these technologies, genomic matchmaking-the matching of cases with similar phenotypic and/or genotypic profiles, to narrow the number of candidate genes or ascertain a condition's etiology with greater certainty-is essential. Yet, due to current limitations on the size of matchmaking networks and data sets available to support them, identifying a match can be difficult. We argue that matchmaking efforts led by affected individuals and their families-participant-led efforts-offer a twofold solution to this need, in that participants both have the capacity to access larger networks and to provide more detailed sets of phenotypic and genotypic data. These features of participant-led efforts have the potential to increase the value of matchmaking networks, both in terms of number of matches and in terms of the overall energy of the network. We provide two examples of participant-led matchmaking, and propose a model for scaling these efforts.
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Affiliation(s)
| | - Stephen A Damiani
- Mission Massimo Foundation, Inc., Elsternwick, Victoria, Australia.,Mission Massimo Foundation, Inc., Westlake Village, California
| | - Matthew Might
- NGLY1.org, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah, United States
| | | | - Sharon F Terry
- Genetic Alliance, Washington, District of Columbia.,PXE International, Inc, Washington, District of Columbia
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125
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Loucks CM, Parboosingh JS, Shaheen R, Bernier FP, McLeod DR, Seidahmed MZ, Puffenberger EG, Ober C, Hegele RA, Boycott KM, Alkuraya FS, Innes AM. Matching two independent cohorts validates DPH1 as a gene responsible for autosomal recessive intellectual disability with short stature, craniofacial, and ectodermal anomalies. Hum Mutat 2015. [PMID: 26220823 DOI: 10.1002/humu.22843] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recently, Alazami et al. (2015) identified 33 putative candidate disease genes for neurogenetic disorders. One such gene was DPH1, in which a homozygous missense mutation was associated with a 3C syndrome-like phenotype in four patients from a single extended family. Here, we report a second homozygous missense variant in DPH1, seen in four members of a founder population, and associated with a phenotype initially reminiscent of Sensenbrenner syndrome. This postpublication "match" validates DPH1 as a gene underlying syndromic intellectual disability with short stature and craniofacial and ectodermal anomalies, reminiscent of, but distinct from, 3C and Sensenbrenner syndromes. This validation took several years after the independent discoveries due to the absence of effective methods for sharing both candidate phenotype and genotype data between investigators. Sharing of data via Web-based anonymous data exchange servers will play an increasingly important role toward more efficient identification of the molecular basis for rare Mendelian disorders.
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Affiliation(s)
- Catrina M Loucks
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jillian S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyhadh, 11211, Saudi Arabia
| | - Francois P Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
| | - D Ross McLeod
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | | | - Carole Ober
- Department of Human Genetics, and Department of Obstetrics and Gynecology, The University of Chicago, Chicago, Illinois
| | - Robert A Hegele
- Department of Paediatrics, University of Western Ontario, London, Ontario, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyhadh, 11211, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, 11442, Saudi Arabia
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
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126
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Sobreira N, Schiettecatte F, Valle D, Hamosh A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum Mutat 2015. [PMID: 26220891 DOI: 10.1002/humu.22844] [Citation(s) in RCA: 1049] [Impact Index Per Article: 116.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Here, we describe an overview and update on GeneMatcher (http://www.genematcher.org), a freely accessible Web-based tool developed as part of the Baylor-Hopkins Center for Mendelian Genomics. We created GeneMatcher with the goal of identifying additional individuals with rare phenotypes who had variants in the same candidate disease gene. We also wanted to facilitate connections to basic scientists working on orthologous genes in model systems with the goal of connecting their work to human Mendelian phenotypes. Meeting these goals will enhance the identification of novel Mendelian genes. Launched in September, 2013, GeneMatcher now has 2,178 candidate genes from 486 submitters spread across 38 countries entered in the database (June 1, 2015). GeneMatcher is also part of the Matchmaker Exchange (http://matchmakerexchange.org/) with an Application Programing Interface enabling submitters to query other databases of genetic variants and phenotypes without having to create accounts and data entries in multiple systems.
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Affiliation(s)
- Nara Sobreira
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - David Valle
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ada Hamosh
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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127
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Jurgens J, Sobreira N, Modaff P, Reiser CA, Seo SH, Seong MW, Park SS, Kim OH, Cho TJ, Pauli RM. Novel COL2A1 variant (c.619G>A, p.Gly207Arg) manifesting as a phenotype similar to progressive pseudorheumatoid dysplasia and spondyloepiphyseal dysplasia, Stanescu type. Hum Mutat 2015; 36:1004-8. [PMID: 26183434 DOI: 10.1002/humu.22839] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/02/2015] [Indexed: 01/09/2023]
Abstract
Progressive pseudorheumatoid dysplasia (PPRD) is a rare, autosomal-recessive condition characterized by mild spondyloepiphyseal dysplasia (SED) and severe, progressive, early-onset arthritis due to WISP3 mutations. SED, Stanescu type, is a vaguely delineated autosomal-dominant dysplasia of unknown genetic etiology. Here, we report three individuals from two unrelated families with radiological features similar to PPRD and SED, Stanescu type who share the same novel COL2A1 variant and were matched following discussion at an academic conference. In the first family, we performed whole-exome sequencing on three family members, two of whom have a PPRD-like phenotype, and identified a heterozygous variant (c.619G>A, p.Gly207Arg) in both affected individuals. Independently, targeted sequencing of the COL2A1 gene in an unrelated proband with a similar phenotype identified the same heterozygous variant. We suggest that the p.Gly207Arg variant causes a distinct type II collagenopathy with features of PPRD and SED, Stanescu type.
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Affiliation(s)
- Julie Jurgens
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205.,Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Peggy Modaff
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, 53705
| | - Catherine A Reiser
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, 53705
| | - Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 110-744, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 110-744, Republic of Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 110-744, Republic of Korea
| | - Ok Hwa Kim
- Department of Radiology, Woorisoa Children's Hospital, Seoul, 152-862, Republic of Korea
| | - Tae-Joon Cho
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, 110-744, Republic of Korea
| | - Richard M Pauli
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, 53705
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128
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Au PYB, You J, Caluseriu O, Schwartzentruber J, Majewski J, Bernier FP, Ferguson M, Valle D, Parboosingh JS, Sobreira N, Innes AM, Kline AD. GeneMatcher aids in the identification of a new malformation syndrome with intellectual disability, unique facial dysmorphisms, and skeletal and connective tissue abnormalities caused by de novo variants in HNRNPK. Hum Mutat 2015; 36:1009-1014. [PMID: 26173930 DOI: 10.1002/humu.22837] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/29/2015] [Indexed: 12/16/2022]
Abstract
We report a new syndrome due to loss-of-function variants in the heterogeneous nuclear ribonucleoprotein K gene (HNRNPK). We describe two probands: one with a de novo frameshift (NM_002140.3: c.953+1dup), and the other with a de novo splice donor site variant (NM_002140.3: c.257G>A). Both probands have intellectual disability, a shared unique craniofacial phenotype, and connective tissue and skeletal abnormalities. The identification of this syndrome was made possible by a new online tool, GeneMatcher, which facilitates connections between clinicians and researchers based on shared interest in candidate genes. This report demonstrates that new Web-based approaches can be effective in helping investigators solve exome sequencing projects, and also highlights the newer paradigm of "reverse phenotyping," where characterization of syndromic features follows the identification of genetic variants.
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Affiliation(s)
- P Y Billie Au
- Department of Medical Genetics, University of Calgary, Cumming School of Medicine, Alberta, Canada
| | - Jing You
- Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Jeremy Schwartzentruber
- Department of Human Genetics, McGill and Genome Quebec Innovation Center, McGill University, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill and Genome Quebec Innovation Center, McGill University, Quebec, Canada
| | - Francois P Bernier
- Department of Medical Genetics, University of Calgary, Cumming School of Medicine, Alberta, Canada.,Alberta Children's Hospital, Research Institute for Child and Maternal Health, University of Calgary, Alberta, Canada
| | - Marcia Ferguson
- Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD
| | | | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jillian S Parboosingh
- Department of Medical Genetics, University of Calgary, Cumming School of Medicine, Alberta, Canada.,Alberta Children's Hospital, Research Institute for Child and Maternal Health, University of Calgary, Alberta, Canada
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - A Micheil Innes
- Department of Medical Genetics, University of Calgary, Cumming School of Medicine, Alberta, Canada.,Alberta Children's Hospital, Research Institute for Child and Maternal Health, University of Calgary, Alberta, Canada
| | - Antonie D Kline
- Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD
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129
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Chong J, Buckingham K, Jhangiani S, Boehm C, Sobreira N, Smith J, Harrell T, McMillin M, Wiszniewski W, Gambin T, Coban Akdemir Z, Doheny K, Scott A, Avramopoulos D, Chakravarti A, Hoover-Fong J, Mathews D, Witmer P, Ling H, Hetrick K, Watkins L, Patterson K, Reinier F, Blue E, Muzny D, Kircher M, Bilguvar K, López-Giráldez F, Sutton V, Tabor H, Leal S, Gunel M, Mane S, Gibbs R, Boerwinkle E, Hamosh A, Shendure J, Lupski J, Lifton R, Valle D, Nickerson D, Bamshad M, Bamshad MJ. The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. Am J Hum Genet 2015; 97:199-215. [PMID: 26166479 DOI: 10.1016/j.ajhg.2015.06.009] [Citation(s) in RCA: 449] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 01/06/2023] Open
Abstract
Discovering the genetic basis of a Mendelian phenotype establishes a causal link between genotype and phenotype, making possible carrier and population screening and direct diagnosis. Such discoveries also contribute to our knowledge of gene function, gene regulation, development, and biological mechanisms that can be used for developing new therapeutics. As of February 2015, 2,937 genes underlying 4,163 Mendelian phenotypes have been discovered, but the genes underlying ∼50% (i.e., 3,152) of all known Mendelian phenotypes are still unknown, and many more Mendelian conditions have yet to be recognized. This is a formidable gap in biomedical knowledge. Accordingly, in December 2011, the NIH established the Centers for Mendelian Genomics (CMGs) to provide the collaborative framework and infrastructure necessary for undertaking large-scale whole-exome sequencing and discovery of the genetic variants responsible for Mendelian phenotypes. In partnership with 529 investigators from 261 institutions in 36 countries, the CMGs assessed 18,863 samples from 8,838 families representing 579 known and 470 novel Mendelian phenotypes as of January 2015. This collaborative effort has identified 956 genes, including 375 not previously associated with human health, that underlie a Mendelian phenotype. These results provide insight into study design and analytical strategies, identify novel mechanisms of disease, and reveal the extensive clinical variability of Mendelian phenotypes. Discovering the gene underlying every Mendelian phenotype will require tackling challenges such as worldwide ascertainment and phenotypic characterization of families affected by Mendelian conditions, improvement in sequencing and analytical techniques, and pervasive sharing of phenotypic and genomic data among researchers, clinicians, and families.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA.
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