1
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Shah YB, Lin P, Chen S, Zheng A, Alcaraz W, Towne MC, Gabriel C, Bhoj EJ, Lambert MP, Olson TS, Frank DM, Ellis CA, Babushok DV. Inherited bone marrow failure with macrothrombocytopenia due to germline tubulin beta class I (TUBB) variant. Br J Haematol 2023; 200:222-228. [PMID: 36207145 PMCID: PMC10989998 DOI: 10.1111/bjh.18491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/30/2022] [Accepted: 09/19/2022] [Indexed: 01/14/2023]
Abstract
Germline mutations in tubulin beta class I (TUBB), which encodes one of the β-tubulin isoforms, were previously associated with neurological and cutaneous abnormalities. Here, we describe the first case of inherited bone marrow (BM) failure, including marked thrombocytopenia, morphological abnormalities, and cortical dysplasia, associated with a de novo p.D249V variant in TUBB. Mutant TUBB had abnormal cellular localisation in transfected cells. Following interferon/ribavirin therapy administered for transfusion-acquired hepatitis C, severe pancytopenia and BM aplasia ensued, which was unresponsive to immunosuppression. Acquired chromosome arm 6p loss of heterozygosity was identified, leading to somatic loss of the mutant TUBB allele.
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Affiliation(s)
- Yash B. Shah
- Comprehensive Bone Marrow Failure Center, Children’s Hospital of Philadelphia, Philadelphia, PA, US
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ping Lin
- Comprehensive Bone Marrow Failure Center, Children’s Hospital of Philadelphia, Philadelphia, PA, US
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Stone Chen
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Alan Zheng
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Courtney Gabriel
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth J. Bhoj
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michele P. Lambert
- Division of Hematology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Timothy S. Olson
- Comprehensive Bone Marrow Failure Center, Children’s Hospital of Philadelphia, Philadelphia, PA, US
- Division of Oncology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dale M. Frank
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Colin A. Ellis
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Daria V. Babushok
- Comprehensive Bone Marrow Failure Center, Children’s Hospital of Philadelphia, Philadelphia, PA, US
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
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2
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Towne MC, Rossi M, Wayburn B, Huang JM, Radtke K, Alcaraz W, Farwell Hagman KD, Shinde DN. Diagnostic testing laboratories are valuable partners for disease gene discovery: 5-year experience with GeneMatcher. Hum Mutat 2022; 43:772-781. [PMID: 35143109 PMCID: PMC9313781 DOI: 10.1002/humu.24342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 12/01/2022]
Abstract
Although the rates of disease gene discovery have steadily increased with the expanding use of genome and exome sequencing by clinical and research laboratories, only ~16% of genes in the genome have confirmed disease associations. Here we describe our clinical laboratory's experience utilizing GeneMatcher, an online portal designed to promote disease gene discovery and data sharing. Since 2016, we submitted 246 candidates from 243 unique genes to GeneMatcher, of which 111 (45%) are now clinically characterized. Submissions meeting our candidate gene‐reporting criteria based on a scoring system using patient and molecular‐weighted evidence were significantly more likely to be characterized as of October 2021 versus genes that did not meet our clinical‐reporting criteria (p = 0.025). We reported relevant findings related to these newly characterized gene–disease associations in 477 probands. In 218 (46%) instances, we issued reclassifications after an initial negative or candidate gene (uncertain) report. We coauthored 104 publications delineating gene–disease relationships, including descriptions of new associations (60%), additional supportive evidence (13%), subsequent descriptive cohorts (23%), and phenotypic expansions (4%). Clinical laboratories are pivotal for disease gene discovery efforts and can screen phenotypes based on genotype matches, contact clinicians of relevant cases, and issue proactive reclassification reports.
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Affiliation(s)
| | - Mari Rossi
- Ambry Genetics, Enterprise, Aliso Viejo, CA, USA
| | - Bess Wayburn
- Ambry Genetics, Enterprise, Aliso Viejo, CA, USA
| | | | - Kelly Radtke
- Ambry Genetics, Enterprise, Aliso Viejo, CA, USA
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3
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Patak J, Gilfert J, Byler M, Neerukonda V, Thiffault I, Cross L, Amudhavalli S, Pacio-Miguez M, Palomares-Bralo M, Garcia-Minaur S, Santos-Simarro F, Powis Z, Alcaraz W, Tang S, Jurgens J, Barry B, England E, Engle E, Hess J, Lebel RR. MAGEL2-related disorders: A study and case series. Clin Genet 2019; 96:493-505. [PMID: 31397880 DOI: 10.1111/cge.13620] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022]
Abstract
Pathogenic MAGEL2 variants result in the phenotypes of Chitayat-Hall syndrome (CHS), Schaaf-Yang syndrome (SYS) and Prader-Willi syndrome (PWS). We present five patients with mutations in MAGEL2, including the first patient reported with a missense variant, adding to the limited literature. Further, we performed a systematic review of the CHS and SYS literature, assess the overlap between CHS, SYS and PWS, and analyze genotype-phenotype correlations among them. We conclude that there is neither a clinical nor etiological difference between CHS and SYS, and propose that the two syndromes simply be referred to as MAGEL2-related disorders.
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Affiliation(s)
- Jameson Patak
- Division of Development, Behavior and Genetics, SUNY Upstate Medical University, Syracuse, New York.,Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, New York.,MD Program, College of Medicine, SUNY Upstate Medical University, Syracuse, New York
| | - James Gilfert
- Division of Development, Behavior and Genetics, SUNY Upstate Medical University, Syracuse, New York
| | - Melissa Byler
- Division of Development, Behavior and Genetics, SUNY Upstate Medical University, Syracuse, New York
| | - Vamsee Neerukonda
- Division of Development, Behavior and Genetics, SUNY Upstate Medical University, Syracuse, New York
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri.,Department of Pathology & Genetics, Children's Mercy Hospitals, Kansas City, Missouri.,Kansas City School of Medicine, University of Missouri, Kansas City, Missouri
| | - Laura Cross
- Department of Pathology & Genetics, Children's Mercy Hospitals, Kansas City, Missouri.,Kansas City School of Medicine, University of Missouri, Kansas City, Missouri
| | - Shivarajan Amudhavalli
- Department of Pathology & Genetics, Children's Mercy Hospitals, Kansas City, Missouri.,Kansas City School of Medicine, University of Missouri, Kansas City, Missouri
| | - Marta Pacio-Miguez
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPaz, Madrid, Spain
| | - Maria Palomares-Bralo
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPaz, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos II (ISCIII), Madrid, Spain
| | - Sixto Garcia-Minaur
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPaz, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos II (ISCIII), Madrid, Spain
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPaz, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos II (ISCIII), Madrid, Spain
| | - Zoe Powis
- Ambry Genetics Corporation, Aliso Viejo, California
| | | | - Sha Tang
- Ambry Genetics Corporation, Aliso Viejo, California
| | - Julie Jurgens
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts.,FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Brenda Barry
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts.,FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Eleina England
- Center for Mendelian Genomics and Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Elizabeth Engle
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts.,FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland.,Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts.,Department of Neurology, Harvard Medical School, Boston, Massachusetts.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
| | - Jonathon Hess
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, New York
| | - Robert R Lebel
- Division of Development, Behavior and Genetics, SUNY Upstate Medical University, Syracuse, New York
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4
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Smith ED, Blanco K, Sajan SA, Hunter JM, Shinde DN, Wayburn B, Rossi M, Huang J, Stevens CA, Muss C, Alcaraz W, Hagman KDF, Tang S, Radtke K. A retrospective review of multiple findings in diagnostic exome sequencing: half are distinct and half are overlapping diagnoses. Genet Med 2019; 21:2199-2207. [PMID: 30894705 PMCID: PMC6774997 DOI: 10.1038/s41436-019-0477-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/25/2019] [Indexed: 12/31/2022] Open
Abstract
PURPOSE We evaluated clinical and genetic features enriched in patients with multiple Mendelian conditions to determine which patients are more likely to have multiple potentially relevant genetic findings (MPRF). METHODS Results of the first 7698 patients who underwent exome sequencing at Ambry Genetics were reviewed. Clinical and genetic features were examined and degree of phenotypic overlap between the genetic diagnoses was evaluated. RESULTS Among patients referred for exome sequencing, 2% had MPRF. MPRF were more common in patients from consanguineous families and patients with greater clinical complexity. The difference in average number of organ systems affected is small: 4.3 (multiple findings) vs. 3.9 (single finding) and may not be distinguished in clinic. CONCLUSION Patients with multiple genetic diagnoses had a slightly higher number of organ systems affected than patients with single genetic diagnoses, largely because the comorbid conditions affected overlapping organ systems. Exome testing may be beneficial for all cases with multiple organ systems affected. The identification of multiple relevant genetic findings in 2% of exome patients highlights the utility of a comprehensive molecular workup and updated interpretation of existing genomic data; a single definitive molecular diagnosis from analysis of a limited number of genes may not be the end of a diagnostic odyssey.
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Affiliation(s)
- Erica D Smith
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Samin A Sajan
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | - Bess Wayburn
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Mari Rossi
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | - Candace Muss
- Children's Hospital at Erlanger, Chattanooga, TN, USA
| | - Wendy Alcaraz
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Sha Tang
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Kelly Radtke
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA.
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5
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Noch E, Henchcliffe C, Hellmers N, Chu ML, Pappas J, Moran E, Alcaraz W, Sarva H. Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers. Mov Disord Clin Pract 2017; 5:92-95. [PMID: 30746398 DOI: 10.1002/mdc3.12567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 10/13/2017] [Accepted: 10/23/2017] [Indexed: 12/19/2022] Open
Affiliation(s)
- Evan Noch
- Department of Neurology Weill Cornell Medicine New York-Presbyterian Hospital New York New York USA
| | - Claire Henchcliffe
- Department of Neurology Weill Cornell Medicine New York-Presbyterian Hospital New York New York USA
| | - Natalie Hellmers
- Department of Neurology Weill Cornell Medicine New York-Presbyterian Hospital New York New York USA
| | - Mary Lynn Chu
- Department of Neurology New York University Langone Medical Center New York New York USA
| | - John Pappas
- Department of Pediatrics New York University Langone Medical Center New York New York USA
| | - Ellen Moran
- Center for Children New York University Hospital for Joint Diseases New York New York USA
| | | | - Harini Sarva
- Department of Neurology Weill Cornell Medicine New York-Presbyterian Hospital New York New York USA
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6
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Ma L, Bayram Y, McLaughlin HM, Cho MT, Krokosky A, Turner CE, Lindstrom K, Bupp CP, Mayberry K, Mu W, Bodurtha J, Weinstein V, Zadeh N, Alcaraz W, Powis Z, Shao Y, Scott DA, Lewis AM, White JJ, Jhangiani SN, Gulec EY, Lalani SR, Lupski JR, Retterer K, Schnur RE, Wentzensen IM, Bale S, Chung WK. De novo missense variants in PPP1CB are associated with intellectual disability and congenital heart disease. Hum Genet 2016; 135:1399-1409. [PMID: 27681385 DOI: 10.1007/s00439-016-1731-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022]
Abstract
Intellectual disabilities are genetically heterogeneous and can be associated with congenital anomalies. Using whole-exome sequencing (WES), we identified five different de novo missense variants in the protein phosphatase-1 catalytic subunit beta (PPP1CB) gene in eight unrelated individuals who share an overlapping phenotype of dysmorphic features, macrocephaly, developmental delay or intellectual disability (ID), congenital heart disease, short stature, and skeletal and connective tissue abnormalities. Protein phosphatase-1 (PP1) is a serine/threonine-specific protein phosphatase involved in the dephosphorylation of a variety of proteins. The PPP1CB gene encodes a PP1 subunit that regulates the level of protein phosphorylation. All five altered amino acids we observed are highly conserved among the PP1 subunit family, and all are predicted to disrupt PP1 subunit binding and impair dephosphorylation. Our data suggest that our heterozygous de novo PPP1CB pathogenic variants are associated with syndromic intellectual disability.
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Affiliation(s)
- Lijiang Ma
- Department of Pediatrics, Columbia University Medical Center, 1150 St. Nicholas Avenue, New York, NY, 10032, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Alyson Krokosky
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | | | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | | | | | - Weiyi Mu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Joann Bodurtha
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Veronique Weinstein
- Division of Genetics and Metabolism, Children's National Medical Center, Washington, DC, USA
| | | | | | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Yunru Shao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalani N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Elif Yilmaz Gulec
- Medical Genetics Section, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, 1150 St. Nicholas Avenue, New York, NY, 10032, USA.
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7
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Amos JS, Huang L, Thevenon J, Kariminedjad A, Beaulieu CL, Masurel-Paulet A, Najmabadi H, Fattahi Z, Beheshtian M, Tonekaboni SH, Tang S, Helbig KL, Alcaraz W, Rivière JB, Faivre L, Innes AM, Lebel RR, Boycott KM. Autosomal recessive mutations in THOC6 cause intellectual disability: syndrome delineation requiring forward and reverse phenotyping. Clin Genet 2016; 91:92-99. [PMID: 27102954 DOI: 10.1111/cge.12793] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 01/21/2023]
Abstract
THOC6 is a part of the THO complex, which is involved in coordinating mRNA processing with export. The THO complex interacts with additional components to form the larger TREX complex (transcription export complex). Previously, a homozygous missense mutation in THOC6 in the Hutterite population was reported in association with syndromic intellectual disability. Using exome sequencing, we identified three unrelated patients with bi-allelic mutations in THOC6 associated with intellectual disability and additional clinical features. Two of the patients were compound heterozygous for a stop and a missense mutation, and the third was homozygous for a missense mutation; the missense mutations were predicted to be pathogenic by in silico analysis and modeling. Clinical features of the three newly identified patients and those previously reported are reviewed; intellectual disability is moderate to severe, and malformations are variable including renal and heart defects, cleft palate, microcephaly, and corpus callosum dysgenesis. Facial features are variable and include tall forehead, short upslanting palpebral fissures +/- deep set eyes, and a long nose with overhanging columella. These subtle facial features render the diagnosis difficult to make in isolation with certainty. Our results expand the mutational and clinical spectrum of this rare disease, confirm that THOC6 is an intellectual disability causing gene, while providing insight into the importance of the THO complex in neurodevelopment.
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Affiliation(s)
- J S Amos
- Medical Genetics Section, SUNY Upstate Medical University, Syracuse, NY, USA
| | - L Huang
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - J Thevenon
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.,EA4271-Génétique des Anomalies du développement, Université de Bourgogne, Dijon, France
| | - A Kariminedjad
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - C L Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - A Masurel-Paulet
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.,EA4271-Génétique des Anomalies du développement, Université de Bourgogne, Dijon, France
| | - H Najmabadi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.,Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Z Fattahi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.,Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Beheshtian
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.,Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - S Tang
- Ambry Genetics Corporation, Aliso Viejo, CA, USA
| | - K L Helbig
- Ambry Genetics Corporation, Aliso Viejo, CA, USA
| | - W Alcaraz
- Ambry Genetics Corporation, Aliso Viejo, CA, USA
| | - J-B Rivière
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.,EA4271-Génétique des Anomalies du développement, Université de Bourgogne, Dijon, France
| | - L Faivre
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.,EA4271-Génétique des Anomalies du développement, Université de Bourgogne, Dijon, France
| | - A M Innes
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - R R Lebel
- Medical Genetics Section, SUNY Upstate Medical University, Syracuse, NY, USA
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
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8
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Butler S, Helbig KL, Alcaraz W, Seaver LH, Hsieh DT, Rohena L. Three cases of Troyer syndrome in two families of Filipino descent. Am J Med Genet A 2016; 170:1780-5. [DOI: 10.1002/ajmg.a.37658] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/25/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Shauna Butler
- Department of Pediatrics; San Antonio Military Medical Center; JBSA Ft Sam Houston Texas
| | | | - Wendy Alcaraz
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
| | - Laurie H. Seaver
- Department of Pediatrics; University of Hawai‘i John A. Burns School of Medicine and Kapi'olani Medical Specialists; Honolulu Hawaii
| | - David T. Hsieh
- Department of Pediatrics; San Antonio Military Medical Center; JBSA Ft Sam Houston Texas
| | - Luis Rohena
- Department of Pediatrics; San Antonio Military Medical Center; JBSA Ft Sam Houston Texas
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9
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Gund C, Powis Z, Alcaraz W, Desai S, Baranano K. Identification of a syndrome comprising microcephaly and intellectual disability but not white matter disease associated with a homozygous c.676C>T p.R226W DEAF1 mutation. Am J Med Genet A 2016; 170A:1330-2. [PMID: 26834045 DOI: 10.1002/ajmg.a.37580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 01/21/2016] [Indexed: 11/07/2022]
Abstract
We evaluated a 13-year-old East Pakistani male affected with microcephaly, apparent intellectual disability, hypotonia, and brisk reflexes without spasticity. His parents were first cousins. The patient also had a brother who was similarly affected and died at 10 years due to an accident. Previous SNP array testing showed a 1.63 Mb duplication at 16p13.11 of uncertain significance along with regions of homozygosity. Exome sequencing identified a known pathogenic homozygous alteration in DEAF1, c.676C>T (p.R226W), in this patient. The alteration had been reported in two individuals from a consanguineous Saudi Arabian family. Both individuals had microcephaly, intellectual disability, hypotonia, feeding difficulties, and poor growth. The patient reported here did not have evidence of white matter disease, as had been reported with prior patients. We conclude that this DEAF1 gene alteration caused this patient's symptoms and that white matter disease should not be considered a obligate feature of this syndrome.
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Affiliation(s)
| | - Zöe Powis
- Ambry Genetics, 15 Argonaut, Aliso Viejo, California
| | - Wendy Alcaraz
- Ambry Genetics, 15 Argonaut, Aliso Viejo, California
| | - Sonal Desai
- Kennedy Krieger Institute, Baltimore, Maryland
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10
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Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, Chiang T, Leduc M, Beuten J, Zhang J, He W, Scull J, Willis A, Landsverk M, Craigen WJ, Bekheirnia MR, Stray-Pedersen A, Liu P, Wen S, Alcaraz W, Cui H, Walkiewicz M, Reid J, Bainbridge M, Patel A, Boerwinkle E, Beaudet AL, Lupski JR, Plon SE, Gibbs RA, Eng CM. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA 2014; 312:1870-9. [PMID: 25326635 PMCID: PMC4326249 DOI: 10.1001/jama.2014.14601] [Citation(s) in RCA: 996] [Impact Index Per Article: 99.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders. OBJECTIVE To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome. DESIGN, SETTING, AND PATIENTS Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay. MAIN OUTCOMES AND MEASURES Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings. RESULTS A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics. CONCLUSIONS AND RELEVANCE Whole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients.
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Affiliation(s)
- Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Zhiyv Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Richard Person
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yan Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Patricia Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Min Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Alicia Hawes
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Magalie Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Joke Beuten
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Weimin He
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jennifer Scull
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Alecia Willis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Megan Landsverk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Mir Reza Bekheirnia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shu Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Wendy Alcaraz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Hong Cui
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jeffrey Reid
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Matthew Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas4Human Genetics Center, University of Texas Health Science Center, Houston
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas2Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Sharon E Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas2Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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