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Ahimaz P, Bergner AL, Florido ME, Harkavy N, Bhattacharyya S. Genetic counselors' utilization of ChatGPT in professional practice: A cross-sectional study. Am J Med Genet A 2024; 194:e63493. [PMID: 38066714 DOI: 10.1002/ajmg.a.63493] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 11/15/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 03/10/2024]
Abstract
PURPOSE The precision medicine era has seen increased utilization of artificial intelligence (AI) in the field of genetics. We sought to explore the ways that genetic counselors (GCs) currently use the publicly accessible AI tool Chat Generative Pre-trained Transformer (ChatGPT) in their work. METHODS GCs in North America were surveyed about how ChatGPT is used in different aspects of their work. Descriptive statistics were reported through frequencies and means. RESULTS Of 118 GCs who completed the survey, 33.8% (40) reported using ChatGPT in their work; 47.5% (19) use it in clinical practice, 35% (14) use it in education, and 32.5% (13) use it in research. Most GCs (62.7%; 74) felt that it saves time on administrative tasks but the majority (82.2%; 97) felt that a paramount challenge was the risk of obtaining incorrect information. The majority of GCs not using ChatGPT (58.9%; 46) felt it was not necessary for their work. CONCLUSION A considerable number of GCs in the field are using ChatGPT in different ways, but it is primarily helpful with tasks that involve writing. It has potential to streamline workflow issues encountered in clinical genetics, but practitioners need to be informed and uniformly trained about its limitations.
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Affiliation(s)
- Priyanka Ahimaz
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Amanda L Bergner
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Michelle E Florido
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Nina Harkavy
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Obstetrics and Gynecology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Sriya Bhattacharyya
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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Freiman A, Rekab A, Bergner AL, Pereira EM, Lin Y, Ahimaz P. Exploring the evolving roles of clinical geneticists and genetic counselors in the era of genomic medicine. Am J Med Genet A 2024; 194:e63502. [PMID: 38102777 DOI: 10.1002/ajmg.a.63502] [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: 11/06/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
The increased utilization of clinical genomic sequencing in the past decade has ushered in the era of genomic medicine, requiring genetics providers to acquire new skills and adapt their practices. The change in workplace responsibilities of clinical/medical geneticists (CMGs) and genetic counselors (GCs) in North America, due to the evolution of genetic testing, has not been studied. We surveyed CMGs (n = 80) and GCs (n = 127) with experience in general/pediatric genetics to describe their current practice of clinical tasks and the change in regularity of performing these tasks over the past 5-10 years. Currently, complementarity of responsibilities between CMGs and GCs clearly exists but providers who have been in the field for longer have noted role changes. Trends indicate that fewer experienced CMGs perform physical exams and select genetic tests than before and fewer experienced GCs complete requisitions and write result letters. The frequency of CMGs and GCs who investigate genetic test results, however, has increased. This study provides insight into the changing landscape of clinical genetics practice. Our findings suggest that the roles and responsibilities of CMGs and GCs have shifted in the past decade.
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Affiliation(s)
- Andrew Freiman
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA
| | - Aisha Rekab
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Pediatrics, Division of Clinical Genetics, Columbia University, New York, New York, USA
| | - Amanda L Bergner
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Elaine M Pereira
- Department of Pediatrics, Division of Clinical Genetics, Columbia University, Vagelos College of Physicians and Surgeons and New York Presbyterian, New York, New York, USA
| | - Yuhuan Lin
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Priyanka Ahimaz
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Pediatrics, Division of Clinical Genetics, Columbia University, New York, New York, USA
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3
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Cheung C, Berger SM, Ross M, Kramer T, Li Y, Andrews C, Dergham KR, Spitz E, Florido ME, Ahimaz P. Assessing management practices for variants of uncertain significance among genetic counselors in pediatrics. J Genet Couns 2024. [PMID: 38217320 DOI: 10.1002/jgc4.1860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/15/2024]
Abstract
Increased utilization of genomic sequencing in pediatric medicine has increased the detection of variants of uncertain significance (VUS). Periodic VUS reinterpretation can clarify clinical significance and increase diagnostic yield, highlighting the importance of systematic VUS tracking and reinterpretation. There are currently no standardized guidelines or established best practices for VUS management, and our understanding of how genetic counselors (GCs) track and manage VUS results for pediatric patients is limited. In this exploratory study, GCs in pediatric clinics in North America were surveyed about their VUS management practices. A total of 124 responses were included in the analysis. The majority (n = 115, 92.7%) of GCs reported that VUS management workflows were at the discretion of each individual provider in their workplace. Approximately half (n = 65, 52%) kept track of patient VUS results over time, and GCs with lower patient volumes were more likely to do so (p = 0.04). While 95% (n = 114) of GCs had requested VUS reinterpretation at least once, only 5% (n = 6) requested it routinely. Most (n = 80, 86%) GCs notified patients when a VUS was reclassified, although methods of recontact differed when the reclassification was an upgrade versus a downgrade. GCs who asked patients to stay in touch through periodic recontact or follow-up appointments were more likely to request VUS reinterpretation (p = 0.01). The most frequently reported barriers to requesting reinterpretation regularly were patients being lost to follow-up (n = 39, 33.1%), insufficient bandwidth (n = 27, 22.9%), and lack of standardized guidelines (n = 25, 21.2%). GCs had consistent overall practices around VUS management around investigation, disclosure, reinterpretation, and recontact, but specific methods used differed and were at the discretion of each provider. These results showcase the current landscape of VUS management workflows in pediatrics and the challenges associated with adopting more uniform practices. The study findings can help inform future strategies to develop standardized guidelines surrounding VUS management.
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Affiliation(s)
- Chloe Cheung
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Clinical Trials Office, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sara M Berger
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Meredith Ross
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Tamar Kramer
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Yuhuan Li
- Department of Biostatistics, Columbia University, New York, New York, USA
| | - Carli Andrews
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Katia R Dergham
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- School of Pharmacy and Health Sciences, Keck Graduate Insititute, Claremont, California, USA
| | - Elana Spitz
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Hematology Oncology, University of Carlifornia, Los Angeles Health, Los Angeles, California, USA
| | - Michelle E Florido
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Priyanka Ahimaz
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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Ahimaz P, Ross M, Foltz J, Sebastin M, Naik K, Kramer T, Bogyo K, Primiano M. Future Frontiers: Exploration of practices, challenges, and educational needs of genetic counselors in emerging subspecialties. J Genet Couns 2023; 32:1238-1248. [PMID: 37975258 DOI: 10.1002/jgc4.1812] [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: 11/30/2022] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 11/19/2023]
Abstract
The augmented use of genomic testing across different medical subspecialties has led to increased involvement of genetic counselors (GCs) in specialized areas of medicine. However, the lack of educational infrastructure required for changing scholastic needs of GCs entering new subspecialties lends to the burden of self-directed learning and inconsistent knowledge. We conducted a cross-sectional study surveying GCs with experience in the emerging genetic subspecialties of Immunology, Dermatology, Endocrinology, and Pulmonology (abbreviated as "IDEP") on current practices, clinical challenges, and educational strategies undertaken while working in these settings. We compared knowledge and confidence in skills related to IDEP patient care between GCs who do (experienced cohort) and do not (control cohort) practice in these settings to assess their comfort with working in subspecialties. Participants were recruited from the National Society of Genetic Counselors membership. A total of 304 GCs (178 experienced and 126 control) completed the survey. Most GCs in the experienced cohort saw IDEP patients by themselves (n = 104; 58.4%) or with a geneticist (n = 97; 54.4%) and almost all (n = 176; 99%) cited GeneReviews as a primary informational source for IDEP genetics but half (n = 91; 51.1%) agreed that a dedicated online course would be the best way to learn about a specific subspecialty. The experienced cohort scored higher on confidence in all skills (p < 0.001, z = 7.32) and knowledge (p < 0.001, z = 5.68) related to IDEP genetics than the control cohort. Previous exposure to IDEP through graduate school coursework and rotations positively correlated with better self-confidence in skills (p = 0.02, z = -2.19; p < 0.001, z = -5.25) and genetic knowledge (p = 0.03, z = -2.09; p < 0.001, z = -2.81) related to IDEP patient care. Years of experience working as a GC did not correlate with better confidence in skills (p = 0.53) or better IDEP genetic knowledge (p = 0.15). Our findings show that provision of opportunities for increased exposure to subspecialties could help maximize GCs' ability to work in emerging niche fields.
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Affiliation(s)
- Priyanka Ahimaz
- Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, USA
| | - Meredith Ross
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, New York, USA
| | - Jennah Foltz
- Genetic Counseling Graduate Program, Columbia University, New York, New York, USA
| | - Monisha Sebastin
- Division of Genetics Medicine, Department of Pediatrics, Montefiore Medical Center, New York, New York, USA
| | - Ketki Naik
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, New York, USA
| | - Tamar Kramer
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, New York, USA
| | - Kelsie Bogyo
- Interdepartmental Genetic Counseling Program, Department of Medicine, Columbia University, New York, New York, USA
| | - Michelle Primiano
- Division of Clinical Genetics, Department of Oncology, Weill Cornell Medical Center, New York, New York, USA
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Chen F, Ahimaz P, Wang K, Chung WK, Ta C, Weng C, Liu C. Phenotype-Driven Molecular Genetic Test Recommendation for Diagnosing Pediatric Rare Disorders. Res Sq 2023:rs.3.rs-3593490. [PMID: 38045411 PMCID: PMC10690317 DOI: 10.21203/rs.3.rs-3593490/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Rare disease patients often endure prolonged diagnostic odysseys and may still remain undiagnosed for years. Selecting the appropriate genetic tests is crucial to lead to timely diagnosis. Phenotypic features offer great potential for aiding genomic diagnosis in rare disease cases. We see great promise in effective integration of phenotypic information into genetic test selection workflow. In this study, we present a phenotype-driven molecular genetic test recommendation (Phen2Test) for pediatric rare disease diagnosis. Phen2Test was constructed using frequency matrix of phecodes and demographic data from the EHR before ordering genetic tests, with the objective to streamline the selection of molecular genetic tests (whole-exome / whole-genome sequencing, or gene panels) for clinicians with minimum genetic training expertise. We developed and evaluated binary classifiers based on 1,005 individuals referred to genetic counselors for potential genetic evaluation. In the evaluation using the gold standard cohort, the model achieved strong performance with an AUROC of 0.82 and an AUPRC of 0.92. Furthermore, we tested the model on another silver standard cohort (n=6,458), achieving an overall AUROC of 0.72 and an AUPRC of 0.671. Phen2Test was adjusted to align with current clinical guidelines, showing superior performance with more recent data, demonstrating its potential for use within a learning healthcare system as a genomic medicine intervention that adapts to guideline updates. This study showcases the practical utility of phenotypic features in recommending molecular genetic tests with performance comparable to clinical geneticists. Phen2Test could assist clinicians with limited genetic training and knowledge to order appropriate genetic tests.
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Affiliation(s)
- Fangyi Chen
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University, New York, NY, USA
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wendy K. Chung
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Casey Ta
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
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Ganapathi M, Matsuoka LS, March M, Li D, Brokamp E, Benito-Sanz S, White SM, Lachlan K, Ahimaz P, Sewda A, Bastarache L, Thomas-Wilson A, Stoler JM, Bramswig NC, Baptista J, Stals K, Demurger F, Cogne B, Isidor B, Bedeschi MF, Peron A, Amiel J, Zackai E, Schacht JP, Iglesias AD, Morton J, Schmetz A, Seidel V, Lucia S, Baskin SM, Thiffault I, Cogan JD, Gordon CT, Chung WK, Bowdin S, Bhoj E. Heterozygous rare variants in NR2F2 cause a recognizable multiple congenital anomaly syndrome with developmental delays. Eur J Hum Genet 2023; 31:1117-1124. [PMID: 37500725 PMCID: PMC10545729 DOI: 10.1038/s41431-023-01434-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023] Open
Abstract
Nuclear receptor subfamily 2 group F member 2 (NR2F2 or COUP-TF2) encodes a transcription factor which is expressed at high levels during mammalian development. Rare heterozygous Mendelian variants in NR2F2 were initially identified in individuals with congenital heart disease (CHD), then subsequently in cohorts of congenital diaphragmatic hernia (CDH) and 46,XX ovotesticular disorders/differences of sexual development (DSD); however, the phenotypic spectrum associated with pathogenic variants in NR2F2 remains poorly characterized. Currently, less than 40 individuals with heterozygous pathogenic variants in NR2F2 have been reported. Here, we review the clinical and molecular details of 17 previously unreported individuals with rare heterozygous NR2F2 variants, the majority of which were de novo. Clinical features were variable, including intrauterine growth restriction (IUGR), CHD, CDH, genital anomalies, DSD, developmental delays, hypotonia, feeding difficulties, failure to thrive, congenital and acquired microcephaly, dysmorphic facial features, renal failure, hearing loss, strabismus, asplenia, and vascular malformations, thus expanding the phenotypic spectrum associated with NR2F2 variants. The variants seen were predicted loss of function, including a nonsense variant inherited from a mildly affected mosaic mother, missense and a large deletion including the NR2F2 gene. Our study presents evidence for rare, heterozygous NR2F2 variants causing a highly variable syndrome of congenital anomalies, commonly associated with heart defects, developmental delays/intellectual disability, dysmorphic features, feeding difficulties, hypotonia, and genital anomalies. Based on the new and previous cases, we provide clinical recommendations for evaluating individuals diagnosed with an NR2F2-associated disorder.
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Affiliation(s)
- Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Michael March
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dong Li
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elly Brokamp
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara Benito-Sanz
- CIBERER, ISCIII. Institute of Medical and Molecular Genetics (INGEMM), Disorder of Sex Development Multidisciplinary Unit, Hospital Universitario La Paz, Madrid, Spain
| | - Susan M White
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Trust, Southampton, UK
- Department of Human Genetics and Genomic Medicine, Southampton University, Southampton, UK
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Anshuman Sewda
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amanda Thomas-Wilson
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Joan M Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Nuria C Bramswig
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Julia Baptista
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
- Peninsula Medical School, Faculty of Health, University of Plymouth, PL4 8AA, Plymouth, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | | | - Benjamin Cogne
- Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000, Nantes, France
| | - Bertrand Isidor
- Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000, Nantes, France
| | | | - Angela Peron
- Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, Università degli Studi di Milano, Milan, Italy
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Jeanne Amiel
- INSERM UMR1163, Institut Imagine, Université Paris-Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Elaine Zackai
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John P Schacht
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandro D Iglesias
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Ariane Schmetz
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Verónica Seidel
- Clinical Genetics, Department of Pediatrics, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Stephanie Lucia
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephanie M Baskin
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA
| | - Joy D Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarah Bowdin
- Department of Clinical Genetics, Addenbrooke's Hospital, Cambridge University Hospitals NHS, Foundation Trust, Cambridge, UK
| | - Elizabeth Bhoj
- Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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Ahimaz P, Foltz JC, Ross MJ, Florido ME, Sebastin M, Yu JE. Exploring the role of genetic counselors in immunology: A study of immunologist and allergist perspectives. J Allergy Clin Immunol Pract 2023; 11:1939-1942.e2. [PMID: 36787825 DOI: 10.1016/j.jaip.2023.01.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 02/16/2023]
Affiliation(s)
- Priyanka Ahimaz
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY; Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, NY.
| | - Jennah C Foltz
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Meredith J Ross
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Michelle E Florido
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY; Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Monisha Sebastin
- Division of Clinical Genetics, Department of Pediatrics, Montefiore Medical Center, New York, NY
| | - Joyce E Yu
- Division of Allergy, Immunology & Rheumatology, Department of Pediatrics, Columbia University, New York, NY
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8
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van Jaarsveld RH, Reilly J, Cornips MC, Hadders MA, Agolini E, Ahimaz P, Anyane-Yeboa K, Bellanger SA, van Binsbergen E, van den Boogaard MJ, Brischoux-Boucher E, Caylor RC, Ciolfi A, van Essen TAJ, Fontana P, Hopman S, Iascone M, Javier MM, Kamsteeg EJ, Kerkhof J, Kido J, Kim HG, Kleefstra T, Lonardo F, Lai A, Lev D, Levy MA, Lewis MES, Lichty A, Mannens MMAM, Matsumoto N, Maya I, McConkey H, Megarbane A, Michaud V, Miele E, Niceta M, Novelli A, Onesimo R, Pfundt R, Popp B, Prijoles E, Relator R, Redon S, Rots D, Rouault K, Saida K, Schieving J, Tartaglia M, Tenconi R, Uguen K, Verbeek N, Walsh CA, Yosovich K, Yuskaitis CJ, Zampino G, Sadikovic B, Alders M, Oegema R. Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature. Genet Med 2023; 25:49-62. [PMID: 36322151 PMCID: PMC9825659 DOI: 10.1016/j.gim.2022.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022] Open
Abstract
PURPOSE Pathogenic variants in genes involved in the epigenetic machinery are an emerging cause of neurodevelopment disorders (NDDs). Lysine-demethylase 2B (KDM2B) encodes an epigenetic regulator and mouse models suggest an important role during development. We set out to determine whether KDM2B variants are associated with NDD. METHODS Through international collaborations, we collected data on individuals with heterozygous KDM2B variants. We applied methylation arrays on peripheral blood DNA samples to determine a KDM2B associated epigenetic signature. RESULTS We recruited a total of 27 individuals with heterozygous variants in KDM2B. We present evidence, including a shared epigenetic signature, to support a pathogenic classification of 15 KDM2B variants and identify the CxxC domain as a mutational hotspot. Both loss-of-function and CxxC-domain missense variants present with a specific subepisignature. Moreover, the KDM2B episignature was identified in the context of a dual molecular diagnosis in multiple individuals. Our efforts resulted in a cohort of 21 individuals with heterozygous (likely) pathogenic variants. Individuals in this cohort present with developmental delay and/or intellectual disability; autism; attention deficit disorder/attention deficit hyperactivity disorder; congenital organ anomalies mainly of the heart, eyes, and urogenital system; and subtle facial dysmorphism. CONCLUSION Pathogenic heterozygous variants in KDM2B are associated with NDD and a specific epigenetic signature detectable in peripheral blood.
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Affiliation(s)
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Marie-Claire Cornips
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Michael A Hadders
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00165 Rome, Italy
| | - Priyanka Ahimaz
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Severine Audebert Bellanger
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Ton A J van Essen
- Department of Medical Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Paolo Fontana
- Medical Genetics Unit, A.O.R.N. San Pio, Benevento, Italy
| | - Saskia Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maria Iascone
- Laboratorio di Genetica Medica - ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Margaret M Javier
- Department of Medical Genetics, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Jun Kido
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Abbe Lai
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program and Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dorit Lev
- The Rina Mor Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach-Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Andre Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon; Institut Jérôme Lejeune, Paris, France
| | - Vincent Michaud
- Department of Medical Genetics, CHU Bordeaux, Bordeaux, France
| | - Evelina Miele
- Department of Pediatric Hematology and Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00165 Rome, Italy
| | - Roberta Onesimo
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany; Center of Functional Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Sylvia Redon
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France; Université de Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Dmitrijs Rots
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Karen Rouault
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France; Université de Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Jolanda Schieving
- Department of Pediatric Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Romano Tenconi
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, Padova, Italy
| | - Kevin Uguen
- Service de Génétique Médicale et de Biologie de la Reproduction, Centre Hospitalier Regional Universitaire Brest, Brest, France
| | - Nienke Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA
| | - Keren Yosovich
- Molecular Genetic Laboratory, Edith Wolfson Medical Center, Holon, Israel
| | - Christopher J Yuskaitis
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Giuseppe Zampino
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Faculty of Medicine and Surgery, Catholic University of Sacred Heart, Rome, Italy
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada.
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.
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9
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Ganapathi M, Buchovecky CM, Cristo F, Ahimaz P, Ruzal-Shapiro C, Wou K, Inácio JM, Iglesias A, Belo JA, Jobanputra V. A novel biallelic loss-of-function variant in DAND5 causes heterotaxy syndrome. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006248. [PMID: 36316122 PMCID: PMC9808554 DOI: 10.1101/mcs.a006248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022] Open
Abstract
The majority of heterotaxy cases do not obtain a molecular diagnosis, although pathogenic variants in more than 50 genes are known to cause heterotaxy. A heterozygous missense variant in DAND5, a nodal inhibitor, which functions in early development for establishment of right-left patterning, has been implicated in heterotaxy. Recently, the first case was reported of a DAND5 biallelic loss-of-function (LoF) variant in an individual with heterotaxy. Here, we describe a second unrelated individual with heterotaxy syndrome and a homozygous frameshift variant in DAND5 (NM_152654.2:c.197del [p.Leu66ArgfsTer22]). Using an in vitro assay, we demonstrate that the DAND5 c.197del variant is unable to inhibit nodal signaling when compared with the wild-type expression construct. This work strengthens the genetic and functional evidence for biallelic LoF variants in DAND5 causing an autosomal recessive heterotaxy syndrome.
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Affiliation(s)
- Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Christie M Buchovecky
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Fernando Cristo
- Stem Cells and Development Laboratory, iNOVA4Health, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1099-085 Lisboa, Portugal
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Carrie Ruzal-Shapiro
- Department of Radiology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Karen Wou
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - José M Inácio
- Stem Cells and Development Laboratory, iNOVA4Health, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1099-085 Lisboa, Portugal
| | - Alejandro Iglesias
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - José A Belo
- Stem Cells and Development Laboratory, iNOVA4Health, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1099-085 Lisboa, Portugal
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, USA
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10
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Ahimaz P, Kramer T, Swaroop P, Mitchell M, Hernan R, Anyane-Yeboa K, Pereira EM. Assessment of the beliefs, needs, and expectations for genetic counseling of patients with hypermobile Ehlers-Danlos syndrome. Am J Med Genet A 2022; 188:3172-3183. [PMID: 36209348 DOI: 10.1002/ajmg.a.62945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/16/2022] [Accepted: 06/19/2022] [Indexed: 01/31/2023]
Abstract
Ehlers-Danlos syndrome, hypermobility type (hEDS) is a heritable connective tissue disorder that currently does not have a known molecular etiology. Previous studies have explored the complex symptomology, clinical diagnosis, and psychological aspects of hEDS. Genetics providers currently aid in the diagnosis and management guidance of patients with hEDS, but there is limited data describing the needs and expectations of individuals with hEDS from a clinical genetics appointment. Our study sought to explore these items through the use of an online survey to assess participants' beliefs, needs and expectations (BNE) for genetic counseling as well as questions about demographics, hEDS symptoms, and current medical care. A total of 460 respondents with hEDS completed the survey. Most participants felt joint pain/weakness (n = 392; 88%) was one of the most disruptive symptoms of hEDS and 63% (n = 289) reported having psychiatric conditions. BNE scores were highest in two domains: expectations to have psychosocial concerns addressed during a genetic counseling appointment (mean score = 4.4/5; SD = 0.56) and desire for positive feelings after a genetic counseling session (mean score = 4.3/5; SD = 0.59). Participants who previously had genetic counseling felt less unsure about their diagnosis (p = 0.02) and had lower need for information about hEDS (p < 0.001). Majority of participants did not feel that their doctors were knowledgeable about hEDS (n = 269; 58%) and strongly supported a multidisciplinary approach to their care (n = 445; 97%). This research provides a framework for genetics providers and other healthcare professionals to assess the needs and expectations of patients with hEDS and consider re-structuring their appointment formats to service this population.
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Affiliation(s)
- Priyanka Ahimaz
- Department of Pediatrics, Division of Molecular Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Tamar Kramer
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Pooja Swaroop
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - McKenzie Mitchell
- Medical Genetics Clinic, University of Alberta Hospital, Edmonton, Alberta, Canada
| | - Rebecca Hernan
- Department of Pediatrics, Division of Molecular Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Vagelos College of Physicians and Surgeons and NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York, USA
| | - Elaine M Pereira
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Vagelos College of Physicians and Surgeons and NewYork-Presbyterian Morgan Stanley Children's Hospital, New York, New York, USA
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11
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Zhong G, Ahimaz P, Edwards NA, Hagen JJ, Faure C, Lu Q, Kingma P, Middlesworth W, Khlevner J, El Fiky M, Schindel D, Fialkowski E, Kashyap A, Forlenza S, Kenny AP, Zorn AM, Shen Y, Chung WK. Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. HGG Adv 2022; 3:100107. [PMID: 35519826 PMCID: PMC9065433 DOI: 10.1016/j.xhgg.2022.100107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 04/06/2022] [Indexed: 11/15/2022] Open
Abstract
Esophageal atresias/tracheoesophageal fistulas (EA/TEF) are rare congenital anomalies caused by aberrant development of the foregut. Previous studies indicate that rare or de novo genetic variants significantly contribute to EA/TEF risk, and most individuals with EA/TEF do not have pathogenic genetic variants in established risk genes. To identify the genetic contributions to EA/TEF, we performed whole genome sequencing of 185 trios (probands and parents) with EA/TEF, including 59 isolated and 126 complex cases with additional congenital anomalies and/or neurodevelopmental disorders. There was a significant burden of protein-altering de novo coding variants in complex cases (p = 3.3 × 10-4), especially in genes that are intolerant of loss-of-function variants in the population. We performed simulation analysis of pathway enrichment based on background mutation rate and identified a number of pathways related to endocytosis and intracellular trafficking that as a group have a significant burden of protein-altering de novo variants. We assessed 18 variants for disease causality using CRISPR-Cas9 mutagenesis in Xenopus and confirmed 13 with tracheoesophageal phenotypes. Our results implicate disruption of endosome-mediated epithelial remodeling as a potential mechanism of foregut developmental defects. Our results suggest significant genetic heterogeneity of EA/TEF and may have implications for the mechanisms of other rare congenital anomalies.
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Affiliation(s)
- Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicole A. Edwards
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Jacob J. Hagen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Christophe Faure
- Division of Pediatric Gastroenterology, CHU Sainte-Justine, Montreal, QC, Canada
| | - Qiao Lu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul Kingma
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William Middlesworth
- Division of Pediatric Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Julie Khlevner
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Columbia University Irving Medical Center, New York, NY, USA
| | - Mahmoud El Fiky
- Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - David Schindel
- Division of Pediatric Surgery, UT Southwestern School of Medicine Dallas, Texas, USA
| | - Elizabeth Fialkowski
- Division of Pediatric Surgery, Oregon Health and Science University, Portland, OR, USA
| | - Adhish Kashyap
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Sophia Forlenza
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Alan P. Kenny
- Division of Neonatology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Aaron M. Zorn
- Center for Stem Cell & Organoid Medicine (CuSTOM), Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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12
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Zhong G, Ahimaz P, Edwards NA, Hagen JJ, Faure C, Lu Q, Kingma P, Middlesworth W, Khlevner J, El Fiky M, Schindel D, Fialkowski E, Kashyap A, Forlenza S, Kenny AP, Zorn AM, Shen Y, Chung WK. Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. Human Genetics and Genomics Advances 2022; 3:100126. [DOI: 10.1016/j.xhgg.2022.100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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13
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Edwards N, Zhong G, Ahimaz P, Kenny A, Kingma P, Wells J, Shen Y, Chung W, Zorn A. Discovering the Developmental Basis of Trachea‐Esophageal Birth Defects: Evidence for Endosome‐opathies. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.0r569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicole Edwards
- Cincinnati Children's Hospital Medical CenterCincinnatiOH
| | | | | | - Alan Kenny
- Cincinnati Children's Hospital Medical CenterCincinnatiOH
| | - Paul Kingma
- Cincinnati Children's Hospital Medical CenterCincinnatiOH
| | - James Wells
- Cincinnati Children's Hospital Medical CenterCincinnatiOH
| | - Yufeng Shen
- Columbia University Medical CenterNew YorkNY
| | - Wendy Chung
- Columbia University Medical CenterNew YorkNY
| | - Aaron Zorn
- Cincinnati Children's Hospital Medical CenterCincinnatiOH
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14
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Guimier A, Achleitner MT, Moreau de Bellaing A, Edwards M, de Pontual L, Mittal K, Dunn KE, Grove ME, Tysoe CJ, Dimartino C, Cameron J, Kanthi A, Shukla A, van den Broek F, Chatterjee D, Alston CL, Knowles CV, Brett L, Till JA, Homfray T, French P, Spentzou G, Elserafy NA, Lichkus KS, Sankaran BP, Kennedy HL, George PM, Kidd A, Wortmann SB, Fisk DG, Koopmann TT, Rafiq MA, Merker JD, Parikh S, Ahimaz P, Weintraub RG, Ma AS, Turner C, Ellaway CJ, Phillips LK, Thorburn DR, Chung WK, Kana SL, Faye-Petersen OM, Thompson ML, Janin A, McLeod K, McGowan R, McFarland R, Girisha KM, Morris-Rosendahl DJ, Hurst ACE, Turner CLS, Hamilton RM, Taylor RW, Bajolle F, Gordon CT, Amiel J, Mayr JA, Doudney K. PPA2-associated sudden cardiac death: extending the clinical and allelic spectrum in 20 new families. Genet Med 2022; 24:967. [PMID: 35394429 DOI: 10.1016/j.gim.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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15
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Ahimaz P, Sabatello M, Qian M, Wang A, Miller EM, Parrott A, Lal AK, Chatfield KC, Rossano JW, Ware SM, Parent JJ, Kantor P, Yue L, Wynn J, Lee TM, Addonizio LJ, Appelbaum PS, Chung WK. Impact of Genetic Testing for Cardiomyopathy on Emotional Well-Being and Family Dynamics: A Study of Parents and Adolescents. Circ Genom Precis Med 2021; 14:e003189. [PMID: 34255550 DOI: 10.1161/circgen.120.003189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Genetic testing is indicated for children with a personal or family history of hereditary cardiomyopathy to determine appropriate management and inform risk stratification for family members. The implications of a positive genetic result for children can potentially impact emotional well-being. Given the nuances of cardiomyopathy genetic testing for minors, this study aimed to understand how parents involve their children in the testing process and investigate the impact of genetic results on family dynamics. METHODS A survey was distributed to participants recruited from the Children's Cardiomyopathy Foundation and 7 North American sites in the Pediatric Cardiomyopathy Registry. The survey explored adolescent and parent participants' emotions upon receiving their/their child's genetic results, parent-child result communication and its impact on family functionality, using the McMaster Family Assessment Device. RESULTS One hundred sixty-two parents of minors and 48 adolescents who were offered genetic testing for a personal or family history of cardiomyopathy completed the survey. Parents whose child had cardiomyopathy were more likely to disclose positive diagnostic genetic results to their child (P=0.014). Parents with unaffected children and positive predictive testing results were more likely to experience negative emotions about the result (P≤0.001) but also had better family functioning scores than those with negative predictive results (P=0.019). Most adolescents preferred results communicated directly to the child, but parents were divided about whether their child's result should first be released to them or their child. CONCLUSIONS These findings have important considerations for how providers structure genetic services for adolescents and facilitate discussion between parents and their children about results.
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Affiliation(s)
- Priyanka Ahimaz
- Division of Molecular Genetics, Department of Pediatrics (P.A., J.W., W.K.C.), Columbia University Irving Medical Center
| | - Maya Sabatello
- Center for Precision Medicine and Genomics, Division of Ethics, Departments of Medicine, Medical Humanities and Ethics (M.S.)
| | - Min Qian
- Department of Biostatistics, Mailman School of Public Health (M.Q., A.W.)
| | - Aijin Wang
- Department of Biostatistics, Mailman School of Public Health (M.Q., A.W.)
| | - Erin M Miller
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children's Hospital Medical Center, Heart Institute Cincinnati, OH (E.M.M.)
| | - Ashley Parrott
- The Heart Institute, Cincinnati Children's Hospital Medical Center, OH (A.P.)
| | - Ashwin K Lal
- Primary Children's Hospital, University of Utah, Salt Lake City (A.K.L.)
| | - Kathryn C Chatfield
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora (K.C.C.)
| | | | - Stephanie M Ware
- Departments of Pediatrics and Medical and Molecular Genetics (S.M.W.), Indiana University School of Medicine, Indianapolis
| | - John J Parent
- Department of Pediatrics (J.J.P.), Indiana University School of Medicine, Indianapolis
| | - Paul Kantor
- Stollery Children's Hospital, Edmonton, Alberta, Canada (P.K.)
| | - Lisa Yue
- Children's Cardiomyopathy Foundation (L.Y.), Columbia University Irving Medical Center
| | - Julia Wynn
- Division of Molecular Genetics, Department of Pediatrics (P.A., J.W., W.K.C.), Columbia University Irving Medical Center
| | - Teresa M Lee
- Division of Cardiology, Department of Pediatrics (T.M.L., L.J.A.), Columbia University Irving Medical Center
| | - Linda J Addonizio
- Division of Cardiology, Department of Pediatrics (T.M.L., L.J.A.), Columbia University Irving Medical Center
| | - Paul S Appelbaum
- Center for Research on Ethical, Legal and Social Implications of Psychiatric, Neurologic and Behavioral Genetics, Department of Psychiatry, Columbia University, New York, NY (P.S.A.)
| | - Wendy K Chung
- Division of Molecular Genetics, Department of Pediatrics (P.A., J.W., W.K.C.), Columbia University Irving Medical Center.,Department of Medicine (W.K.C.), Columbia University Irving Medical Center
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16
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Ahimaz P, Giordano J, Disco M, Harrington E, Levinson E, Spiegel E, Andrews C, Griffin E, Hernan R, Wynn J. COVID contingencies: Early epicenter experiences of different genetics clinics at a New York City institution inform emergency adaptation strategies. J Genet Couns 2021; 30:938-948. [PMID: 33734519 PMCID: PMC8250804 DOI: 10.1002/jgc4.1409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/30/2022]
Abstract
The unique situational challenges of the COVID‐19 pandemic have demanded creative modifications to the delivery of genetic services. Institutions across the country have adapted workflows to continue to provide quality care while minimizing the need for physical visits. As the first epicenter of the pandemic in the country, New York City healthcare workers and residents had to make rapid, unprecedented changes to their way of life. This article describes the workflow adaptations of genetic counselors across various clinical settings at New York Presbyterian/Columbia University Irving Medical Center, the largest provider of genetics care in New York City, during the height of the COVID‐19 pandemic. The authors observe how the adaptations impacted clinical care and the genetic counselors. Our lived experience and account can provide guidance for others during the current and future pandemics.
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Affiliation(s)
- Priyanka Ahimaz
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Jessica Giordano
- Division of Maternal-Fetal Medicine-Research, Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Michele Disco
- Interdepartmental Genetic Counseling Program, Department of Pathology, Columbia University, New York, NY, USA
| | - Elizabeth Harrington
- Division of Neuromuscular Medicine, Department of Neurology, Columbia University, New York, NY, USA
| | - Elana Levinson
- Department of Medical Hematology and Oncology, Columbia University, New York, NY, USA
| | - Erica Spiegel
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Carli Andrews
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Emily Griffin
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Rebecca Hernan
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Julia Wynn
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY, USA
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Al-Deri N, Okur V, Ahimaz P, Milev M, Valivullah Z, Hagen J, Sheng Y, Chung W, Sacher M, Ganapathi M. A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function. J Med Genet 2020; 58:592-601. [PMID: 32843486 DOI: 10.1136/jmedgenet-2020-107016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/25/2020] [Accepted: 06/26/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Next-generation sequencing has facilitated the diagnosis of neurodevelopmental disorders with variable and non-specific clinical findings. Recently, a homozygous missense p.(Asp37Tyr) variant in TRAPPC2L, a core subunit of TRAPP complexes which function as tethering factors during membrane trafficking, was reported in two unrelated individuals with neurodevelopmental delay, post-infectious encephalopathy-associated developmental arrest, tetraplegia and accompanying rhabdomyolysis. METHODS We performed whole genome sequencing on members of an Ashkenazi Jewish pedigree to identify the underlying genetic aetiology of global developmental delay/intellectual disability in three affected siblings. To assess the effect of the identified TRAPPC2L variant, we performed biochemical and cell biological functional studies on the TRAPPC2L protein. RESULTS A rare homozygous predicted deleterious missense variant, p.(Ala2Gly), in TRAPPC2L was identified in the affected siblings and it segregated with the neurodevelopmental phenotype within the family. Using a yeast two-hybrid assay and in vitro binding, we demonstrate that the p.(Ala2Gly) variant, but not the p.(Asp37Tyr) variant, disrupted the interaction between TRAPPC2L and another core TRAPP protein, TRAPPC6a. Size exclusion chromatography suggested that this variant affects the assembly of TRAPP complexes. Employing two different membrane trafficking assays using fibroblasts from one of the affected siblings, we found a delay in traffic into and out of the Golgi. Similar to the p.(Asp37Tyr) variant, the p.(Ala2Gly) variant resulted in an increase in the levels of active RAB11. CONCLUSION Our data fill in a gap in the knowledge of TRAPP architecture with TRAPPC2L interacting with TRAPPC6a, positioning it as a putative adaptor for other TRAPP subunits. Collectively, our findings support the pathogenicity of the TRAPPC2L p.(Ala2Gly) variant.
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Affiliation(s)
- Noraldin Al-Deri
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Volkan Okur
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Miroslav Milev
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Zaheer Valivullah
- Center for Mendelian Genomics, Broad Institute Harvard, Cambridge, Massachusetts, USA
| | - Jacob Hagen
- Department of Biomedical Sciences, Columbia University Medical Center, New York, New York, USA
| | - Yufeng Sheng
- Department of Biomedical Sciences, Columbia University Medical Center, New York, New York, USA
| | - Wendy Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA.,Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada .,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
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18
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Pereira EM, Ahimaz P, Andrews C, Anyane-Yeboa K, Arsov T, Berger SM, Chilton I, Cory DM, Chung WK, Dergham KR, Disco MM, Ernst ME, Forman T, Galloway S, Geltzeiler AR, Giordano JL, Griffin E, Guzman E, Harkavy N, Hernan R, Hetzler AK, Iglesias A, Kakar R, Kentros C, Khonje TC, Koval C, Levinson E, Pereira EM, Robinson S, Ross MJ, Sadeque-Iqbal F, Spiegel E, Spitz E, Wapner RJ, Chung WK. COVID-19’s Impact on Genetics at One Medical Center in New York. Genet Med 2020; 22:1467-1469. [PMID: 32499605 PMCID: PMC8740647 DOI: 10.1038/s41436-020-0857-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/22/2020] [Indexed: 11/18/2022] Open
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19
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Hernan R, Cho MT, Wilson AL, Ahimaz P, Au C, Berger SM, Guzman E, Primiano M, Shaw JE, Ross M, Tabanfar L, Chilton I, Griffin E, Ratner C, Anyane-Yeboa K, Iglesias A, Pisani L, Roohi J, Duong J, Martinez J, Appelbaum P, Klitzman R, Ottman R, Chung WK, Wynn J. Impact of patient education videos on genetic counseling outcomes after exome sequencing. Patient Educ Couns 2020; 103:127-135. [PMID: 31521424 PMCID: PMC9667716 DOI: 10.1016/j.pec.2019.08.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/05/2019] [Accepted: 08/16/2019] [Indexed: 05/05/2023]
Abstract
OBJECTIVE Growing use of clinical exome sequencing (CES) has led to an increased burden of genomic education. Self-guided educational tools can minimize the educational burden for genetic counselors (GCs). The effectiveness of these tools must be evaluated. METHODS Parents of patients offered CES were randomized to watch educational videos before their visit or to receive routine care. Parents and GCs were surveyed about their experiences following the sessions. The responses of the video (n = 102) and no-video (n = 105) groups were compared. RESULTS GCs reported no significant differences between parents in the video and no-video groups on genetics knowledge or CES knowledge. In contrast, parents' scores on genetics knowledge questions were lower in the video than no-video group (p = 0.007). Most parents reported the videos were informative, and the groups did not differ in satisfaction with GCs or decisions to have CES. CONCLUSION GCs and parents perceived the videos to be beneficial. However, lower scores on genetics knowledge questions highlight the need for careful development of educational tools. PRACTICE IMPLICATIONS Educational tools should be developed and assessed for effectiveness with the input of all stakeholders before widespread implementation. Better measures of the effectiveness of these educational tools are needed.
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Affiliation(s)
- Rebecca Hernan
- Sarah Lawrence College, Joan H. Marks Graduate Program in Human Genetics, Bronxville, NY, USA; Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Megan T Cho
- Sarah Lawrence College, Joan H. Marks Graduate Program in Human Genetics, Bronxville, NY, USA; GeneDx, 207 Perry Parkway, Gaithersburg, MD, USA
| | - Ashley L Wilson
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY, USA
| | - Priyanka Ahimaz
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Catherine Au
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY, USA
| | - Sara M Berger
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY, USA
| | - Edwin Guzman
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY, USA
| | - Michelle Primiano
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY, USA
| | - Jessica E Shaw
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY, USA
| | - Meredith Ross
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY, USA
| | - Leyla Tabanfar
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY, USA
| | - Ilana Chilton
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Emily Griffin
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Chana Ratner
- Long Island University, LIU Post Genetic Counseling Graduate Program, Brookville, NY, USA
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandro Iglesias
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Laura Pisani
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jasmin Roohi
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jimmy Duong
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Josue Martinez
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center and NY State Psychiatric Institute, New York, NY, USA
| | - Robert Klitzman
- G.H. Sergievsky Center and Departments of Epidemiology and Neurology, Columbia University Irving Medical Center, and NY State Psychiatric Institute, New York, NY, USA
| | - Ruth Ottman
- G.H. Sergievsky Center and Departments of Epidemiology and Neurology, Columbia University Irving Medical Center, and NY State Psychiatric Institute, New York, NY, USA
| | - Wendy K Chung
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Julia Wynn
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.
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20
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Wynn J, Ottman R, Duong J, Wilson AL, Ahimaz P, Martinez J, Rabin R, Rosen E, Webster R, Au C, Cho MT, Egan C, Guzman E, Primiano M, Shaw JE, Sisson R, Klitzman RL, Appelbaum PS, Lichter-Konecki U, Anyane-Yeboa K, Iglesias A, Chung WK. Diagnostic exome sequencing in children: A survey of parental understanding, experience and psychological impact. Clin Genet 2018; 93:1039-1048. [PMID: 29266212 DOI: 10.1111/cge.13200] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 09/21/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022]
Abstract
Clinical exome sequencing (CES) is increasingly being used as an effective diagnostic tool in the field of pediatric genetics. We sought to evaluate the parental experience, understanding and psychological impact of CES by conducting a survey study of English-speaking parents of children who had diagnostic CES. Parents of 192 unique patients participated. The parent's interpretation of the child's result agreed with the clinician's interpretation in 79% of cases, with more frequent discordance when the clinician's interpretation was uncertain. The majority (79%) reported no regret with the decision to have CES. Most (65%) reported complete satisfaction with the genetic counseling experience, and satisfaction was positively associated with years of genetic counselor (GC) experience. The psychological impact of CES was greatest for parents of children with positive results and for parents with anxiety or depression. The results of this study are important for helping clinicians to prepare families for the possible results and variable psychological impact of CES. The frequency of parental misinterpretation of test results indicates the need for additional clarity in the communication of results. Finally, while the majority of patients were satisfied with their genetic counseling, satisfaction was lower for new GCs, suggesting a need for targeted GC training for genomic testing.
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Affiliation(s)
- J Wynn
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York
| | - R Ottman
- G.H. Sergievsky Center and Departments of Epidemiology and Neurology, Columbia University Medical Center and NY State Psychiatric Institute, New York, New York
| | - J Duong
- Department of Sociomedical Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - A L Wilson
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, New York
| | - P Ahimaz
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York
| | - J Martinez
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York
| | - R Rabin
- College of Liberal Arts and Sciences, Long Island University - Post Campus, Brookville, New York
| | - E Rosen
- College of Liberal Arts and Sciences, Long Island University - Post Campus, Brookville, New York
| | - R Webster
- Columbia University Medical School, New York, New York
| | - C Au
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, New York
| | - M T Cho
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, New York.,GeneDx, Gaithersburg, Maryland
| | - C Egan
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, New York
| | - E Guzman
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, New York
| | - M Primiano
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, New York
| | - J E Shaw
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, New York
| | - R Sisson
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, New York
| | - R L Klitzman
- Department of Psychiatry, Columbia University Medical Center and NY State Psychiatric Institute, New York, New York
| | - P S Appelbaum
- Department of Psychiatry, Columbia University Medical Center and NY State Psychiatric Institute, New York, New York
| | - U Lichter-Konecki
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York
| | - K Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York
| | - A Iglesias
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York
| | - W K Chung
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York.,Department of Medicine, Columbia University Medical Center, New York, New York
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21
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Lu HC, Tan Q, Rousseaux MWC, Wang W, Kim JY, Richman R, Wan YW, Yeh SY, Patel JM, Liu X, Lin T, Lee Y, Fryer JD, Han J, Chahrour M, Finnell RH, Lei Y, Zurita-Jimenez ME, Ahimaz P, Anyane-Yeboa K, Van Maldergem L, Lehalle D, Jean-Marcais N, Mosca-Boidron AL, Thevenon J, Cousin MA, Bro DE, Lanpher BC, Klee EW, Alexander N, Bainbridge MN, Orr HT, Sillitoe RV, Ljungberg MC, Liu Z, Schaaf CP, Zoghbi HY. Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans. Nat Genet 2017; 49:527-536. [PMID: 28288114 DOI: 10.1038/ng.3808] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 02/10/2017] [Indexed: 12/18/2022]
Abstract
Gain-of-function mutations in some genes underlie neurodegenerative conditions, whereas loss-of-function mutations in the same genes have distinct phenotypes. This appears to be the case with the protein ataxin 1 (ATXN1), which forms a transcriptional repressor complex with capicua (CIC). Gain of function of the complex leads to neurodegeneration, but ATXN1-CIC is also essential for survival. We set out to understand the functions of the ATXN1-CIC complex in the developing forebrain and found that losing this complex results in hyperactivity, impaired learning and memory, and abnormal maturation and maintenance of upper-layer cortical neurons. We also found that CIC activity in the hypothalamus and medial amygdala modulates social interactions. Informed by these neurobehavioral features in mouse mutants, we identified five individuals with de novo heterozygous truncating mutations in CIC who share similar clinical features, including intellectual disability, attention deficit/hyperactivity disorder (ADHD), and autism spectrum disorder. Our study demonstrates that loss of ATXN1-CIC complexes causes a spectrum of neurobehavioral phenotypes.
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Affiliation(s)
- Hsiang-Chih Lu
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA
| | - Qiumin Tan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maxime W C Rousseaux
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ji-Yoen Kim
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ronald Richman
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Szu-Ying Yeh
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA
| | - Jay M Patel
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Xiuyun Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Tao Lin
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Yoontae Lee
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - John D Fryer
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jing Han
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maria Chahrour
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Richard H Finnell
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Yunping Lei
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Maria E Zurita-Jimenez
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | | | - Daphne Lehalle
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France
| | - Nolwenn Jean-Marcais
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France
| | - Anne-Laure Mosca-Boidron
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France.,Chromosomal and Molecular Genetics Laboratory, Biological Center, Dijon University Hospital, Dijon, France
| | - Julien Thevenon
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Della E Bro
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Matthew N Bainbridge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Codified Genomics, LLC, Houston, Texas, USA
| | - Harry T Orr
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Roy V Sillitoe
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - M Cecilia Ljungberg
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Christian P Schaaf
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Huda Y Zoghbi
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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22
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Tanaka AJ, Bai R, Cho MT, Anyane-Yeboa K, Ahimaz P, Wilson AL, Kendall F, Hay B, Moss T, Nardini M, Bauer M, Retterer K, Juusola J, Chung WK. De novo mutations in PURA are associated with hypotonia and developmental delay. Cold Spring Harb Mol Case Stud 2016; 1:a000356. [PMID: 27148565 PMCID: PMC4850890 DOI: 10.1101/mcs.a000356] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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] [Indexed: 12/30/2022] Open
Abstract
PURA is the leading candidate gene responsible for the developmental phenotype in the 5q31.3 microdeletion syndrome. De novo mutations in PURA were recently reported in 15 individuals with developmental features similar to the 5q31.3 microdeletion syndrome. Here we describe six unrelated children who were identified by clinical whole-exome sequencing (WES) to have novel de novo variants in PURA with a similar phenotype of hypotonia and developmental delay and frequently associated with seizures. The protein Purα (encoded by PURA) is involved in neuronal proliferation, dendrite maturation, and the transport of mRNA to translation sites during neuronal development. Mutations in PURA may alter normal brain development and impair neuronal function, leading to developmental delay and the seizures observed in patients with mutations in PURA.
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Affiliation(s)
- Akemi J Tanaka
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Renkui Bai
- GeneDx, Gaithersburg, Maryland 20877, USA
| | | | - Kwame Anyane-Yeboa
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Ashley L Wilson
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Fran Kendall
- VMP Genetics, Roswell, Georgia 30076, USA;; Department of Kinesiology, University of Georgia, Athens, Georgia 30605, USA
| | - Beverly Hay
- Division of Genetics, UMass Memorial Medical Center, Worcester, Massachusetts 01655, USA
| | - Timothy Moss
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Monica Nardini
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Mislen Bauer
- Department of Genetics, Miami Children's Hospital, Miami, Florida 33155, USA
| | | | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA;; Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
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