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Meester JAN, Hebert A, Bastiaansen M, Rabaut L, Bastianen J, Boeckx N, Ashcroft K, Atwal PS, Benichou A, Billon C, Blankensteijn JD, Brennan P, Bucks SA, Campbell IM, Conrad S, Curtis SL, Dasouki M, Dent CL, Eden J, Goel H, Hartill V, Houweling AC, Isidor B, Jackson N, Koopman P, Korpioja A, Kraatari-Tiri M, Kuulavainen L, Lee K, Low KJ, Lu AC, McManus ML, Oakley SP, Oliver J, Organ NM, Overwater E, Revencu N, Trainer AH, Trivedi B, Turner CLS, Whittington R, Zankl A, Zentner D, Van Laer L, Verstraeten A, Loeys BL. Expanding the clinical spectrum of biglycan-related Meester-Loeys syndrome. NPJ Genom Med 2024; 9:22. [PMID: 38531898 PMCID: PMC10966070 DOI: 10.1038/s41525-024-00413-z] [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: 12/01/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Pathogenic loss-of-function variants in BGN, an X-linked gene encoding biglycan, are associated with Meester-Loeys syndrome (MRLS), a thoracic aortic aneurysm/dissection syndrome. Since the initial publication of five probands in 2017, we have considerably expanded our MRLS cohort to a total of 18 probands (16 males and 2 females). Segregation analyses identified 36 additional BGN variant-harboring family members (9 males and 27 females). The identified BGN variants were shown to lead to loss-of-function by cDNA and Western Blot analyses of skin fibroblasts or were strongly predicted to lead to loss-of-function based on the nature of the variant. No (likely) pathogenic missense variants without additional (predicted) splice effects were identified. Interestingly, a male proband with a deletion spanning the coding sequence of BGN and the 5' untranslated region of the downstream gene (ATP2B3) presented with a more severe skeletal phenotype. This may possibly be explained by expressional activation of the downstream ATPase ATP2B3 (normally repressed in skin fibroblasts) driven by the remnant BGN promotor. This study highlights that aneurysms and dissections in MRLS extend beyond the thoracic aorta, affecting the entire arterial tree, and cardiovascular symptoms may coincide with non-specific connective tissue features. Furthermore, the clinical presentation is more severe and penetrant in males compared to females. Extensive analysis at RNA, cDNA, and/or protein level is recommended to prove a loss-of-function effect before determining the pathogenicity of identified BGN missense and non-canonical splice variants. In conclusion, distinct mechanisms may underlie the wide phenotypic spectrum of MRLS patients carrying loss-of-function variants in BGN.
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Affiliation(s)
- Josephina A N Meester
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Anne Hebert
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Maaike Bastiaansen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Laura Rabaut
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Jarl Bastianen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Nele Boeckx
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Kathryn Ashcroft
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals, NHS Foundation Trust, Leeds, UK
| | - Paldeep S Atwal
- Genomic and Personalized Medicine, Atwal Clinic, Palm Beach, FL, USA
| | - Antoine Benichou
- Department of Internal and Vascular Medicine, CHU Nantes, Nantes Université, Nantes, France
| | - Clarisse Billon
- Service de Médecine Génomique des Maladies Rares, Groupe Hospitalier Universitaire Centre, Paris, Assistance Publique Hôpitaux de Paris, Paris, France
- Université de Paris Cité, Inserm, PARCC, Paris, France
| | - Jan D Blankensteijn
- Department of Vascular Surgery, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Paul Brennan
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Ian M Campbell
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Solène Conrad
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Stephanie L Curtis
- Bristol Heart Institute, University Hospitals Bristol & Weston NHS Foundation Trust, Bristol, UK
| | - Majed Dasouki
- Department of Medical Genetics & Genomics, AdventHealth Medical Group, Orlando, FL, USA
| | - Carolyn L Dent
- South West Genomic Laboratory Hub, Bristol Genetics Laboratory, Bristol, UK
| | - James Eden
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester, UK
| | | | - Verity Hartill
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals, NHS Foundation Trust, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Arjan C Houweling
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Nicola Jackson
- Clinical Genetics Service, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Pieter Koopman
- Department of Cardiology, Heart Centre Hasselt, Jessa Hospital, Hasselt, Belgium
| | - Anita Korpioja
- Department of Clinical Genetics, Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Minna Kraatari-Tiri
- Department of Clinical Genetics, Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Liina Kuulavainen
- Department of Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kelvin Lee
- Department of Medical Genetics & Genomics, AdventHealth Medical Group, Orlando, FL, USA
| | - Karen J Low
- Clinical Genetics Department, University Hospitals Bristol and Weston NHS Foundation Trust St Michael's Hospital, Bristol, UK
- University of Bristol, Canynge Hall, Bristol, UK
| | - Alan C Lu
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Morgan L McManus
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stephen P Oakley
- John Hunter Hospital, New Lambton Heights, NSW, Australia
- College of Health, Medicine and Wellbeing, School of Medicine, University of Newcastle, Newcastle, NSW, Australia
| | - James Oliver
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Nicole M Organ
- John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Eline Overwater
- Department of Human Genetics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Nicole Revencu
- Center for Human Genetics, Cliniques Universitaires Saint-Luc and Université Catholique de Louvain, Brussels, Belgium
| | - Alison H Trainer
- Department of Genomic Medicine, The Royal Melbourne Hospital and University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Bhavya Trivedi
- Department of Medical Genetics & Genomics, AdventHealth Medical Group, Orlando, FL, USA
| | - Claire L S Turner
- Department of Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | | | - Andreas Zankl
- Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, NSW, Australia
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Dominica Zentner
- Department of Genomic Medicine, The Royal Melbourne Hospital and University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Lut Van Laer
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Aline Verstraeten
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Bart L Loeys
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.
- Department of Clinical Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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Pendleton KE, Hernandez-Garcia A, Lyu JM, Campbell IM, Shaw CA, Vogt J, High FA, Donahoe PK, Chung WK, Scott DA. FOXP1 Haploinsufficiency Contributes to the Development of Congenital Diaphragmatic Hernia. J Pediatr Genet 2024; 13:29-34. [PMID: 38567173 PMCID: PMC10984716 DOI: 10.1055/s-0043-1767731] [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: 10/28/2021] [Accepted: 04/11/2022] [Indexed: 03/30/2023]
Abstract
FOXP1 encodes a transcription factor involved in tissue regulation and cell-type-specific functions. Haploinsufficiency of FOXP1 is associated with a neurodevelopmental disorder: autosomal dominant mental retardation with language impairment with or without autistic features. More recently, heterozygous FOXP1 variants have also been shown to cause a variety of structural birth defects including central nervous system (CNS) anomalies, congenital heart defects, congenital anomalies of the kidney and urinary tract, cryptorchidism, and hypospadias. In this report, we present a previously unpublished case of an individual with congenital diaphragmatic hernia (CDH) who carries an approximately 3.8 Mb deletion. Based on this deletion, and deletions previously reported in two other individuals with CDH, we define a CDH critical region on chromosome 3p13 that includes FOXP1 and four other protein-coding genes. We also provide detailed clinical descriptions of two previously reported individuals with CDH who carry de novo, pathogenic variants in FOXP1 that are predicted to trigger nonsense-mediated mRNA decay. A subset of individuals with putatively deleterious FOXP4 variants has also been shown to develop CDH. Since FOXP proteins function as homo- or heterodimers and the homologs of FOXP1 and FOXP4 are expressed at the same time points in the embryonic mouse diaphragm, they may function together as a dimer, or in parallel as homodimers, to regulate gene expression during diaphragm development. Not all individuals with heterozygous, loss-of-function changes in FOXP1 develop CDH. Hence, we conclude that FOXP1 acts as a susceptibility factor that contributes to the development of CDH in conjunction with other genetic, epigenetic, environmental, and/or stochastic factors.
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Affiliation(s)
- Katherine E. Pendleton
- Genetics and Genomics Program, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Jennifer M. Lyu
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Ian M. Campbell
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, United Kingdom
| | - Frances A. High
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Patricia K. Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States
| | - Wendy K. Chung
- Departments of Pediatrics, Columbia University, New York, New York, United States
- Department of Medicine, Columbia University, New York, New York, United States
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States
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Weissenbacher D, Rawal S, Zhao X, Priestley JRC, Szigety KM, Schmidt SF, Higgins MJ, Magge A, O'Connor K, Gonzalez-Hernandez G, Campbell IM. PhenoID, a language model normalizer of physical examinations from genetics clinical notes. medRxiv 2024:2023.10.16.23296894. [PMID: 37904943 PMCID: PMC10614999 DOI: 10.1101/2023.10.16.23296894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Background Phenotypes identified during dysmorphology physical examinations are critical to genetic diagnosis and nearly universally documented as free-text in the electronic health record (EHR). Variation in how phenotypes are recorded in free-text makes large-scale computational analysis extremely challenging. Existing natural language processing (NLP) approaches to address phenotype extraction are trained largely on the biomedical literature or on case vignettes rather than actual EHR data. Methods We implemented a tailored system at the Children's Hospital of Philadelpia that allows clinicians to document dysmorphology physical exam findings. From the underlying data, we manually annotated a corpus of 3136 organ system observations using the Human Phenotype Ontology (HPO). We provide this corpus publicly. We trained a transformer based NLP system to identify HPO terms from exam observations. The pipeline includes an extractor, which identifies tokens in the sentence expected to contain an HPO term, and a normalizer, which uses those tokens together with the original observation to determine the specific term mentioned. Findings We find that our labeler and normalizer NLP pipeline, which we call PhenoID, achieves state-of-the-art performance for the dysmorphology physical exam phenotype extraction task. PhenoID's performance on the test set was 0.717, compared to the nearest baseline system (Pheno-Tagger) performance of 0.633. An analysis of our system's normalization errors shows possible imperfections in the HPO terminology itself but also reveals a lack of semantic understanding by our transformer models. Interpretation Transformers-based NLP models are a promising approach to genetic phenotype extraction and, with recent development of larger pre-trained causal language models, may improve semantic understanding in the future. We believe our results also have direct applicability to more general extraction of medical signs and symptoms. Funding US National Institutes of Health.
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Campbell IM, Karavite DJ, Mcmanus ML, Cusick FC, Junod DC, Sheppard SE, Lourie EM, Shelov ED, Hakonarson H, Luberti AA, Muthu N, Grundmeier RW. Clinical decision support with a comprehensive in-EHR patient tracking system improves genetic testing follow up. J Am Med Inform Assoc 2023; 30:1274-1283. [PMID: 37080563 PMCID: PMC10280356 DOI: 10.1093/jamia/ocad070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/10/2023] [Accepted: 04/11/2023] [Indexed: 04/22/2023] Open
Abstract
OBJECTIVE We sought to develop and evaluate an electronic health record (EHR) genetic testing tracking system to address the barriers and limitations of existing spreadsheet-based workarounds. MATERIALS AND METHODS We evaluated the spreadsheet-based system using mixed effects logistic regression to identify factors associated with delayed follow up. These factors informed the design of an EHR-integrated genetic testing tracking system. After deployment, we assessed the system in 2 ways. We analyzed EHR access logs and note data to assess patient outcomes and performed semistructured interviews with users to identify impact of the system on work. RESULTS We found that patient-reported race was a significant predictor of documented genetic testing follow up, indicating a possible inequity in care. We implemented a CDS system including a patient data capture form and management dashboard to facilitate important care tasks. The system significantly sped review of results and significantly increased documentation of follow-up recommendations. Interviews with key system users identified a range of sociotechnical factors (ie, tools, tasks, collaboration) that contribute to safer and more efficient care. DISCUSSION Our new tracking system ended decades of workarounds for identifying and communicating test results and improved clinical workflows. Interview participants related that the system decreased cognitive and time burden which allowed them to focus on direct patient interaction. CONCLUSION By assembling a multidisciplinary team, we designed a novel patient tracking system that improves genetic testing follow up. Similar approaches may be effective in other clinical settings.
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Affiliation(s)
- Ian M Campbell
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Clinical Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of General Pediatrics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dean J Karavite
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Morgan L Mcmanus
- Division of Clinical Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Fred C Cusick
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - David C Junod
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sarah E Sheppard
- Division of Clinical Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Eli M Lourie
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of General Pediatrics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Eric D Shelov
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Anthony A Luberti
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Naveen Muthu
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Robert W Grundmeier
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of General Pediatrics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Campbell IM, Crowley TB, Jobaliya C, Bailey A, McGinn DE, Gaiser K, Bassett A, Gur RE, Morrow B, Emanuel BS, Franco AT, French D, Zackai EH, McDonald-McGinn DM, Lambert MP. Platelet findings in 22q11.2 deletion syndrome correlate with disease manifestations but do not correlate with GPIb surface expression. Clin Genet 2023; 103:109-113. [PMID: 36075864 PMCID: PMC9742133 DOI: 10.1111/cge.14227] [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: 07/18/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 01/21/2023]
Abstract
Prior studies have demonstrated that patients with chromosome 22q11.2 deletion syndrome (22q11.2DS) have lower platelet counts (PC) compared to non-deleted populations. They also have an increased mean platelet volume. The mechanism for this has been postulated to be haploinsufficiency of the GPIBB gene. We examined platelet parameters, deletion size and factors known to influence counts, including status of thyroid hormone and congenital heart disease (CHD), in a population of 825 patients with 22q11.2DS. We also measured surface expression of GPIB-IX complex by flow cytometry. The major determinant of PC was deletion status of GP1BB, regardless of surface expression or other factors. Patients with nested distal chromosome 22q11.2 deletions (those with GP1BB present) had higher PCs than those with proximal deletions where GP1BB is deleted. Patients with 22q11.2DS also demonstrated an accelerated PC decrease with age, occurring in childhood. These data demonstrate that genes within the proximal deletion segment drive PC differences in 22q11.2DS and suggest that PC reference ranges may need to be adjusted for age and deletion size in 22q11.2DS populations. Bleeding did not correlate with either platelet count or GPIb expression. Further studies into drivers of expression of GPIb and associations with severe thrombocytopenia and immune thrombocytopenia are needed to inform clinical care.
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Affiliation(s)
- Ian M. Campbell
- Division of Human Genetics and 22q and You Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - T. Blaine Crowley
- Division of Human Genetics and 22q and You Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Chintan Jobaliya
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Alice Bailey
- Division of Human Genetics and 22q and You Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Daniel E. McGinn
- Division of Human Genetics and 22q and You Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kimberly Gaiser
- Division of Human Genetics and 22q and You Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Anne Bassett
- Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Raquel E. Gur
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Bernice Morrow
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY
| | - Beverly S. Emanuel
- Division of Human Genetics and 22q and You Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Aime T. Franco
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Division of Endocrinology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Deborah French
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Elaine H. Zackai
- Division of Human Genetics and 22q and You Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Donna M. McDonald-McGinn
- Division of Human Genetics and 22q and You Center, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michele P. Lambert
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
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Priestley JR, Pace LM, Sen K, Aggarwal A, Alves CAP, Campbell IM, Cuddapah SR, Engelhardt NM, Eskandar M, Jolín García PC, Gropman A, Helbig I, Hong X, Gowda VK, Lusk L, Trapane P, Srinivasan VM, Suwannarat P, Ganetzky RD. Malate dehydrogenase 2 deficiency is an emerging cause of pediatric epileptic encephalopathy with a recognizable biochemical signature. Mol Genet Metab Rep 2022; 33:100931. [DOI: 10.1016/j.ymgmr.2022.100931] [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] [Received: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/18/2022] Open
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7
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Campbell IM, Crowley TB, Keena B, Donoghue S, McManus ML, Zackai EH. The experience of one pediatric geneticist with telemedicine-based clinical diagnosis. Am J Med Genet A 2022; 188:3416-3422. [PMID: 35906847 DOI: 10.1002/ajmg.a.62920] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/11/2022] [Accepted: 07/05/2022] [Indexed: 01/31/2023]
Abstract
Telemedicine has long been considered as an attractive alternative methodology in clinical genetics to improve patient access and convenience. Given the importance of the dysmorphology physical examination and anthropometric measurement in clinical genetics, many have wondered if lost information would hamper diagnosis. We previously addressed this question by analyzing thousands of diagnostic encounters in a single practice involving multiple practitioners and found no evidence for a difference in new molecular diagnosis rates. However, our previous study design resulted in variability in providers between in-person and telemedicine evaluation groups. To address this in our present study, we expanded our analysis to 1104 new patient evaluations seen by one highly experienced clinical geneticist across two 10-month periods before and after the start of the COVID-19 pandemic. Comparing patients seen in-person to those seen by telemedicine, we found significant differences in race and ethnicity, preferred language, and home zip code median income. The clinical geneticist intended to send more genetic testing for those patients seen by telemedicine, but due to issues with test authorization and sample collection, there was no difference in ultimate completion rate between groups. We found no significant difference in new molecular diagnosis rate. Overall, we find telemedicine to be an acceptable alternative to in-person evaluation for routine pediatric clinical genetics care.
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Affiliation(s)
- Ian M Campbell
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - T Blaine Crowley
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Beth Keena
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sarah Donoghue
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Morgan L McManus
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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8
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Hardcastle A, Berry AM, Campbell IM, Zhao X, Liu P, Gerard AE, Rosenfeld JA, Sisoudiya SD, Hernandez-Garcia A, Loddo S, Di Tommaso S, Novelli A, Dentici ML, Capolino R, Digilio MC, Graziani L, Rustad CF, Neas K, Ferrero GB, Brusco A, Di Gregorio E, Wellesley D, Beneteau C, Joubert M, Van Den Bogaert K, Boogaerts A, McMullan DJ, Dean J, Giuffrida MG, Bernardini L, Varghese V, Shannon NL, Harrison RE, Lam WWK, McKee S, Turnpenny PD, Cole T, Morton J, Eason J, Jones MC, Hall R, Wright M, Horridge K, Shaw CA, Chung WK, Scott DA. Identifying phenotypic expansions for congenital diaphragmatic hernia plus (CDH+) using DECIPHER data. Am J Med Genet A 2022; 188:2958-2968. [PMID: 35904974 PMCID: PMC9474674 DOI: 10.1002/ajmg.a.62919] [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: 03/01/2022] [Revised: 06/28/2022] [Accepted: 07/10/2022] [Indexed: 01/31/2023]
Abstract
Congenital diaphragmatic hernia (CDH) can occur in isolation or in conjunction with other birth defects (CDH+). A molecular etiology can only be identified in a subset of CDH cases. This is due, in part, to an incomplete understanding of the genes that contribute to diaphragm development. Here, we used clinical and molecular data from 36 individuals with CDH+ who are cataloged in the DECIPHER database to identify genes that may play a role in diaphragm development and to discover new phenotypic expansions. Among this group, we identified individuals who carried putatively deleterious sequence or copy number variants affecting CREBBP, SMARCA4, UBA2, and USP9X. The role of these genes in diaphragm development was supported by their expression in the developing mouse diaphragm, their similarity to known CDH genes using data from a previously published and validated machine learning algorithm, and/or the presence of CDH in other individuals with their associated genetic disorders. Our results demonstrate how data from DECIPHER, and other public databases, can be used to identify new phenotypic expansions and suggest that CREBBP, SMARCA4, UBA2, and USP9X play a role in diaphragm development.
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Affiliation(s)
- Amy Hardcastle
- Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Aliska M. Berry
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ian M. Campbell
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Amanda E. Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Saumya D. Sisoudiya
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Sara Loddo
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Silvia Di Tommaso
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Maria L. Dentici
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Rossella Capolino
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Maria C. Digilio
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ludovico Graziani
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
- Medical Genetics Unit, Tor Vergata Hospital, Rome, Italy
| | - Cecilie F. Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Giovanni B. Ferrero
- Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Città della Salute e della Scienza University Hospital, Torino, Italy
| | | | - Diana Wellesley
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, Hampshire, UK
- University Hospital Southampton, Southampton, Hampshire, UK
| | - Claire Beneteau
- Nantes Université, CHU de Nantes, UF 9321 de Fœtopathologie et Génétique, Nantes, France
| | - Madeleine Joubert
- Nantes Université, CHU de Nantes, UF 9321 de Fœtopathologie et Génétique, Nantes, France
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals Leuven–KU Leuven, Leuven, Belgium
| | - Anneleen Boogaerts
- Center for Human Genetics, University Hospitals Leuven–KU Leuven, Leuven, Belgium
| | - Dominic J. McMullan
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s NHS Foundation Trust, UK
| | - John Dean
- Clinical Genetics Service, Ashgrove House, NHS Grampian, Aberdeen, UK
| | - Maria G. Giuffrida
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Laura Bernardini
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Nora L Shannon
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Rachel E. Harrison
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Wayne W. K. Lam
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, Scotland
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Peter D. Turnpenny
- Clinical Genetics Department, Royal Devon and Exeter Hospital, Exeter, UK
| | - Trevor Cole
- Clinical Genetics Unit, Birmingham Women’s Hospital, Birmingham, UK
| | - Jenny Morton
- Clinical Genetics Unit, Birmingham Women’s Hospital, Birmingham, UK
| | - Jacqueline Eason
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Marilyn C. Jones
- University of California, San Diego and Rady Children’s Hospital, San Diego, CA, USA
| | - Rebecca Hall
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michael Wright
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Karen Horridge
- South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
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9
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Szigety KM, Crowley TB, Gaiser KB, Chen EY, Priestley JRC, Williams LS, Rangu SA, Wright CM, Adusumalli P, Ahrens-Nicklas RC, Calderon B, Cuddapah SR, Edmondson A, Ficicioglu C, Ganetzky R, Kalish JM, Krantz ID, McDonald-McGinn DM, Medne L, Muraresku C, Pyle LC, Zackai EH, Campbell IM, Sheppard SE. Clinical Effectiveness of Telemedicine-Based Pediatric Genetics Care. Pediatrics 2022; 150:188195. [PMID: 35642503 PMCID: PMC9724118 DOI: 10.1542/peds.2021-054520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/01/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Telemedicine may increase access to medical genetics care. However, in the pediatric setting, how telemedicine may affect the diagnostic rate is unknown, partially because of the perceived importance of the dysmorphology physical examination. We studied the clinical effectiveness of telemedicine for patients with suspected or confirmed genetic conditions. METHODS We conducted a retrospective cohort study of outpatient encounters before and after the widespread implementation of telemedicine (N = 5854). Visit types, diagnoses, patient demographic characteristics, and laboratory data were acquired from the electronic health record. Patient satisfaction was assessed through survey responses. New molecular diagnosis was the primary end point. RESULTS Patients seen by telemedicine were more likely to report non-Hispanic White ancestry, prefer to speak English, live in zip codes with higher median incomes, and have commercial insurance (all P < .01). Genetic testing was recommended for more patients evaluated by telemedicine than in person (79.5% vs 70.9%; P < .001). Patients seen in person were more likely to have a sample collected, resulting in similar test completion rates (telemedicine, 51.2%; in person, 55.1%; P = .09). There was no significant difference in molecular diagnosis rate between visit modalities (telemedicine, 13.8%; in person, 12.4%; P = .40). CONCLUSIONS Telemedicine and traditional in-person evaluation resulted in similar molecular diagnosis rates. However, improved methodologies for remote sample collection may be required. This study reveals the feasibility of telemedicine in a large academic medical genetics practice and is applicable to other pediatric specialties with perceived importance of physical examination.
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Affiliation(s)
- Katherine M. Szigety
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Terrence B. Crowley
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kimberly B. Gaiser
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Erin Y. Chen
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jessica R. C. Priestley
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Lydia S. Williams
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Sneha A. Rangu
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Christina M. Wright
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Priyanka Adusumalli
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | | | - Brandon Calderon
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Sanmati R. Cuddapah
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Andrew Edmondson
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Can Ficicioglu
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Rebecca Ganetzky
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jennifer M. Kalish
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Ian D. Krantz
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Donna M. McDonald-McGinn
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Livija Medne
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Colleen Muraresku
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Louise C. Pyle
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Elaine H. Zackai
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Ian M. Campbell
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Sarah E. Sheppard
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
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10
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Scott TM, Campbell IM, Hernandez-Garcia A, Lalani SR, Liu P, Shaw CA, Rosenfeld JA, Scott DA. Clinical exome sequencing data reveal high diagnostic yields for congenital diaphragmatic hernia plus (CDH+) and new phenotypic expansions involving CDH. J Med Genet 2022; 59:270-278. [PMID: 33461977 PMCID: PMC8286264 DOI: 10.1136/jmedgenet-2020-107317] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 07/04/2020] [Revised: 11/17/2020] [Accepted: 12/26/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Congenital diaphragmatic hernia (CDH) is a life-threatening birth defect that often co-occurs with non-hernia-related anomalies (CDH+). While copy number variant (CNV) analysis is often employed as a diagnostic test for CDH+, clinical exome sequencing (ES) has not been universally adopted. METHODS We analysed a clinical database of ~12 000 test results to determine the diagnostic yields of ES in CDH+ and to identify new phenotypic expansions. RESULTS Among the 76 cases with an indication of CDH+, a molecular diagnosis was made in 28 cases for a diagnostic yield of 37% (28/76). A provisional diagnosis was made in seven other cases (9%; 7/76). Four individuals had a diagnosis of Kabuki syndrome caused by frameshift variants in KMT2D. Putatively deleterious variants in ALG12 and EP300 were each found in two individuals, supporting their role in CDH development. We also identified individuals with de novo pathogenic variants in FOXP1 and SMARCA4, and compound heterozygous pathogenic variants in BRCA2. The role of these genes in CDH development is supported by the expression of their mouse homologs in the developing diaphragm, their high CDH-specific pathogenicity scores generated using a previously validated algorithm for genome-scale knowledge synthesis and previously published case reports. CONCLUSION We conclude that ES should be ordered in cases of CDH+ when a specific diagnosis is not suspected and CNV analyses are negative. Our results also provide evidence in favour of phenotypic expansions involving CDH for genes associated with ALG12-congenital disorder of glycosylation, Rubinstein-Taybi syndrome, Fanconi anaemia, Coffin-Siris syndrome and FOXP1-related disorders.
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Affiliation(s)
- Tiana M. Scott
- Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, 84602, USA,Texas Children’s Hospital, Houston, TX, 77030, USA
| | - Ian M. Campbell
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R. Lalani
- Texas Children’s Hospital, Houston, TX, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA,Baylor Genetics, Houston, TX, 77021, USA
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daryl A. Scott
- Texas Children’s Hospital, Houston, TX, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA,Correspondence Daryl A. Scott, R813, One Baylor Plaza. BCM225, Houston, TX 77030, USA, , Phone: +1 713-203-7242
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11
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Crowley TB, Campbell IM, Liebling EJ, Lambert MP, Levitt Katz LE, Heimall J, Bailey A, McGinn DE, McDonald McGinn DM, Sullivan KE. Distinct immune trajectories in patients with chromosome 22q11.2 deletion syndrome and immune-mediated diseases. J Allergy Clin Immunol 2021; 149:445-450. [PMID: 34144109 DOI: 10.1016/j.jaci.2021.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 04/28/2021] [Revised: 06/02/2021] [Accepted: 06/10/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Identification of biomarkers associated with immune-mediated diseases in 22q11.2 deletion syndrome is an evolving field. OBJECTIVES We sought to use a carefully phenotyped cohort to study immune parameters associated with autoimmunity and atopy in 22q11.2 deletion syndrome to define biomarkers associated with immune-mediated disease in this syndrome. METHODS Chart review validated autoimmune disease and atopic condition diagnoses. Laboratory data were extracted for each subcohort and plotted according to age. A random-effects model was used to define statistical significance. RESULTS CD19, CD4, and CD4/45RA lymphocyte populations were not different from the general cohort for patients with atopic conditions. CD4/45RA T cells were significantly lower in the subjects with immune thrombocytopenia compared with the general cohort, and CD4 T-cell counts were lower in patients with autoimmune thyroid disease. CONCLUSIONS The mechanisms of autoimmunity in cytopenias may be distinct from those of solid-organ autoimmunity in 22q11.2 deletion syndrome. This study identifies potential biomarkers for risk stratification among commonly obtained laboratory studies.
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Affiliation(s)
- T Blaine Crowley
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa
| | - Ian M Campbell
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa
| | - Emily J Liebling
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa
| | - Michele P Lambert
- Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa
| | - Lorraine E Levitt Katz
- Division of Endocrinol & Diabetes, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa
| | - Jennifer Heimall
- Division of Allergy and Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa
| | - Alice Bailey
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa
| | - Daniel E McGinn
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa
| | - Donna M McDonald McGinn
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa.
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12
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Sheppard SE, Campbell IM, Harr MH, Gold N, Li D, Bjornsson HT, Cohen JS, Fahrner JA, Fatemi A, Harris JR, Nowak C, Stevens CA, Grand K, Au M, Graham JM, Sanchez-Lara PA, Campo MD, Jones MC, Abdul-Rahman O, Alkuraya FS, Bassetti JA, Bergstrom K, Bhoj E, Dugan S, Kaplan JD, Derar N, Gripp KW, Hauser N, Innes AM, Keena B, Kodra N, Miller R, Nelson B, Nowaczyk MJ, Rahbeeni Z, Ben-Shachar S, Shieh JT, Slavotinek A, Sobering AK, Abbott MA, Allain DC, Amlie-Wolf L, Au PYB, Bedoukian E, Beek G, Barry J, Berg J, Bernstein JA, Cytrynbaum C, Chung BHY, Donoghue S, Dorrani N, Eaton A, Flores-Daboub JA, Dubbs H, Felix CA, Fong CT, Fung JLF, Gangaram B, Goldstein A, Greenberg R, Ha TK, Hersh J, Izumi K, Kallish S, Kravets E, Kwok PY, Jobling RK, Knight Johnson AE, Kushner J, Lee BH, Levin B, Lindstrom K, Manickam K, Mardach R, McCormick E, McLeod DR, Mentch FD, Minks K, Muraresku C, Nelson SF, Porazzi P, Pichurin PN, Powell-Hamilton NN, Powis Z, Ritter A, Rogers C, Rohena L, Ronspies C, Schroeder A, Stark Z, Starr L, Stoler J, Suwannarat P, Velinov M, Weksberg R, Wilnai Y, Zadeh N, Zand DJ, Falk MJ, Hakonarson H, Zackai EH, Quintero-Rivera F. Expanding the genotypic and phenotypic spectrum in a diverse cohort of 104 individuals with Wiedemann-Steiner syndrome. Am J Med Genet A 2021; 185:1649-1665. [PMID: 33783954 DOI: 10.1002/ajmg.a.62124] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 09/28/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/19/2022]
Abstract
Wiedemann-Steiner syndrome (WSS) is an autosomal dominant disorder caused by monoallelic variants in KMT2A and characterized by intellectual disability and hypertrichosis. We performed a retrospective, multicenter, observational study of 104 individuals with WSS from five continents to characterize the clinical and molecular spectrum of WSS in diverse populations, to identify physical features that may be more prevalent in White versus Black Indigenous People of Color individuals, to delineate genotype-phenotype correlations, to define developmental milestones, to describe the syndrome through adulthood, and to examine clinicians' differential diagnoses. Sixty-nine of the 82 variants (84%) observed in the study were not previously reported in the literature. Common clinical features identified in the cohort included: developmental delay or intellectual disability (97%), constipation (63.8%), failure to thrive (67.7%), feeding difficulties (66.3%), hypertrichosis cubiti (57%), short stature (57.8%), and vertebral anomalies (46.9%). The median ages at walking and first words were 20 months and 18 months, respectively. Hypotonia was associated with loss of function (LoF) variants, and seizures were associated with non-LoF variants. This study identifies genotype-phenotype correlations as well as race-facial feature associations in an ethnically diverse cohort, and accurately defines developmental trajectories, medical comorbidities, and long-term outcomes in individuals with WSS.
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Affiliation(s)
- Sarah E Sheppard
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ian M Campbell
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Margaret H Harr
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nina Gold
- Mass General Hospital for Children, Division of Medical Genetics and Metabolism and Harvard Medical School, Boston, Massachusetts, USA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Landspitali University Hospital, Iceland
| | - Julie S Cohen
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ali Fatemi
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline R Harris
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Catherine Nowak
- Division of Genetics and Genomics, Boston Children's Hospital, The Feingold Center for Children, Boston, Massachusetts, USA
| | - Cathy A Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, Tennessee, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Margaret Au
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Miguel Del Campo
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Marilyn C Jones
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Omar Abdul-Rahman
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jennifer A Bassetti
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Katherine Bergstrom
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Elizabeth Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sarah Dugan
- Division of Medical Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Julie D Kaplan
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nada Derar
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Karen W Gripp
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Natalie Hauser
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - A Micheil Innes
- Department of Medical Genetics, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Beth Keena
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Neslida Kodra
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Rebecca Miller
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Beverly Nelson
- Department of Clinical Skills, St. George's University, True Blue, Grenada
| | | | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shay Ben-Shachar
- Genetic Institute, Tel-Aviv Medical Center, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joseph T Shieh
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Andrew K Sobering
- Department of Biochemistry, St. George's University, True Blue, Grenada
| | - Mary-Alice Abbott
- Medical Genetics, Department of Pediatrics, University of Massachusetts Medical School - Baystate, Springfield, Massachusetts, USA
| | - Dawn C Allain
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Louise Amlie-Wolf
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Ping Yee Billie Au
- Department of Medical Genetics, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Emma Bedoukian
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Geoffrey Beek
- Children's Hospital of Minnesota, Minneapolis, Minnesota, USA
| | - James Barry
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Janet Berg
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Sarah Donoghue
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Naghmeh Dorrani
- Department of Pediatrics, University of California Los Angeles, California, Los Angeles, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, California, Los Angeles, USA
| | - Alison Eaton
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | | | - Holly Dubbs
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Carolyn A Felix
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Chin-To Fong
- Department of Pediatrics, Division of Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jasmine Lee Fong Fung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Balram Gangaram
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Amy Goldstein
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rotem Greenberg
- Genetic Institute, Tel-Aviv Medical Center, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Thoa K Ha
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Joseph Hersh
- Weisskopf Child Evaluation Center, Department of Pediatrics, University of Louisville, Louisville, Kentucky, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Staci Kallish
- Division of Translational Medicine and Human Genetics Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elijah Kravets
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Pui-Yan Kwok
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Rebekah K Jobling
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | | | - Jessica Kushner
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Bo Hoon Lee
- Department of Neurology, Division of Child Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Brooke Levin
- MD Anderson Cancer Center at Cooper, Cooper University Health Care, Camden, New Jersey, USA
| | | | - Kandamurugu Manickam
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Rebecca Mardach
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Elizabeth McCormick
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - D Ross McLeod
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - Frank D Mentch
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kelly Minks
- Department of Neurology, Division of Child Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Colleen Muraresku
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stanley F Nelson
- UCLA Clinical Genomics Center, University of California Los Angeles, California, Los Angeles, USA.,Department of Human Genetics, Center for Duchenne Muscular Dystrophy University of California Los Angeles, California, Los Angeles, USA
| | - Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Pavel N Pichurin
- Clinical Genomics Center, University of California Los Angeles, Los Angeles, California, USA
| | - Nina N Powell-Hamilton
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Zoe Powis
- Quest Diagnostics Kalamzoo, Kalamzoo, Michigan, USA
| | - Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Caleb Rogers
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Luis Rohena
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Carey Ronspies
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Audrey Schroeder
- Department of Pediatrics, Division of Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Lois Starr
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joan Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Pim Suwannarat
- Mid-Atlantic Permanente Medical Group, Rockville, Maryland, USA
| | - Milen Velinov
- NYS Institute for Basic Research in developmental Disabilities, Staten Island, New York, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Yael Wilnai
- Genetic Institute, Sourasky Medical Center, Te-Aviv, Tel Aviv, Israel
| | - Neda Zadeh
- Genetics Center and CHOC Children's Hospital, Orange, California, USA
| | - Dina J Zand
- Rare Disease Institute, Children's National Medical Center, Washington, District of Columbia, USA
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Fabiola Quintero-Rivera
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, California, Los Angeles, USA
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13
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Tencer J, Virupakshaiah A, Campbell IM, Zackai EH, Zarnow D, Agarwal S. A Case of Prenatally Diagnosed Periventricular Nodular Heterotopia in a Surviving Male Patient with FLNA Mutation. Journal of Pediatric Neurology 2021. [DOI: 10.1055/s-0041-1725017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
FLNA is a gene on the X chromosome that encodes Filamin A, a widely expressed protein crucial for forming the cell cytoskeleton and mediating cell signaling. Loss-of-function mutations have been associated with periventricular nodular heterotopia (PVNH) with associated epilepsy and intellectual deficits, as well as cardiovascular disease, connective tissue disorders, pulmonary disease, bleeding diathesis, and gastrointestinal disease. Alternatively, gain-of-function mutations have been described with otopalatodigital spectrum disorders.The loss-of-function variants of FLNA associated with PVNH have historically been considered lethal in males, often prenatally or by the first year of life. However, more surviving males with FLNA variants are being described. Most of the surviving males have missense or distal truncating mutations or a degree of mosaicism. Others are thought to have splice site mutations or in-frame exon skipping leading to production of some degree of functional Filamin A as possible mechanisms of survival.Here, we presented a case of a 20-month-old small but developmentally appropriate and healthy male infant who was prenatally diagnosed with PVNH, and postnatally found to have a nonsense variant of the FLNA gene. This mutation has not been previously clinically described or published to our knowledge.
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Affiliation(s)
- Jaclyn Tencer
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Akash Virupakshaiah
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Ian M. Campbell
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Elaine H. Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Deborah Zarnow
- Division of Radiology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Sonika Agarwal
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
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14
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Walters ME, Lacassie Y, Azamian M, Franciskovich R, Zapata G, Hernandez PP, Liu P, Campbell IM, Bostwick BL, Lalani SR. Vertical transmission of a large calvarial ossification defect due to heterozygous variants of ALX4 and TWIST1. Am J Med Genet A 2020; 185:916-922. [PMID: 33369125 DOI: 10.1002/ajmg.a.62036] [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: 08/27/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 11/08/2022]
Abstract
ALX4 is a homeobox gene expressed in the mesenchyme of developing bone and is known to play an important role in the regulation of osteogenesis. Enlarged parietal foramina (EPF) is a phenotype of delayed intramembranous ossification of calvarial bones due to variants of ALX4. The contrasting phenotype of premature ossification of sutures is observed with heterozygous loss-of-function variants of TWIST1, which is an important regulator of osteoblast differentiation. Here, we describe an individual with a large cranium defect, with dominant transmission from the mother, both carrying disease causing heterozygous variants in ALX4 and TWIST1. The distinct phenotype of absent superior and posterior calvarium in the child and his mother was in sharp contrast to the other affected maternal relatives with a recognizable ALX4-related EPF phenotype. This report demonstrates comorbid disorders of Saethre-Chotzen syndrome and EPF in a mother and her child, resulting in severe skull defects reminiscent of calvarial abnormalities observed with bilallelic ALX4 variants. To our knowledge this is the first instance of ALX4 and TWIST1 variants acting synergistically to cause a unique phenotype influencing skull ossification.
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Affiliation(s)
- Michelle E Walters
- Division of Dermatology, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Yves Lacassie
- Division of Genetics, Department of Pediatrics, Louisiana State University Health Sciences Center School of Medicine, and Children's Hospital, New Orleans, Louisiana, USA
| | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Rachel Franciskovich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Gladys Zapata
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Patricia P Hernandez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Ian M Campbell
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Bret L Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
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15
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Affiliation(s)
- Ian M Campbell
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Morgan Congdon
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter S Capucilli
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - William W Fox
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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16
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Campbell IM, Sheppard SE, Crowley TB, McGinn DE, Bailey A, McGinn MJ, Unolt M, Homans JF, Chen EY, Salmons HI, Gaynor JW, Goldmuntz E, Jackson OA, Katz LE, Mascarenhas MR, Deeney VFX, Castelein RM, Zur KB, Elden L, Kallish S, Kolon TF, Hopkins SE, Chadehumbe MA, Lambert MP, Forbes BJ, Moldenhauer JS, Schindewolf EM, Solot CB, Moss EM, Gur RE, Sullivan KE, Emanuel BS, Zackai EH, McDonald-McGinn DM. What is new with 22q? An update from the 22q and You Center at the Children's Hospital of Philadelphia. Am J Med Genet A 2019; 176:2058-2069. [PMID: 30380191 DOI: 10.1002/ajmg.a.40637] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022]
Abstract
22q11.2 deletion syndrome (22q11.2DS) is a disorder caused by recurrent, chromosome-specific, low copy repeat (LCR)-mediated copy-number losses of chromosome 22q11. The Children's Hospital of Philadelphia has been involved in the clinical care of individuals with what is now known as 22q11.2DS since our initial report of the association with DiGeorge syndrome in 1982. We reviewed the medical records on our continuously growing longitudinal cohort of 1,421 patients with molecularly confirmed 22q11.2DS from 1992 to 2018. Most individuals are Caucasian and older than 8 years. The mean age at diagnosis was 3.9 years. The majority of patients (85%) had typical LCR22A-LCR22D deletions, and only 7% of these typical deletions were inherited from a parent harboring the deletion constitutionally. However, 6% of individuals harbored other nested deletions that would not be identified by traditional 22q11.2 FISH, thus requiring an orthogonal technology to diagnose. Major medical problems included immune dysfunction or allergies (77%), palatal abnormalities (67%), congenital heart disease (64%), gastrointestinal difficulties (65%), endocrine dysfunction (>50%), scoliosis (50%), renal anomalies (16%), and airway abnormalities. Median full-scale intelligence quotient was 76, with no significant difference between individuals with and without congenital heart disease or hypocalcemia. Characteristic dysmorphic facial features were present in most individuals, but dermatoglyphic patterns of our cohort are similar to normal controls. This is the largest longitudinal study of patients with 22q11.2DS, helping to further describe the condition and aid in diagnosis and management. Further surveillance will likely elucidate additional clinically relevant findings as they age.
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Affiliation(s)
- Ian M Campbell
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sarah E Sheppard
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - T Blaine Crowley
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Daniel E McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Davidson College, Davidson, North Carolina
| | - Alice Bailey
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael J McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Marta Unolt
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Cardiology, Bambino Gesu Hospital, Rome, Italy
| | - Jelle F Homans
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Orthopaedic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Erin Y Chen
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Johns Hopkins University, Baltimore, Maryland
| | - Harold I Salmons
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - J William Gaynor
- Division of Cardiothoracic Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Oksana A Jackson
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Plastic Surgery, Department of Pediatric Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Plastic Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lorraine E Katz
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Endocrinology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Maria R Mascarenhas
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Gastroenterology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Vincent F X Deeney
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Orthopaedics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - René M Castelein
- Department of Orthopaedic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Karen B Zur
- Division of Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lisa Elden
- Division of Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Staci Kallish
- Department of Medicine, Division of Translational Medicine and Human Genetics, The Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Thomas F Kolon
- Division of Pediatric Urology, Department of Pediatric Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Surgery (Urology), Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sarah E Hopkins
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Madeline A Chadehumbe
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michele P Lambert
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Brian J Forbes
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Julie S Moldenhauer
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Fetal Diagnosis and Treatment at Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Erica M Schindewolf
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Center for Fetal Diagnosis and Treatment at Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cynthia B Solot
- Center for Childhood Communication, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Edward M Moss
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Malamut and Moss, Bryn Mawr, Pennsylvania
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kathleen E Sullivan
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Beverly S Emanuel
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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17
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Campbell IM, Sheppard SE, Crowley TB, McGinn DE, Bailey A, McGinn MJ, Unolt M, Homans JF, Chen EY, Salmons HI, Gaynor JW, Goldmuntz E, Jackson OA, Katz LE, Mascarenhas MR, Deeney VFX, Castelein RM, Zur KB, Elden L, Kallish S, Kolon TF, Hopkins SE, Chadehumbe MA, Lambert MP, Forbes BJ, Moldenhauer JS, Schindewolf EM, Solot CB, Moss EM, Gur RE, Sullivan KE, Emanuel BS, Zackai EH, McDonald-McGinn DM. Cover Image, Volume 176A, Number 10, October 2018. Am J Med Genet A 2018. [DOI: 10.1002/ajmg.a.60697] [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: 11/08/2022]
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18
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Song X, Beck CR, Du R, Campbell IM, Coban-Akdemir Z, Gu S, Breman AM, Stankiewicz P, Ira G, Shaw CA, Lupski JR. Predicting human genes susceptible to genomic instability associated with Alu/ Alu-mediated rearrangements. Genome Res 2018; 28:1228-1242. [PMID: 29907612 PMCID: PMC6071635 DOI: 10.1101/gr.229401.117] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 06/06/2018] [Indexed: 12/14/2022]
Abstract
Alu elements, the short interspersed element numbering more than 1 million copies per human genome, can mediate the formation of copy number variants (CNVs) between substrate pairs. These Alu/Alu-mediated rearrangements (AAMRs) can result in pathogenic variants that cause diseases. To investigate the impact of AAMR on gene variation and human health, we first characterized Alus that are involved in mediating CNVs (CNV-Alus) and observed that these Alus tend to be evolutionarily younger. We then computationally generated, with the assistance of a supercomputer, a test data set consisting of 78 million Alu pairs and predicted ∼18% of them are potentially susceptible to AAMR. We further determined the relative risk of AAMR in 12,074 OMIM genes using the count of predicted CNV-Alu pairs and experimentally validated the predictions with 89 samples selected by correlating predicted hotspots with a database of CNVs identified by clinical chromosomal microarrays (CMAs) on the genomes of approximately 54,000 subjects. We fine-mapped 47 duplications, 40 deletions, and two complex rearrangements and examined a total of 52 breakpoint junctions of simple CNVs. Overall, 94% of the candidate breakpoints were at least partially Alu mediated. We successfully predicted all (100%) of Alu pairs that mediated deletions (n = 21) and achieved an 87% positive predictive value overall when including AAMR-generated deletions and duplications. We provided a tool, AluAluCNVpredictor, for assessing AAMR hotspots and their role in human disease. These results demonstrate the utility of our predictive model and provide insights into the genomic features and molecular mechanisms underlying AAMR.
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Affiliation(s)
- Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Baylor Genetics, Houston, Texas 77021, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Baylor Genetics, Houston, Texas 77021, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Baylor Genetics, Houston, Texas 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Texas Children's Hospital, Houston, Texas 77030, USA
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19
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Callaway DA, Campbell IM, Stover SR, Hernandez-Garcia A, Jhangiani SN, Punetha J, Paine IS, Posey JE, Muzny D, Lally KP, Lupski JR, Shaw CA, Fernandes CJ, Scott DA. Prioritization of Candidate Genes for Congenital Diaphragmatic Hernia in a Critical Region on Chromosome 4p16 using a Machine-Learning Algorithm. J Pediatr Genet 2018; 7:164-173. [PMID: 30430034 DOI: 10.1055/s-0038-1655755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 12/01/2017] [Accepted: 04/10/2018] [Indexed: 02/07/2023]
Abstract
Wolf-Hirschhorn syndrome (WHS) is caused by partial deletion of the short arm of chromosome 4 and is characterized by dysmorphic facies, congenital heart defects, intellectual/developmental disability, and increased risk for congenital diaphragmatic hernia (CDH). In this report, we describe a stillborn girl with WHS and a large CDH. A literature review revealed 15 cases of WHS with CDH, which overlap a 2.3-Mb CDH critical region. We applied a machine-learning algorithm that integrates large-scale genomic knowledge to genes within the 4p16.3 CDH critical region and identified FGFRL1 , CTBP1 , NSD2 , FGFR3 , CPLX1 , MAEA , CTBP1-AS2 , and ZNF141 as genes whose haploinsufficiency may contribute to the development of CDH.
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Affiliation(s)
- Danielle A Callaway
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States
| | - Ian M Campbell
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Samantha R Stover
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Ingrid S Paine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Kevin P Lally
- Department of Pediatric Surgery, McGovern Medical School at UT Health, Houston, Texas, United States
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States.,Division of Neonatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Caraciolo J Fernandes
- Division of Neonatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States
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20
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Liu P, Yuan B, Carvalho CMB, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SW, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell 2017; 168:830-842.e7. [PMID: 28235197 DOI: 10.1016/j.cell.2017.01.037] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 10/13/2016] [Accepted: 01/27/2017] [Indexed: 01/07/2023]
Abstract
De novo copy number variants (dnCNVs) arising at multiple loci in a personal genome have usually been considered to reflect cancer somatic genomic instabilities. We describe a multiple dnCNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional dnCNVs. These CNVs originate from independent formation incidences, are predominantly tandem duplications or complex gains, exhibit breakpoint junction features reminiscent of replicative repair, and show increased de novo point mutations flanking the rearrangement junctions. The active CNV mutation shower appears to be restricted to a transient perizygotic period. We propose that a defect in the CNV formation process is responsible for the "CNV-mutator state," and this state is dampened after early embryogenesis. The constitutional MdnCNV phenomenon resembles chromosomal instability in various cancers. Investigations of this phenomenon may provide unique access to understanding genomic disorders, structural variant mutagenesis, human evolution, and cancer biology.
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Affiliation(s)
- Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA.
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur Wuster
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Ling Zhang
- Collaborative Innovation Center of Genetics and Development, Institute of Reproduction and Development, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zechen Chong
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Violet Gelowani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Karin Writzl
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Marjorie Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Joanna Wiszniewska
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer Scull
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Zhang
- Collaborative Innovation Center of Genetics and Development, Institute of Reproduction and Development, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Janice Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | | | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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21
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James RA, Campbell IM, Chen ES, Boone PM, Rao MA, Bainbridge MN, Lupski JR, Yang Y, Eng CM, Posey JE, Shaw CA. A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. Genome Med 2016; 8:13. [PMID: 26838676 PMCID: PMC4736244 DOI: 10.1186/s13073-016-0261-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/05/2016] [Indexed: 12/22/2022] Open
Abstract
Background Genome-wide data are increasingly important in the clinical evaluation of human disease. However, the large number of variants observed in individual patients challenges the efficiency and accuracy of diagnostic review. Recent work has shown that systematic integration of clinical phenotype data with genotype information can improve diagnostic workflows and prioritization of filtered rare variants. We have developed visually interactive, analytically transparent analysis software that leverages existing disease catalogs, such as the Online Mendelian Inheritance in Man database (OMIM) and the Human Phenotype Ontology (HPO), to integrate patient phenotype and variant data into ranked diagnostic alternatives. Methods Our tool, “OMIM Explorer” (http://www.omimexplorer.com), extends the biomedical application of semantic similarity methods beyond those reported in previous studies. The tool also provides a simple interface for translating free-text clinical notes into HPO terms, enabling clinical providers and geneticists to contribute phenotypes to the diagnostic process. The visual approach uses semantic similarity with multidimensional scaling to collapse high-dimensional phenotype and genotype data from an individual into a graphical format that contextualizes the patient within a low-dimensional disease map. The map proposes a differential diagnosis and algorithmically suggests potential alternatives for phenotype queries—in essence, generating a computationally assisted differential diagnosis informed by the individual’s personal genome. Visual interactivity allows the user to filter and update variant rankings by interacting with intermediate results. The tool also implements an adaptive approach for disease gene discovery based on patient phenotypes. Results We retrospectively analyzed pilot cohort data from the Baylor Miraca Genetics Laboratory, demonstrating performance of the tool and workflow in the re-analysis of clinical exomes. Our tool assigned to clinically reported variants a median rank of 2, placing causal variants in the top 1 % of filtered candidates across the 47 cohort cases with reported molecular diagnoses of exome variants in OMIM Morbidmap genes. Our tool outperformed Phen-Gen, eXtasy, PhenIX, PHIVE, and hiPHIVE in the prioritization of these clinically reported variants. Conclusions Our integrative paradigm can improve efficiency and, potentially, the quality of genomic medicine by more effectively utilizing available phenotype information, catalog data, and genomic knowledge. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0261-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Regis A James
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ian M Campbell
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Edward S Chen
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Philip M Boone
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mitchell A Rao
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew N Bainbridge
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chad A Shaw
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Department of Statistics, Rice University, Houston, TX, 77005, USA.
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22
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Campbell IM, Shaw CA, Stankiewicz P, Lupski JR. Erratum to: Somatic Mosaicism: Implications for Disease and Transmission Genetics. Trends Genet 2016; 32:138. [DOI: 10.1016/j.tig.2015.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Campbell IM, Gambin T, Jhangiani S, Grove ML, Veeraraghavan N, Muzny DM, Shaw CA, Gibbs RA, Boerwinkle E, Yu F, Lupski JR. Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses. Hum Mutat 2015; 37:231-234. [PMID: 26670213 DOI: 10.1002/humu.22944] [Citation(s) in RCA: 16] [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: 08/10/2015] [Accepted: 12/03/2015] [Indexed: 11/11/2022]
Abstract
As the amount of human genomic sequence available from personal genomes and exomes has increased, so too has the observation of genomic positions having two or more alternative alleles, so-called multiallelic sites. For portions of the haploid genome that are present in more than one copy, including segmental duplications, variation at such multisite variant positions becomes even more complex. Despite the frequency of multiallelic variants, a number of commonly used resources and tools in genomic research and diagnostics do not support these multiallelic variants all together or require special modifications. Here, we explore the frequency of multiallelic sites in large samples with whole exome sequencing and discuss potential outcomes of failing to account for multiple variant alleles. We also briefly discuss some commonly utilized resources that fully support multiallelic sites.
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Affiliation(s)
- Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Megan L Grove
- Human Genetics Center, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
| | | | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genetics Center, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
| | - Fuli Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Hospital, Houston, TX 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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24
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Yuan B, Liu P, Gupta A, Beck CR, Tejomurtula A, Campbell IM, Gambin T, Simmons AD, Withers MA, Harris RA, Rogers J, Schwartz DC, Lupski JR. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates. PLoS Genet 2015; 11:e1005686. [PMID: 26641089 PMCID: PMC4671654 DOI: 10.1371/journal.pgen.1005686] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 10/29/2015] [Indexed: 11/30/2022] Open
Abstract
Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases—about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual’s susceptibility to acquiring disease-associated alleles. Genomic instability due to the intrinsic sequence architecture of the genome, such as low copy repeats (LCRs), is a major contributor to de novo mutations that can occur in the process of human genome evolution. LCRs can mediate genomic rearrangements associated with genomic disorders by acting as substrates for nonallelic homologous recombination. Juvenile-onset nephronophthisis 1 is the most frequent genetic cause of renal failure in children. An LCR-mediated, homozygous common recurrent deletion encompassing NPHP1 is found in the majority of affected subjects, while heterozygous deletion representing the nephronophthisis 1 recessive carrier state is frequently observed amongst world populations. Interestingly, the human NPHP1 locus is located proximal to the head-to-head fusion site of two ancestral chromosomes that occurred in the great apes, which resulted in a reduction of chromosome number from 48 in nonhuman primates to the current 46 in humans. In this study, we characterized and provided evidence for the diverse genomic architecture at the NPHP1 locus and potential structural variant haplotypes in the human population. Furthermore, our analyses of primate genomes shed light on the massive changes of genomic architecture at the human NPHP1 locus and delineated a model for the emergence of the LCRs during primate evolution.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Aditya Gupta
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and The UW-Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christine R. Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anusha Tejomurtula
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ian M. Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alexandra D. Simmons
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Marjorie A. Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jeffrey Rogers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and The UW-Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
- * E-mail:
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25
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Mayle R, Campbell IM, Beck CR, Yu Y, Wilson M, Shaw CA, Bjergbaek L, Lupski JR, Ira G. DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage. Science 2015; 349:742-7. [PMID: 26273056 DOI: 10.1126/science.aaa8391] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most spontaneous DNA double-strand breaks (DSBs) result from replication-fork breakage. Break-induced replication (BIR), a genome rearrangement-prone repair mechanism that requires the Pol32/POLD3 subunit of eukaryotic DNA Polδ, was proposed to repair broken forks, but how genome destabilization is avoided was unknown. We show that broken fork repair initially uses error-prone Pol32-dependent synthesis, but that mutagenic synthesis is limited to within a few kilobases from the break by Mus81 endonuclease and a converging fork. Mus81 suppresses template switches between both homologous sequences and diverged human Alu repetitive elements, highlighting its importance for stability of highly repetitive genomes. We propose that lack of a timely converging fork or Mus81 may propel genome instability observed in cancer.
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Affiliation(s)
- Ryan Mayle
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yang Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Marenda Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Lotte Bjergbaek
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus 8000, Denmark
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Department of Pediatrics, and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Texas Children's Hospital, Houston, TX 77030, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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26
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Gambin T, Jhangiani SN, Below JE, Campbell IM, Wiszniewski W, Muzny DM, Staples J, Morrison AC, Bainbridge MN, Penney S, McGuire AL, Gibbs RA, Lupski JR, Boerwinkle E. Secondary findings and carrier test frequencies in a large multiethnic sample. Genome Med 2015. [PMID: 26195989 PMCID: PMC4507324 DOI: 10.1186/s13073-015-0171-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Besides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potential clinical utility for physicians, patients and their families. We analyzed the frequency and nature of single nucleotide variants (SNVs) considered secondary findings and recessive disease allele carrier status in the exomes of 8554 individuals from a large, randomly sampled cohort study and 2514 patients from a study of presumed Mendelian disease having undergone WES. METHODS We used the same sequencing platform and data processing pipeline to analyze all samples and characterized the distributions of reported pathogenic (ClinVar, Human Gene Mutation Database (HGMD)) and predicted deleterious variants in the pre-specified American College of Medical Genetics and Genomics (ACMG) secondary findings and recessive disease genes in different ethnic groups. RESULTS In the 56 ACMG secondary findings genes, the average number of predicted deleterious variants per individual was 0.74, and the mean number of ClinVar reported pathogenic variants was 0.06. We observed an average of 10 deleterious and 0.78 ClinVar reported pathogenic variants per individual in 1423 autosomal recessive disease genes. By repeatedly sampling pairs of exomes, 0.5 % of the randomly generated couples were at 25 % risk of having an affected offspring for an autosomal recessive disorder based on the ClinVar variants. CONCLUSIONS By investigating reported pathogenic and novel, predicted deleterious variants we estimated the lower and upper limits of the population fraction for which exome sequencing may reveal additional medically relevant information. We suggest that the observed wide range for the lower and upper limits of these frequency numbers will be gradually reduced due to improvement in classification databases and prediction algorithms.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA ; Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665 Poland
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jennifer E Below
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jeffrey Staples
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Alanna C Morrison
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Matthew N Bainbridge
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Samantha Penney
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA ; Texas Children's Hospital, Houston, TX 77030 USA
| | - Amy L McGuire
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA ; Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030 USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA ; The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA ; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA ; Texas Children's Hospital, Houston, TX 77030 USA
| | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA ; Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
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27
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Gu S, Yuan B, Campbell IM, Beck CR, Carvalho CMB, Nagamani SCS, Erez A, Patel A, Bacino CA, Shaw CA, Stankiewicz P, Cheung SW, Bi W, Lupski JR. Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3. Hum Mol Genet 2015; 24:4061-77. [PMID: 25908615 DOI: 10.1093/hmg/ddv146] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/20/2015] [Indexed: 01/05/2023] Open
Abstract
Alu repetitive elements are known to be major contributors to genome instability by generating Alu-mediated copy-number variants (CNVs). Most of the reported Alu-mediated CNVs are simple deletions and duplications, and the mechanism underlying Alu-Alu-mediated rearrangement has been attributed to non-allelic homologous recombination (NAHR). Chromosome 17 at the p13.3 genomic region lacks extensive low-copy repeat architecture; however, it is highly enriched for Alu repetitive elements, with a fraction of 30% of total sequence annotated in the human reference genome, compared with the 10% genome-wide and 18% on chromosome 17. We conducted mechanistic studies of the 17p13.3 CNVs by performing high-density oligonucleotide array comparative genomic hybridization, specifically interrogating the 17p13.3 region with ∼150 bp per probe density; CNV breakpoint junctions were mapped to nucleotide resolution by polymerase chain reaction and Sanger sequencing. Studied rearrangements include 5 interstitial deletions, 14 tandem duplications, 7 terminal deletions and 13 complex genomic rearrangements (CGRs). Within the 17p13.3 region, Alu-Alu-mediated rearrangements were identified in 80% of the interstitial deletions, 46% of the tandem duplications and 50% of the CGRs, indicating that this mechanism was a major contributor for formation of breakpoint junctions. Our studies suggest that Alu repetitive elements facilitate formation of non-recurrent CNVs, CGRs and other structural aberrations of chromosome 17 at p13.3. The common observation of Alu-mediated rearrangement in CGRs and breakpoint junction sequences analysis further demonstrates that this type of mechanism is unlikely attributed to NAHR, but rather may be due to a recombination-coupled DNA replicative repair process.
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Affiliation(s)
- Shen Gu
- Department of Molecular & Human Genetics
| | - Bo Yuan
- Department of Molecular & Human Genetics
| | | | | | | | - Sandesh C S Nagamani
- Department of Molecular & Human Genetics, Texas Children's Hospital, Houston, TX 77030, USA and
| | - Ayelet Erez
- Department of Molecular & Human Genetics, Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Carlos A Bacino
- Department of Molecular & Human Genetics, Texas Children's Hospital, Houston, TX 77030, USA and
| | | | | | | | - Weimin Bi
- Department of Molecular & Human Genetics
| | - James R Lupski
- Department of Molecular & Human Genetics, Department of Pediatrics and Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA, Texas Children's Hospital, Houston, TX 77030, USA and
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28
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Abstract
Variant interpretation is a central challenge in genomic medicine. A recent study demonstrates the power of Bayesian statistical approaches to improve interpretation of variants in the context of specific genes and syndromes. Such Bayesian approaches combine frequency (in the form of observed genetic variation in cases and controls) with biological annotations to determine a probability of pathogenicity. These Bayesian approaches complement other efforts to catalog human variation. See related Research; 10.1186/s13073-014-0120-4
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Affiliation(s)
- Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ; Department of Statistics, Rice University, Houston, TX 77005 USA ; Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Startek M, Szafranski P, Gambin T, Campbell IM, Hixson P, Shaw CA, Stankiewicz P, Gambin A. Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination. Nucleic Acids Res 2015; 43:2188-98. [PMID: 25613453 PMCID: PMC4344489 DOI: 10.1093/nar/gku1394] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Nonallelic homologous recombination (NAHR), occurring between low-copy repeats (LCRs) >10 kb in size and sharing >97% DNA sequence identity, is responsible for the majority of recurrent genomic rearrangements in the human genome. Recent studies have shown that transposable elements (TEs) can also mediate recurrent deletions and translocations, indicating the features of substrates that mediate NAHR may be significantly less stringent than previously believed. Using >4 kb length and >95% sequence identity criteria, we analyzed of the genome-wide distribution of long interspersed element (LINE) retrotransposon and their potential to mediate NAHR. We identified 17 005 directly oriented LINE pairs located <10 Mbp from each other as potential NAHR substrates, placing 82.8% of the human genome at risk of LINE-LINE-mediated instability. Cross-referencing these regions with CNVs in the Baylor College of Medicine clinical chromosomal microarray database of 36 285 patients, we identified 516 CNVs potentially mediated by LINEs. Using long-range PCR of five different genomic regions in a total of 44 patients, we confirmed that the CNV breakpoints in each patient map within the LINE elements. To additionally assess the scale of LINE-LINE/NAHR phenomenon in the human genome, we tested DNA samples from six healthy individuals on a custom aCGH microarray targeting LINE elements predicted to mediate CNVs and identified 25 LINE-LINE rearrangements. Our data indicate that LINE-LINE-mediated NAHR is widespread and under-recognized, and is an important mechanism of structural rearrangement contributing to human genomic variability.
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Affiliation(s)
- Michał Startek
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Patricia Hixson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Anna Gambin
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawińskiego street, 02-106 Warsaw, Poland
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Bayer DK, Martinez CA, Sorte HS, Forbes LR, Demmler-Harrison GJ, Hanson IC, Pearson NM, Noroski LM, Zaki SR, Bellini WJ, Leduc MS, Yang Y, Eng CM, Patel A, Rodningen OK, Muzny DM, Gibbs RA, Campbell IM, Shaw CA, Baker MW, Zhang V, Lupski JR, Orange JS, Seeborg FO, Stray-Pedersen A. Vaccine-associated varicella and rubella infections in severe combined immunodeficiency with isolated CD4 lymphocytopenia and mutations in IL7R detected by tandem whole exome sequencing and chromosomal microarray. Clin Exp Immunol 2014; 178:459-69. [PMID: 25046553 PMCID: PMC4238873 DOI: 10.1111/cei.12421] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2014] [Indexed: 12/22/2022] Open
Abstract
In areas without newborn screening for severe combined immunodeficiency (SCID), disease-defining infections may lead to diagnosis, and in some cases, may not be identified prior to the first year of life. We describe a female infant who presented with disseminated vaccine-acquired varicella (VZV) and vaccine-acquired rubella infections at 13 months of age. Immunological evaluations demonstrated neutropenia, isolated CD4 lymphocytopenia, the presence of CD8(+) T cells, poor lymphocyte proliferation, hypergammaglobulinaemia and poor specific antibody production to VZV infection and routine immunizations. A combination of whole exome sequencing and custom-designed chromosomal microarray with exon coverage of primary immunodeficiency genes detected compound heterozygous mutations (one single nucleotide variant and one intragenic copy number variant involving one exon) within the IL7R gene. Mosaicism for wild-type allele (20-30%) was detected in pretransplant blood and buccal DNA and maternal engraftment (5-10%) demonstrated in pretransplant blood DNA. This may be responsible for the patient's unusual immunological phenotype compared to classical interleukin (IL)-7Rα deficiency. Disseminated VZV was controlled with anti-viral and immune-based therapy, and umbilical cord blood stem cell transplantation was successful. Retrospectively performed T cell receptor excision circle (TREC) analyses completed on neonatal Guthrie cards identified absent TREC. This case emphasizes the danger of live viral vaccination in severe combined immunodeficiency (SCID) patients and the importance of newborn screening to identify patients prior to high-risk exposures. It also illustrates the value of aggressive pathogen identification and treatment, the influence newborn screening can have on morbidity and mortality and the significant impact of newer genomic diagnostic tools in identifying the underlying genetic aetiology for SCID patients.
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Affiliation(s)
- D K Bayer
- Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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31
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Abstract
MOTIVATION Set-based network similarity metrics are increasingly used to productively analyze genome-wide data. Conventional approaches, such as mean shortest path and clique-based metrics, have been useful but are not well suited to all applications. Computational scientists in other disciplines have developed communicability as a complementary metric. Network communicability considers all paths of all lengths between two network members. Given the success of previous network analyses of protein-protein interactions, we applied the concepts of network communicability to this problem. Here we show that our communicability implementation has advantages over traditional approaches. Overall, analyses suggest network communicability has considerable utility in analysis of large-scale biological networks. AVAILABILITY AND IMPLEMENTATION We provide our method as an R package for use in both human protein-protein interaction network analyses and analyses of arbitrary networks along with a tutorial at http://www.shawlab.org/NetComm/.
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Affiliation(s)
- Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77054, USA
| | - Regis A James
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77054, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77054, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77054, USA
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32
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Campbell IM, Gambin T, Dittwald P, Beck CR, Shuvarikov A, Hixson P, Patel A, Gambin A, Shaw CA, Rosenfeld JA, Stankiewicz P. Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination. BMC Biol 2014; 12:74. [PMID: 25246103 PMCID: PMC4195946 DOI: 10.1186/s12915-014-0074-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 11/13/2022] Open
Abstract
Background Recurrent rearrangements of the human genome resulting in disease or variation are mainly mediated by non-allelic homologous recombination (NAHR) between low-copy repeats. However, other genomic structures, including AT-rich palindromes and retroviruses, have also been reported to underlie recurrent structural rearrangements. Notably, recurrent deletions of Yq12 conveying azoospermia, as well as non-pathogenic reciprocal duplications, are mediated by human endogenous retroviral elements (HERVs). We hypothesized that HERV elements throughout the genome can serve as substrates for genomic instability and result in human copy-number variation (CNV). Results We developed parameters to identify HERV elements similar to those that mediate Yq12 rearrangements as well as recurrent deletions of 3q13.2q13.31. We used these parameters to identify HERV pairs genome-wide that may cause instability. Our analysis highlighted 170 pairs, flanking 12.1% of the genome. We cross-referenced these predicted susceptibility regions with CNVs from our clinical databases for potentially HERV-mediated rearrangements and identified 78 CNVs. We subsequently molecularly confirmed recurrent deletion and duplication rearrangements at four loci in ten individuals, including reciprocal rearrangements at two loci. Breakpoint sequencing revealed clustering in regions of high sequence identity enriched in PRDM9-mediated recombination hotspot motifs. Conclusions The presence of deletions and reciprocal duplications suggests NAHR as the causative mechanism of HERV-mediated CNV, even though the length and the sequence homology of the HERV elements are less than currently thought to be required for NAHR. We propose that in addition to HERVs, other repetitive elements, such as long interspersed elements, may also be responsible for the formation of recurrent CNVs via NAHR. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0074-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, USA.
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Karaca E, Weitzer S, Pehlivan D, Shiraishi H, Gogakos T, Hanada T, Jhangiani SN, Wiszniewski W, Withers M, Campbell IM, Erdin S, Isikay S, Franco LM, Gonzaga-Jauregui C, Gambin T, Gelowani V, Hunter JV, Yesil G, Koparir E, Yilmaz S, Brown M, Briskin D, Hafner M, Morozov P, Farazi TA, Bernreuther C, Glatzel M, Trattnig S, Friske J, Kronnerwetter C, Bainbridge MN, Gezdirici A, Seven M, Muzny DM, Boerwinkle E, Ozen M, Clausen T, Tuschl T, Yuksel A, Hess A, Gibbs RA, Martinez J, Penninger JM, Lupski JR. Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function. Cell 2014; 157:636-50. [PMID: 24766809 DOI: 10.1016/j.cell.2014.02.058] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 12/19/2013] [Accepted: 02/21/2014] [Indexed: 10/25/2022]
Abstract
CLP1 is a RNA kinase involved in tRNA splicing. Recently, CLP1 kinase-dead mice were shown to display a neuromuscular disorder with loss of motor neurons and muscle paralysis. Human genome analyses now identified a CLP1 homozygous missense mutation (p.R140H) in five unrelated families, leading to a loss of CLP1 interaction with the tRNA splicing endonuclease (TSEN) complex, largely reduced pre-tRNA cleavage activity, and accumulation of linear tRNA introns. The affected individuals develop severe motor-sensory defects, cortical dysgenesis, and microcephaly. Mice carrying kinase-dead CLP1 also displayed microcephaly and reduced cortical brain volume due to the enhanced cell death of neuronal progenitors that is associated with reduced numbers of cortical neurons. Our data elucidate a neurological syndrome defined by CLP1 mutations that impair tRNA splicing. Reduction of a founder mutation to homozygosity illustrates the importance of rare variations in disease and supports the clan genomics hypothesis.
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Affiliation(s)
- Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stefan Weitzer
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hiroshi Shiraishi
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Tasos Gogakos
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Toshikatsu Hanada
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, 1030 Vienna, Austria; Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marjorie Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Serkan Erdin
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sedat Isikay
- Gaziantep Children's Hospital, Gaziantep 27560, Turkey
| | - Luis M Franco
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Violet Gelowani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill V Hunter
- Department of Pediatric Radiology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Gozde Yesil
- Department of Medical Genetics, Bezmialem University, Istanbul 34093, Turkey
| | - Erkan Koparir
- Department of Medical Genetics, Cerrahpasa Medical School of Istanbul University, Istanbul 34098, Turkey
| | - Sarenur Yilmaz
- Istanbul Medeniyet University, Faculty of Medicine, Department of Medical Genetics, Istanbul 34730, Turkey
| | - Miguel Brown
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Daniel Briskin
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Markus Hafner
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Pavel Morozov
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Thalia A Farazi
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Christian Bernreuther
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Siegfried Trattnig
- Department of Radiology, MR Center of Excellence, Medical University of Vienna, Vienna 1090, Austria
| | - Joachim Friske
- Department of Radiology, MR Center of Excellence, Medical University of Vienna, Vienna 1090, Austria
| | - Claudia Kronnerwetter
- Department of Radiology, MR Center of Excellence, Medical University of Vienna, Vienna 1090, Austria
| | - Matthew N Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Cerrahpasa Medical School of Istanbul University, Istanbul 34098, Turkey
| | - Mehmet Seven
- Department of Medical Genetics, Cerrahpasa Medical School of Istanbul University, Istanbul 34098, Turkey
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Mustafa Ozen
- Department of Medical Genetics, Cerrahpasa Medical School of Istanbul University, Istanbul 34098, Turkey
| | | | - Tim Clausen
- Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Adnan Yuksel
- Department of Medical Genetics, Cerrahpasa Medical School of Istanbul University, Istanbul 34098, Turkey
| | - Andreas Hess
- Institute for Experimental Pharmacology, Friedrich-Alexander University Erlangen-Nuremberg, 91054 Erlangen, Germany; Campus Support Facility (CSF), Vienna BioCentre, Vienna 1030, Austria
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Javier Martinez
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, 1030 Vienna, Austria.
| | - Josef M Penninger
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, 1030 Vienna, Austria.
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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Gonzaga-Jauregui C, Lotze T, Jamal L, Penney S, Campbell IM, Pehlivan D, Hunter JV, Woodbury SL, Raymond G, Adesina AM, Jhangiani SN, Reid JG, Muzny DM, Boerwinkle E, Lupski JR, Gibbs RA, Wiszniewski W. Mutations in VRK1 associated with complex motor and sensory axonal neuropathy plus microcephaly. JAMA Neurol 2014; 70:1491-8. [PMID: 24126608 DOI: 10.1001/jamaneurol.2013.4598] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Patients with rare diseases and complex clinical presentations represent a challenge for clinical diagnostics. Genomic approaches are allowing the identification of novel variants in genes for very rare disorders, enabling a molecular diagnosis. Genomics is also revealing a phenotypic expansion whereby the full spectrum of clinical expression conveyed by mutant alleles at a locus can be better appreciated. OBJECTIVE To elucidate the molecular cause of a complex neuropathy phenotype in 3 patients by applying genomic sequencing strategies. DESIGN, SETTING, AND PARTICIPANTS Three affected individuals from 2 unrelated families presented with a complex neuropathy phenotype characterized by axonal sensorimotor neuropathy and microcephaly. They were recruited into the Centers for Mendelian Genomics research program to identify the molecular cause of their phenotype. Whole-genome, targeted whole-exome sequencing, and high-resolution single-nucleotide polymorphism arrays were performed in genetics clinics of tertiary care pediatric hospitals and biomedical research institutions. MAIN OUTCOMES AND MEASURES Whole-genome and whole-exome sequencing identified the variants responsible for the patients' clinical phenotype. RESULTS We identified compound heterozygous alleles in 2 affected siblings from 1 family and a homozygous nonsense variant in the third unrelated patient in the vaccinia-related kinase 1 gene (VRK1). In the latter subject, we found a common haplotype on which the nonsense mutation occurred and that segregates in the Ashkenazi Jewish population. CONCLUSIONS AND RELEVANCE We report the identification of disease-causing alleles in 3 children from 2 unrelated families with a previously uncharacterized complex axonal motor and sensory neuropathy accompanied by severe nonprogressive microcephaly and cerebral dysgenesis. Our data raise the question of whether VRK1 mutations disturb cell cycle progression and may result in apoptosis of cells in the nervous system. The application of unbiased genomic approaches allows the identification of potentially pathogenic mutations in unsuspected genes in highly genetically heterogeneous and uncharacterized neurological diseases.
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Affiliation(s)
| | | | - Leila Jamal
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland
| | - Samantha Penney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas2Texas Children's Hospital, Houston
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | | | - Gerald Raymond
- Department of Neurology, University of Minnesota, Minneapolis
| | | | | | - Jeffrey G Reid
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas6Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas2Texas Children's Hospital, Houston5Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas5Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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35
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Campbell IM, Rao M, Arredondo SD, Lalani SR, Xia Z, Kang SHL, Bi W, Breman AM, Smith JL, Bacino CA, Beaudet AL, Patel A, Cheung SW, Lupski JR, Stankiewicz P, Ramocki MB, Shaw CA. Fusion of large-scale genomic knowledge and frequency data computationally prioritizes variants in epilepsy. PLoS Genet 2013; 9:e1003797. [PMID: 24086149 PMCID: PMC3784560 DOI: 10.1371/journal.pgen.1003797] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022] Open
Abstract
Curation and interpretation of copy number variants identified by genome-wide testing is challenged by the large number of events harbored in each personal genome. Conventional determination of phenotypic relevance relies on patterns of higher frequency in affected individuals versus controls; however, an increasing amount of ascertained variation is rare or private to clans. Consequently, frequency data have less utility to resolve pathogenic from benign. One solution is disease-specific algorithms that leverage gene knowledge together with variant frequency to aid prioritization. We used large-scale resources including Gene Ontology, protein-protein interactions and other annotation systems together with a broad set of 83 genes with known associations to epilepsy to construct a pathogenicity score for the phenotype. We evaluated the score for all annotated human genes and applied Bayesian methods to combine the derived pathogenicity score with frequency information from our diagnostic laboratory. Analysis determined Bayes factors and posterior distributions for each gene. We applied our method to subjects with abnormal chromosomal microarray results and confirmed epilepsy diagnoses gathered by electronic medical record review. Genes deleted in our subjects with epilepsy had significantly higher pathogenicity scores and Bayes factors compared to subjects referred for non-neurologic indications. We also applied our scores to identify a recently validated epilepsy gene in a complex genomic region and to reveal candidate genes for epilepsy. We propose a potential use in clinical decision support for our results in the context of genome-wide screening. Our approach demonstrates the utility of integrative data in medical genomics.
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Affiliation(s)
- Ian M. Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mitchell Rao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sean D. Arredondo
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Zhilian Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sung-Hae L. Kang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Amy M. Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Janice L. Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Melissa B. Ramocki
- Texas Children's Hospital, Houston, Texas, United States of America
- Department of Pediatrics, Section of Pediatric Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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36
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Shuvarikov A, Campbell IM, Dittwald P, Neill NJ, Bialer MG, Moore C, Wheeler PG, Wallace SE, Hannibal MC, Murray MF, Giovanni MA, Terespolsky D, Sodhi S, Cassina M, Viskochil D, Moghaddam B, Herman K, Brown CW, Beck CR, Gambin A, Cheung SW, Patel A, Lamb AN, Shaffer LG, Ellison JW, Ravnan JB, Stankiewicz P, Rosenfeld JA. Recurrent HERV-H-mediated 3q13.2-q13.31 deletions cause a syndrome of hypotonia and motor, language, and cognitive delays. Hum Mutat 2013; 34:1415-23. [PMID: 23878096 DOI: 10.1002/humu.22384] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/11/2013] [Indexed: 11/09/2022]
Abstract
We describe the molecular and clinical characterization of nine individuals with recurrent, 3.4-Mb, de novo deletions of 3q13.2-q13.31 detected by chromosomal microarray analysis. All individuals have hypotonia and language and motor delays; they variably express mild to moderate cognitive delays (8/9), abnormal behavior (7/9), and autism spectrum disorders (3/9). Common facial features include downslanting palpebral fissures with epicanthal folds, a slightly bulbous nose, and relative macrocephaly. Twenty-eight genes map to the deleted region, including four strong candidate genes, DRD3, ZBTB20, GAP43, and BOC, with important roles in neural and/or muscular development. Analysis of the breakpoint regions based on array data revealed directly oriented human endogenous retrovirus (HERV-H) elements of ~5 kb in size and of >95% DNA sequence identity flanking the deletion. Subsequent DNA sequencing revealed different deletion breakpoints and suggested nonallelic homologous recombination (NAHR) between HERV-H elements as a mechanism of deletion formation, analogous to HERV-I-flanked and NAHR-mediated AZFa deletions. We propose that similar HERV elements may also mediate other recurrent deletion and duplication events on a genome-wide scale. Observation of rare recurrent chromosomal events such as these deletions helps to further the understanding of mechanisms behind naturally occurring variation in the human genome and its contribution to genetic disease.
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Affiliation(s)
- Andrey Shuvarikov
- Signature Genomic Laboratories, PerkinElmer, Inc, Spokane, Washington
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Wiszniewski W, Hunter J, Hanchard N, Willer J, Shaw C, Tian Q, Illner A, Wang X, Cheung S, Patel A, Campbell IM, Gelowani V, Hixson P, Ester A, Azamian M, Potocki L, Zapata G, Hernandez P, Ramocki M, Santos-Cortez R, Wang G, York M, Justice MJ, Chu Z, Bader P, Omo-Griffith L, Madduri N, Scharer G, Crawford H, Yanatatsaneejit P, Eifert A, Kerr J, Bacino C, Franklin A, Goin-Kochel RP, Simpson G, Immken L, Haque M, Stosic M, Williams M, Morgan T, Pruthi S, Omary R, Boyadjiev S, Win K, Thida A, Hurles M, Hibberd M, Khor C, Van Vinh Chau N, Gallagher T, Mutirangura A, Stankiewicz P, Beaudet A, Maletic-Savatic M, Rosenfeld J, Shaffer L, Davis E, Belmont J, Dunstan S, Simmons CP, Bonnen PE, Leal S, Katsanis N, Lupski J, Lalani S. TM4SF20 ancestral deletion and susceptibility to a pediatric disorder of early language delay and cerebral white matter hyperintensities. Am J Hum Genet 2013; 93:197-210. [PMID: 23810381 DOI: 10.1016/j.ajhg.2013.05.027] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/07/2013] [Accepted: 05/30/2013] [Indexed: 11/26/2022] Open
Abstract
White matter hyperintensities (WMHs) of the brain are important markers of aging and small-vessel disease. WMHs are rare in healthy children and, when observed, often occur with comorbid neuroinflammatory or vasculitic processes. Here, we describe a complex 4 kb deletion in 2q36.3 that segregates with early childhood communication disorders and WMH in 15 unrelated families predominantly from Southeast Asia. The premature brain aging phenotype with punctate and multifocal WMHs was observed in ~70% of young carrier parents who underwent brain MRI. The complex deletion removes the penultimate exon 3 of TM4SF20, a gene encoding a transmembrane protein of unknown function. Minigene analysis showed that the resultant net loss of an exon introduces a premature stop codon, which, in turn, leads to the generation of a stable protein that fails to target to the plasma membrane and accumulates in the cytoplasm. Finally, we report this deletion to be enriched in individuals of Vietnamese Kinh descent, with an allele frequency of about 1%, embedded in an ancestral haplotype. Our data point to a constellation of early language delay and WMH phenotypes, driven by a likely toxic mechanism of TM4SF20 truncation, and highlight the importance of understanding and managing population-specific low-frequency pathogenic alleles.
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Harrison SM, Campbell IM, Keays M, Granberg CF, Villanueva C, Tannin G, Zinn AR, Castrillon DH, Shaw CA, Stankiewicz P, Baker LA. Screening and familial characterization of copy-number variations in NR5A1 in 46,XY disorders of sex development and premature ovarian failure. Am J Med Genet A 2013; 161A:2487-94. [PMID: 23918653 DOI: 10.1002/ajmg.a.36084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 05/12/2013] [Indexed: 11/08/2022]
Abstract
The NR5A1 gene encodes for steroidogenic factor 1, a nuclear receptor that regulates proper adrenal and gonadal development and function. Mutations identified by NR5A1 sequencing have been associated with disorders of sex development (DSD), ranging from sex reversal to severe hypospadias in 46,XY patients and premature ovarian failure (POF) in 46,XX patients. Previous reports have identified four families with a history of both 46,XY DSD and 46,XX POF carrying segregating NR5A1 sequence mutations. Recently, three 46,XY DSD sporadic cases with NR5A1 microdeletions have been reported. Here, we identify the first NR5A1 microdeletion transmitted in a pedigree with both 46,XY DSD and 46,XX POF. A 46,XY individual with DSD due to gonadal dysgenesis was born to a young mother who developed POF. Array CGH analysis revealed a maternally inherited 0.23 Mb microdeletion of chromosome 9q33.3, including the NR5A1 gene. Based on this finding, we screened patients with unexplained 46,XY DSD (n = 11), proximal hypospadias (n = 21) and 46,XX POF (n = 36) for possible NR5A1 copy-number variations (CNVs) via multiplex ligation-dependent probe amplification (MLPA), but did not identify any additional CNVs involving NR5A1. These data suggest that NR5A1 CNVs are an infrequent cause of these disorders but that array CGH and MLPA are useful genomic screening tools to uncover the genetic basis of such unexplained cases. This case is the first report of a familial NR5A1 CNV transmitting in a pedigree, causing both the male and female phenotypes associated with NR5A1 mutations, and the first report of a NR5A1 CNV associated with POF.
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Affiliation(s)
- Steven M Harrison
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
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Boone PM, Campbell IM, Baggett BC, Soens ZT, Rao MM, Hixson PM, Patel A, Bi W, Cheung SW, Lalani SR, Beaudet AL, Stankiewicz P, Shaw CA, Lupski JR. Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles. Genome Res 2013; 23:1383-94. [PMID: 23685542 PMCID: PMC3759716 DOI: 10.1101/gr.156075.113] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Over 1200 recessive disease genes have been described in humans. The prevalence, allelic architecture, and per-genome load of pathogenic alleles in these genes remain to be fully elucidated, as does the contribution of DNA copy-number variants (CNVs) to carrier status and recessive disease. We mined CNV data from 21,470 individuals obtained by array-comparative genomic hybridization in a clinical diagnostic setting to identify deletions encompassing or disrupting recessive disease genes. We identified 3212 heterozygous potential carrier deletions affecting 419 unique recessive disease genes. Deletion frequency of these genes ranged from one occurrence to 1.5%. When compared with recessive disease genes never deleted in our cohort, the 419 recessive disease genes affected by at least one carrier deletion were longer and located farther from known dominant disease genes, suggesting that the formation and/or prevalence of carrier CNVs may be affected by both local and adjacent genomic features and by selection. Some subjects had multiple carrier CNVs (307 subjects) and/or carrier deletions encompassing more than one recessive disease gene (206 deletions). Heterozygous deletions spanning multiple recessive disease genes may confer carrier status for multiple single-gene disorders, for complex syndromes resulting from the combination of two or more recessive conditions, or may potentially cause clinical phenotypes due to a multiply heterozygous state. In addition to carrier mutations, we identified homozygous and hemizygous deletions potentially causative for recessive disease. We provide further evidence that CNVs contribute to the allelic architecture of both carrier and recessive disease-causing mutations. Thus, a complete recessive carrier screening method or diagnostic test should detect CNV alleles.
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Affiliation(s)
- Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Chotewutmontri P, Reddick LE, McWilliams DR, Campbell IM, Bruce BD. Differential transit peptide recognition during preprotein binding and translocation into flowering plant plastids. Plant Cell 2012; 24:3040-59. [PMID: 22829148 PMCID: PMC3426131 DOI: 10.1105/tpc.112.098327] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 06/04/2012] [Accepted: 07/09/2012] [Indexed: 05/03/2023]
Abstract
Despite the availability of thousands of transit peptide (TP) primary sequences, the structural and/or physicochemical properties that determine TP recognition by components of the chloroplast translocon are not well understood. By combining a series of in vitro and in vivo experiments, we reveal that TP recognition is determined by sequence-independent interactions and vectorial-specific recognition domains. Using both native and reversed TPs for two well-studied precursors, small subunit of ribulose-1,5-bis-phosphate carboxylase/oxygenase, and ferredoxin, we exposed these two modes of recognition. Toc34 receptor (34-kD subunit of the translocon of the outer envelope) recognition in vitro, preprotein binding in organellar, precursor binding in vivo, and the recognition of TPs by the major stromal molecular motor Hsp70 are specific for the physicochemical properties of the TP. However, translocation in organellar and in vivo demonstrates strong specificity to recognition domain organization. This organization specificity correlates with the N-terminal placement of a strong Hsp70 recognition element. These results are discussed in light of how individual translocon components sequentially interact with the precursor during binding and translocation and helps explain the apparent lack of sequence conservation in chloroplast TPs.
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Affiliation(s)
- Prakitchai Chotewutmontri
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996
| | - L. Evan Reddick
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - David R. McWilliams
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996
| | - Ian M. Campbell
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Barry D. Bruce
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
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Campbell IM, Yatsenko SA, Hixson P, Reimschisel T, Thomas M, Wilson W, Dayal U, Wheless JW, Crunk A, Curry C, Parkinson N, Fishman L, Riviello JJ, Nowaczyk MJM, Zeesman S, Rosenfeld JA, Bejjani BA, Shaffer LG, Cheung SW, Lupski JR, Stankiewicz P, Scaglia F. Novel 9q34.11 gene deletions encompassing combinations of four Mendelian disease genes: STXBP1, SPTAN1, ENG, and TOR1A. Genet Med 2012; 14:868-76. [PMID: 22722545 DOI: 10.1038/gim.2012.65] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
PURPOSE A number of genes in the 9q34.11 region may be haploinsufficient. However, studies analyzing genotype-phenotype correlations of deletions encompassing multiple dosage-sensitive genes in the region are lacking. METHODS We mapped breakpoints of 10 patients with 9q34.11 deletions using high-resolution 9q34-specific array comparative genomic hybridization (CGH) to determine deletion size and gene content. RESULTS The 9q34.11 deletions range in size from 67 kb to 2.8 Mb. Six patients exhibit intellectual disability and share a common deleted region including STXBP1; four manifest variable epilepsy. In five subjects, deletions include SPTAN1, previously associated with early infantile epileptic encephalopathy, infantile spasms, intellectual disability, and hypomyelination. In four patients, the deletion includes endoglin (ENG), causative of hereditary hemorrhagic telangiectasia. Finally, in four patients, deletions involve TOR1A, of which molecular defects lead to early-onset primary dystonia. Ninety-four other RefSeq genes also map to the genomic intervals investigated. CONCLUSION STXBP1 haploinsufficiency results in progressive encephalopathy characterized by intellectual disability and may be accompanied by epilepsy, movement disorders, and autism. We propose that 9q34.11 genomic deletions involving ENG, TOR1A, STXBP1, and SPTAN1 are responsible for multisystemic vascular dysplasia, early-onset primary dystonia, epilepsy, and intellectual disability, therefore revealing cis-genetic effects leading to complex phenotypes.
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Affiliation(s)
- Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Campbell IM, Kolodziejska KE, Quach MM, Wolf VL, Cheung SW, Lalani SR, Ramocki MB, Stankiewicz P. TGFBR2 deletion in a 20-month-old female with developmental delay and microcephaly. Am J Med Genet A 2011; 155A:1442-7. [PMID: 21567932 DOI: 10.1002/ajmg.a.34015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 03/07/2011] [Indexed: 11/07/2022]
Abstract
To date, over 70 mutations in the TGFBR2 gene have been reported in patients with Loeys-Dietz syndrome (LDS), Marfan syndrome type 2 (MFS2), or other hereditary thoracic aortic aneurysms and dissections. Whereas almost all of mutations analyzed thus far are predicted to disrupt the constitutively active C-terminal serine/threonine kinase domain of TGFBR2, mounting evidence suggests that the molecular mechanism underlying these diseases is more complex than simple haploinsufficiency. Using exon-targeted oligonucleotide array comparative genomic hybridization, we identified an ∼896 kb deletion of TGFBR2 in a 20-month-old female with microcephaly and global developmental delay, but no stigmata of LDS. FISH analysis showed no evidence of this deletion in the parental peripheral blood samples; however, somatic mosaicism was detected using PCR in the paternal DNA from peripheral blood lymphocytes and lymphoblasts. Our data suggest that TGFBR2 haploinsufficiency may cause a phenotype, which is distinct from LDS. Moreover, we propose that somatic mosaicism below the detection threshold of FISH analysis in asymptomatic parents of children with genomic disorders may be more common than previously recognized.
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Affiliation(s)
- Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Bartman CD, Doerfler DL, Bird BA, Remaley AT, Peace JN, Campbell IM. Mycophenolic Acid Production by Penicillium brevicompactum on Solid Media. Appl Environ Microbiol 2010; 41:729-36. [PMID: 16345733 PMCID: PMC243768 DOI: 10.1128/aem.41.3.729-736.1981] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When grown on Czapek-Dox agar, Penicillium brevicompactum produced mycophenolic acid after a vegetative mycelium had been formed and as aerial hyphae were developing. Nutrients were still plenteous in the agar when the synthesis began. If aerial hyphal development was prevented by placing a dialysis membrane over the growing fungus, no mycophenolic acid was produced. When the dialysis membrane was peeled back and, as a consequence, production of aerial hyphae began, mycophenolic acid biosynthesis was observed. We concluded that mycophenolic acid was produced only by P. brevicompactum colonies that possessed an aerial mycelium.
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Affiliation(s)
- C D Bartman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
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Abstract
A unique aspect of protein transport into plastids is the coordinate involvement of two GTPases in the translocon of the outer chloroplast membrane (Toc). There are two subfamilies in Arabidopsis, the small GTPases (Toc33 and Toc34) and the large acidic GTPases (Toc90, Toc120, Toc132, and Toc159). In chloroplasts, Toc34 and Toc159 are implicated in precursor binding, yet mechanistic details are poorly understood. How the GTPase cycle is modulated by precursor binding is complex and in need of careful dissection. To this end, we have developed novel in vitro assays to quantitate nucleotide binding and hydrolysis of the Toc GTPases. Here we present the first systematic kinetic characterization of four Toc GTPases (cytosolic domains of atToc33, atToc34, psToc34, and the GTPase domain of atToc159) to permit their direct comparison. We report the KM, Vmax, and Ea values for GTP hydrolysis and the Kd value for nucleotide binding for each protein. We demonstrate that GTP hydrolysis by psToc34 is stimulated by chloroplast transit peptides; however, this activity is not stimulated by homodimerization and is abolished by the R133A mutation. Furthermore, we show peptide stimulation of hydrolytic rates are not because of accelerated nucleotide exchange, indicating that transit peptides function as GTPase-activating proteins and not guanine nucleotide exchange factors in modulating the activity of psToc34. Finally, by using the psToc34 structure, we have developed molecular models for atToc33, atToc34, and atToc159G. By combining these models with the measured enzymatic properties of the Toc GTPases, we provide new insights of how the chloroplast protein import cycle may be regulated.
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Affiliation(s)
- L Evan Reddick
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville 37996, USA
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Rosenblum ER, Stauber RE, Van Thiel DH, Campbell IM, Gavaler JS. Assessment of the estrogenic activity of phytoestrogens isolated from bourbon and beer. Alcohol Clin Exp Res 1993; 17:1207-9. [PMID: 8116832 DOI: 10.1111/j.1530-0277.1993.tb05230.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Phytoestrogenic substances have previously been isolated and identified in two alcoholic beverages: bourbon and beer. To delineate the relative potencies of the estrogenic substances of plant origin thus far identified in these commonly consumed alcoholic beverages, we evaluated the ability of biochanin A, beta-sitosterol, genistein, and daidzein to bind to cytosolic estrogen receptor binding sites. The in vitro studies demonstrated that each of the contained substances was capable of effectively competing for cytosolic estrogen receptor binding sites of rat liver and uterus. Further, the two phytoestrogenic constituents of bourbon, beta-sitosterol and biochanin A, were less potent than those present in beer. Given the high concentration of beta-sitosterol in bourbon, we chose to evaluate the estrogenicity of beta-sitosterol in vivo using ovariectomized rats. beta-sitosterol was administered either daily or intermittently at 3 doses, based on amounts previously determined to be present in bourbon. The in vivo studies demonstrated that beta-sitosterol is capable of producing a weak estrogenic effect only at the lowest dose (6.2 micrograms/dl) administered intermittently. These responses suggest that beta-sitosterol may be weakly estrogenic at low doses, but is unable to maintain such an effect at higher doses.
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Affiliation(s)
- E R Rosenblum
- Oklahoma Transplant Institute, Baptist Medical Center, Oklahoma City 73112
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Abstract
Two estrogenic substances of plant origin have been identified in beer using gas chromatography/mass spectrometry. These phytoestrogens, daidzein and genistein, have previously been shown to be biologically active in animals. Confirming the presence of biologically active phytoestrogens in beer and their possible presence in other beverages, suggests that there may be clinically significant effects related to sustained exposure to phytoestrogens contained in alcoholic beverages.
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Affiliation(s)
- E R Rosenblum
- Department of Medicine, University of Pittsburgh School of Medicine, PA
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Abstract
Four phytoestrogens have previously been isolated and identified in alcoholic beverages. Before studies to evaluate the degree of estrogenicity of these substances can be performed, it is necessary to determine appropriate doses to be administered to experimental animals. Because beta-sitosterol is the most plentiful, being present in bourbon at microgram/dl quantities, we have chosen to begin our quantitation work with this compound. The variability of the amount of beta-sitosterol contained in various brands of bourbon and in different lots of the same brand of bourbon have been assessed using combined gas chromatography/mass spectrometry (GC/MS) for quantitation following a simplified procedure to extract compounds of interest from bourbon.
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Affiliation(s)
- E R Rosenblum
- Department of Medicine, University of Pittsburgh School of Medicine, PA 15261
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48
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Abstract
In the present study an assessment strategy was developed which adapted the Articulated Thoughts during Simulated Situations (ATSS) paradigm devised by Davison, Robins & Johnson (1983). That strategy was applied to the assessment of social anxiety. Responses of 10 socially anxious and 10 non-anxious males were compared as they imagined themselves participating in videotaped simulations of heterosocial interactions. Each time the subject was aware of a reaction to the events depicted, he stopped the videotape, and then articulated his thoughts. Consistent with cognitive conceptualizations of social anxiety, the articulated thoughts of anxious males were distinguished by a greater focus upon the self in general and by a concentration upon irrational concerns in particular. In contrast, non-anxious males provided larger proportions of thoughts directed towards the environment and in particular, provided more positive thoughts both about other persons and their interactions in general. The theoretical and methodological implications of the data are discussed.
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Affiliation(s)
- G W Bates
- Department of Psychology, University of Melbourne, Parkville, Victoria, Australia
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Campbell IM. Does climate affect host-plant quality? Annual variation in the quality of balsam fir as food for spruce budworm. Oecologia 1989; 81:341-344. [DOI: 10.1007/bf00377081] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/1989] [Accepted: 06/14/1989] [Indexed: 11/28/2022]
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Abstract
The present study aimed to determine whether the negative symptoms of patients with schizophrenia were better predictors of social competence than a range of other variables pertaining to demographics, illness, hospitalization, and premorbid functioning. Independent raters assessed social skills performance on a video-taped role-play test and 5 min conversation in 53 inpatients with a DSM-III diagnosis of schizophrenia. Patients' social skills were also assessed by ward nurses. Project clinicians assessed depression, medication side effects and positive and negative symptoms. Multiple-regression analyses demonstrated that, generally, negative symptoms were the best predictors of social skills performance.
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Affiliation(s)
- H J Jackson
- National Health and Medical Research Council Schizophrenia Research Unit, Royal Park Hospital, Parkville, Australia
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