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Schubert C, Milverton J, Goodall S, Merlin T. A systematic review to assess the utility of genomic autopsy using exome or genome sequencing in cases of congenital anomalies and perinatal death. Genet Med 2024; 26:101159. [PMID: 38704678 DOI: 10.1016/j.gim.2024.101159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024] Open
Abstract
PURPOSE Exome or genome sequencing (ES or GS) can identify genetic causes of otherwise unexplained congenital anomaly and perinatal death (PND) but is not routine practice. The evidence base for "genomic autopsy" after termination of pregnancy for fetal anomaly (TOPFA) and PND has been synthesized to determine the value of this investigation. METHODS We conducted a systematic review and meta-analysis of studies meeting prespecified inclusion criteria and containing ≥10 cases of TOPFA or PND (with or without major congenital abnormality), in which ES or GS was conducted. We determined test performance, including diagnostic yield, accuracy, and reliability. We also reported outcomes associated with clinical utility and harms, where described. RESULTS From 2245 potentially eligible studies, 32 publications were eligible and had data extracted, representing 2120 cases that could be meta-analyzed. No diagnostic accuracy or comparative studies were identified, although some analysis of concordance between different ES/GS methodologies could be performed. Studies reporting parent-related outcomes or long-term follow-up did not do so in a systematic or quantifiable manner. CONCLUSION Evidence suggests that approximately one-fourth to one-third of fetal losses associated with TOPFA or unexplained PND are associated with a genetic cause identifiable on ES or GS-albeit this estimate varies depending on phenotypic and background risk factors. Despite the large body of evidence on ES and GS, little research has attempted to validate the accuracy of testing, nor measure the clinical or societal outcomes in families that follow the diagnostic investigation in this context.
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Affiliation(s)
- Camille Schubert
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia.
| | - Joanne Milverton
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia
| | - Stephen Goodall
- Centre for Health Economics Research and Evaluation, Faculty of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Tracy Merlin
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia
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2
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Fortin O, Mulkey SB, Fraser JL. Advancing fetal diagnosis and prognostication using comprehensive prenatal phenotyping and genetic testing. Pediatr Res 2024:10.1038/s41390-024-03343-9. [PMID: 38937640 DOI: 10.1038/s41390-024-03343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/14/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
Prenatal diagnoses of congenital malformations have increased significantly in recent years with use of high-resolution prenatal imaging. Despite more precise radiological diagnoses, discussions with expectant parents remain challenging because congenital malformations are associated with a wide spectrum of outcomes. Comprehensive prenatal genetic testing has become an essential tool that improves the accuracy of prognostication. Testing strategies include chromosomal microarray, exome sequencing, and genome sequencing. The diagnostic yield varies depending on the specific malformations, severity of the abnormalities, and multi-organ involvement. The utility of prenatal genetic diagnosis includes increased diagnostic clarity for clinicians and families, informed pregnancy decision-making, neonatal care planning, and reproductive planning. Turnaround time for results of comprehensive genetic testing remains a barrier, especially for parents that are decision-making, although this has improved over time. Uncertainty inherent to many genetic testing results is a challenge. Appropriate genetic counseling is essential for parents to understand the diagnosis and prognosis and to make informed decisions. Recent research has investigated the yield of exome or genome sequencing in structurally normal fetuses, both with non-invasive screening methods and invasive diagnostic testing; the prenatal diagnostic community must evaluate and analyze the significant ethical considerations associated with this practice prior to generalizing its use. IMPACT: Reviews available genetic testing options during the prenatal period in detail. Discusses the impact of prenatal genetic testing on care using case-based examples. Consolidates the current literature on the yield of genetic testing for prenatal diagnosis of congenital malformations.
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Affiliation(s)
- Olivier Fortin
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
| | - Sarah B Mulkey
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
- Department of Neurology and Rehabilitation Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jamie L Fraser
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA.
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA.
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
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3
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Blayney GV, Laffan E, Jacob PA, Baptiste CD, Gabriel H, Sparks TN, Yaron Y, Norton ME, Diderich K, Wang Y, Chong K, Chitayat D, Saini N, Aggarwal S, Pauta M, Borrell A, Gilmore K, Chandler NJ, Allen S, Vora N, Noor A, Monaghan C, Kilby MD, Wapner RJ, Chitty LS, Mone F. Monogenic conditions and central nervous system anomalies: A prospective study, systematic review and meta-analysis. Prenat Diagn 2024; 44:422-431. [PMID: 38054560 PMCID: PMC11044826 DOI: 10.1002/pd.6466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 12/07/2023]
Abstract
OBJECTIVES Determine the incremental diagnostic yield of prenatal exome sequencing (pES) over chromosome microarray (CMA) or G-banding karyotype in fetuses with central nervous system (CNS) abnormalities. METHODS Data were collected via electronic searches from January 2010 to April 2022 in MEDLINE, Cochrane, Web of Science and EMBASE. The NHS England prenatal exome cohort was also included. Incremental yield was calculated as a pooled value using a random-effects model. RESULTS Thirty studies were included (n = 1583 cases). The incremental yield with pES for any CNS anomaly was 32% [95%CI 27%-36%; I2 = 72%]. Subgroup analysis revealed apparent incremental yields in; (a) isolated CNS anomalies; 27% [95%CI 19%-34%; I2 = 74%]; (b) single CNS anomaly; 16% [95% CI 10%-23%; I2 = 41%]; (c) more than one CNS anomaly; 31% [95% Cl 21%-40%; I2 = 56%]; and (d) the anatomical subtype with the most optimal yield was Type 1 malformation of cortical development, related to abnormal cell proliferation or apoptosis, incorporating microcephalies, megalencephalies and dysplasia; 40% (22%-57%; I2 = 68%). The commonest syndromes in isolated cases were Lissencephaly 3 and X-linked hydrocephalus. CONCLUSIONS Prenatal exome sequencing provides a high incremental diagnostic yield in fetuses with CNS abnormalities with optimal yields in cases with multiple CNS anomalies, particularly those affecting the midline, posterior fossa and cortex.
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Affiliation(s)
- Gillian V. Blayney
- Fetal Medicine Department, Royal Jubilee Maternity Service, Belfast Health and Social Care Trust, Belfast, UK
| | - Eoghan Laffan
- Department of Radiology, Children’ Health Ireland at Crumlin, Dublin, Ireland
| | | | | | | | - Teresa N. Sparks
- Department of Obstetrics, Gynaecology & Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
| | - Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mary E. Norton
- Department of Obstetrics, Gynaecology & Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
| | - Karin Diderich
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Yiming Wang
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Karen Chong
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics & Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics & Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Neelam Saini
- Department of Medical Genetics, Nizam’s Institute of Medical Sciences, Hyderabad, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam’s Institute of Medical Sciences, Hyderabad, India
| | - Montse Pauta
- Insitut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), BCNatal, Barcelona, Spain
| | - Antoni Borrell
- Insitut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), BCNatal, Barcelona, Spain
| | - Kelly Gilmore
- Department of Obstetrics and Gynaecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, South and Central Genomic Laboratory Hub, Birmingham, UK
| | - Neeta Vora
- Department of Obstetrics and Gynaecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Abdul Noor
- Division of Diagnostic Medical Genetics, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Caitriona Monaghan
- Fetal Medicine Department, Royal Jubilee Maternity Service, Belfast Health and Social Care Trust, Belfast, UK
| | - Mark D. Kilby
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
- Fetal Medicine Centre, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | | | - Lyn S. Chitty
- North Thames Genomic Laboratory Hub, NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Fionnuala Mone
- Centre for Public Health, Queen’s University Belfast, Belfast, UK
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4
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Mustafa HJ, Barbera JP, Sambatur EV, Pagani G, Yaron Y, Baptiste CD, Wapner RJ, Brewer CJ, Khalil A. Diagnostic yield of exome sequencing in prenatal agenesis of corpus callosum: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:312-320. [PMID: 37519216 DOI: 10.1002/uog.27440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/25/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
OBJECTIVES To determine the incremental diagnostic yield of exome sequencing (ES) after negative chromosomal microarray analysis (CMA) in cases of prenatally diagnosed agenesis of the corpus callosum (ACC) and to identify the associated genes and variants. METHODS A systematic search was performed to identify relevant studies published up until June 2022 using four databases: PubMed, SCOPUS, Web of Science and The Cochrane Library. Studies in English reporting on the diagnostic yield of ES following negative CMA in prenatally diagnosed partial or complete ACC were included. Authors of cohort studies were contacted for individual participant data and extended cohorts were provided for two of them. The increase in diagnostic yield with ES for pathogenic/likely pathogenic (P/LP) variants was assessed in all cases of ACC, isolated ACC, ACC with other cranial anomalies and ACC with extracranial anomalies. To identify all reported genetic variants, the systematic review included all ACC cases; however, for the meta-analysis, only studies with ≥ three ACC cases were included. Meta-analysis of proportions was employed using a random-effects model. Quality assessment of the included studies was performed using modified Standards for Reporting of Diagnostic Accuracy criteria. RESULTS A total of 28 studies, encompassing 288 prenatally diagnosed ACC cases that underwent ES following negative CMA, met the inclusion criteria of the systematic review. We classified 116 genetic variants in 83 genes associated with prenatal ACC with a full phenotypic description. There were 15 studies, encompassing 268 cases, that reported on ≥ three ACC cases and were included in the meta-analysis. Of all the included cases, 43% had a P/LP variant on ES. The highest yield was for ACC with extracranial anomalies (55% (95% CI, 35-73%)), followed by ACC with other cranial anomalies (43% (95% CI, 30-57%)) and isolated ACC (32% (95% CI, 18-51%)). CONCLUSIONS ES demonstrated an incremental diagnostic yield in cases of prenatally diagnosed ACC following negative CMA. While the greatest diagnostic yield was observed in ACC with extracranial anomalies and ACC with other central nervous system anomalies, ES should also be considered in cases of isolated ACC. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- H J Mustafa
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Riley Children and Indiana University Health Fetal Center, Indianapolis, IN, USA
| | - J P Barbera
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - E V Sambatur
- Research Division, Houston Center for Maternal Fetal Medicine, Houston, TX, USA
| | - G Pagani
- Maternal Fetal Medicine Unit, Department of Obstetrics and Gynecology, ASST-Papa Giovanni XXIII, Bergamo, Italy
| | - Y Yaron
- Prenatal Genetic Diagnosis Unit, Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - C D Baptiste
- Obstetrics and Gynecology, Reproductive Genetics, Columbia University Medical Center, New York, NY, USA
| | - R J Wapner
- Obstetrics and Gynecology, Reproductive Genetics, Columbia University Medical Center, New York, NY, USA
| | - C J Brewer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - A Khalil
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, University of London, London, UK
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
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5
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Zhao E, Bomback M, Khan A, Murthy SK, Solowiejczyk D, Vora NL, Gilmore KL, Giordano JL, Wapner RJ, Sanna-Cherchi S, Lyford A, Jelin AC, Gharavi AG, Hays T. The expanded spectrum of human disease associated with GREB1L likely includes complex congenital heart disease. Prenat Diagn 2024; 44:343-351. [PMID: 38285371 PMCID: PMC11040453 DOI: 10.1002/pd.6527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
OBJECTIVE GREB1L has been linked prenatally to Potter's sequence, as well as less severe anomalies of the kidney, uterus, inner ear, and heart. The full phenotypic spectrum is unknown. The purpose of this study was to characterize known and novel pre- and postnatal phenotypes associated with GREB1L. METHODS We solicited cases from the Fetal Sequencing Consortium, screened a population-based genomic database, and conducted a comprehensive literature search to identify disease cases associated with GREB1L. We present a detailed phenotypic spectrum and molecular changes. RESULTS One hundred twenty-seven individuals with 51 unique pathogenic or likely pathogenic GREB1L variants were identified. 24 (47%) variants were associated with isolated kidney anomalies, 19 (37%) with anomalies of multiple systems, including one case of hypoplastic left heart syndrome, five (10%) with isolated sensorineural hearing loss, two (4%) with isolated uterine agenesis; and one (2%) with isolated tetralogy of Fallot. CONCLUSION GREB1L may cause complex congenital heart disease (CHD) in humans. Clinicians should consider GREB1L testing in the setting of CHD, and cardiac screening in the setting of GREB1L variants.
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Affiliation(s)
- Emily Zhao
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Miles Bomback
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Sarath Krishna Murthy
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - David Solowiejczyk
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Kelly L. Gilmore
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Jessica L. Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Simone Sanna-Cherchi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Alex Lyford
- Department of Mathematics and Statistics, Middlebury College, Middlebury, Vermont, USA
| | - Angie C. Jelin
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ali G. Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Thomas Hays
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
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6
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Fan L, Shen G, Liu M, Liang Y, Yao J, Ding Z, Li Z, Feng X, Zhang J, Shen X. Renal Hypodysplasia/Aplasia 3 Caused by a Rare Variant of GREB1L With Incomplete Penetrance in a Chinese Family. Urology 2024; 185:49-53. [PMID: 38309594 DOI: 10.1016/j.urology.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/15/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
Renal agenesis represents the most severe form of congenital anomalies of the kidney and urinary tract. Bilateral renal agenesis is almost invariably fatal at birth and has high genetic heterogeneity. Here we report on a Chinese family with two pregnancies affected by a prenatal form of bilateral renal agenesis. Trio-WES was conducted to explore the underlying genetic cause and identified a novel nonsense variant (c .2621G>A: p. Trp874Ter) in the GREB1L gene. Based on previous research, pathogenic mutations in GREB1L can cause renal hypodysplasia/aplasia-3 (RHDA3) with autosomal dominant inheritance. Sanger sequencing performed on the family members revealed that the variant was vertically transmitted from the maternal grandfather through the unaffected mother to the two affected fetuses, fully demonstrating the incomplete dominance of the disease. Our study extends the mutational spectrum associated with RHDA3 and contributes to a more general understanding for the complex genetic inheritance of GREB1L.
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Affiliation(s)
- Lihong Fan
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Guosong Shen
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Mingsong Liu
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Yufei Liang
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Juan Yao
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Zhongying Ding
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Zhi Li
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Xiangping Feng
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Jinghui Zhang
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Xueping Shen
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China.
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7
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Sonner S, Reilly K, Woolf AS, Chandler N, Kilby MD, Maher ER, Flanagan C, McKnight AJ, Mone F. When should we offer antenatal sequencing for urinary tract malformations? A systematic review, cohort study and meta-analysis. Prenat Diagn 2024; 44:187-195. [PMID: 38056891 DOI: 10.1002/pd.6479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
OBJECTIVE Determine the incremental yield of prenatal exome sequencing (PES) over chromosome microarray (CMA) and/or karyotype for urinary tract malformations (UTMs). METHOD A prospective cohort study encompassing data from the English Genomic Medicine Service North Thames Laboratory Hub for fetuses with bilateral echogenic kidneys (BEKs) was combined with data from a systematic review. MEDLINE, EMBASE, Web of Science, MedRxiv and GreyLit were searched from 01/2010-02/2023 for studies reporting on the yield of PES over CMA or karyotype in fetuses with UTMs. Pooled incremental yield was determined using a random effects model. PROSPERO CRD42023364544. RESULTS Fourteen studies (410 cases) were included. The incremental yield for multisystem UTMs, any isolated UTMs, and BEKs was 31% [95% CI, 18%-46%; I2 = 78%], 16% [95% CI, 6%-26%; I2 = 80%] and 51% [95% CI, 27%-75%; I2 = 34%]. The most common clinical diseases and syndromes identified, based on the variant genes detected, were Bardet-Biedl syndrome (BBS genes), dominant and recessive polycystic kidney diseases (PKD1, PKD2 and PKHD1) and renal cysts and diabetes syndrome (HNF1B). CONCLUSION There was a notable incremental genetic diagnostic yield when PES was applied to multisystem UTMs and BEKs. There was a modest incremental yield when this technique was used for UTMs other than BEKs.
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Affiliation(s)
- Sarah Sonner
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Kelly Reilly
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Mark D Kilby
- Fetal Medicine Centre, Birmingham Women's & Children's Foundation Trust, Birmingham, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Medical Genomics Research Group, Illumina, Cambridge, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Cheryl Flanagan
- Institute of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | | | - Fionnuala Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
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8
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Martino J, Liu Q, Vukojevic K, Ke J, Lim TY, Khan A, Gupta Y, Perez A, Yan Z, Milo Rasouly H, Vena N, Lippa N, Giordano JL, Saraga M, Saraga-Babic M, Westland R, Bodria M, Piaggio G, Bendapudi PK, Iglesias AD, Wapner RJ, Tasic V, Wang F, Ionita-Laza I, Ghiggeri GM, Kiryluk K, Sampogna RV, Mendelsohn CL, D'Agati VD, Gharavi AG, Sanna-Cherchi S. Mouse and human studies support DSTYK loss of function as a low-penetrance and variable expressivity risk factor for congenital urinary tract anomalies. Genet Med 2023; 25:100983. [PMID: 37746849 DOI: 10.1016/j.gim.2023.100983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 09/26/2023] Open
Abstract
PURPOSE Previous work identified rare variants in DSTYK associated with human congenital anomalies of the kidney and urinary tract (CAKUT). Here, we present a series of mouse and human studies to clarify the association, penetrance, and expressivity of DSTYK variants. METHODS We phenotypically characterized Dstyk knockout mice of 3 separate inbred backgrounds and re-analyzed the original family segregating the DSTYK c.654+1G>A splice-site variant (referred to as "SSV" below). DSTYK loss of function (LOF) and SSVs were annotated in individuals with CAKUT, epilepsy, or amyotrophic lateral sclerosis vs controls. A phenome-wide association study analysis was also performed using United Kingdom Biobank (UKBB) data. RESULTS Results demonstrate ∼20% to 25% penetrance of obstructive uropathy, at least, in C57BL/6J and FVB/NJ Dstyk-/- mice. Phenotypic penetrance increased to ∼40% in C3H/HeJ mutants, with mild-to-moderate severity. Re-analysis of the original family segregating the rare SSV showed low penetrance (43.8%) and no alternative genetic causes for CAKUT. LOF DSTYK variants burden showed significant excess for CAKUT and epilepsy vs controls and an exploratory phenome-wide association study supported association with neurological disorders. CONCLUSION These data support causality for DSTYK LOF variants and highlights the need for large-scale sequencing studies (here >200,000 cases) to accurately assess causality for genes and variants to lowly penetrant traits with common population prevalence.
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Affiliation(s)
- Jeremiah Martino
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Qingxue Liu
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Katarina Vukojevic
- Department of Medicine, Columbia University Irving Medical Center, New York, NY; Department of Anatomy, Histology and Embryology, University of Split School of Medicine, Split, Croatia
| | - Juntao Ke
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Tze Y Lim
- Department of Medicine, Columbia University Irving Medical Center, New York, NY; Unit of Genomic Variability and Complex Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Yask Gupta
- Department of Medicine, Columbia University Irving Medical Center, New York, NY; Institute for Inflammation Medicine, University of Lubeck, Germany
| | - Alejandra Perez
- Department of Medicine, Columbia University Irving Medical Center, New York, NY; Department of Urology, Mount Sinai Medical Center, Miami, FL
| | - Zonghai Yan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Hila Milo Rasouly
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Natalie Vena
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Natalie Lippa
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Jessica L Giordano
- Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia; School of Medicine, University of Split, Split, Croatia
| | - Mirna Saraga-Babic
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, Split, Croatia
| | - Rik Westland
- Department of Pediatric Nephrology, Emma Children's Hospital, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Monica Bodria
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Pavan K Bendapudi
- Division of Hematology and Blood Transfusion Service, Massachusetts General Hospital, Boston, MA; Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Boston, MA; Harvard Medical School, Boston, MA
| | - Alejandro D Iglesias
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Ronald J Wapner
- Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Velibor Tasic
- Medical Faculty of Skopje, University Children's Hospital, Skopje, Macedonia
| | - Fan Wang
- Department of Biostatistics, Columbia University, New York, NY
| | | | - Gian Marco Ghiggeri
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Krzysztof Kiryluk
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Rosemary V Sampogna
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Cathy L Mendelsohn
- Department of Urology, Columbia University Irving Medical Center, New York, NY; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY; Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY
| | - Vivette D D'Agati
- The Renal Pathology Laboratory of the Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Ali G Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Simone Sanna-Cherchi
- Department of Medicine, Columbia University Irving Medical Center, New York, NY.
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9
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Mustafa HJ, Sambatur EV, Barbera JP, Pagani G, Yaron Y, Baptiste CD, Wapner RJ, Khalil A. Diagnostic yield with exome sequencing in prenatal severe bilateral ventriculomegaly: a systematic review and meta-analysis. Am J Obstet Gynecol MFM 2023; 5:101048. [PMID: 37311485 DOI: 10.1016/j.ajogmf.2023.101048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
OBJECTIVE This study aimed to determine the incremental diagnostic yield of prenatal exome sequencing after negative chromosomal microarray analysis results in prenatally diagnosed bilateral severe ventriculomegaly or hydrocephalus; another objective was to categorize the associated genes and variants. DATA SOURCES A systematic search was performed to identify relevant studies published until June 2022 using 4 databases (Cochrane Library, Web of Science, Scopus, and MEDLINE). STUDY ELIGIBILITY CRITERIA Studies in English reporting on the diagnostic yield of exome sequencing following negative chromosomal microarray analysis results in cases of prenatally diagnosed bilateral severe ventriculomegaly were included. METHODS Authors of cohort studies were contacted for individual participant data, and 2 studies provided their extended cohort data. The incremental diagnostic yield of exome sequencing was assessed for pathogenic/likely pathogenic findings in cases of: (1) all severe ventriculomegaly; (2) isolated severe ventriculomegaly (as the only cranial anomaly); (3) severe ventriculomegaly with other cranial anomalies; and (4) nonisolated severe ventriculomegaly (with extracranial anomalies). To be able to identify all reported genetic associations, the systematic review portion was not limited to any minimal severe ventriculomegaly case numbers; however, for the synthetic meta-analysis, we included studies with ≥3 severe ventriculomegaly cases. Meta-analysis of proportions was done using a random-effects model. Quality assessment of the included studies was performed using the modified STARD (Standards for Reporting of Diagnostic Accuracy Studies) criteria. RESULTS A total of 28 studies had 1988 prenatal exome sequencing analyses performed following negative chromosomal microarray analysis results for various prenatal phenotypes; this included 138 cases with prenatal bilateral severe ventriculomegaly. We categorized 59 genetic variants in 47 genes associated with prenatal severe ventriculomegaly along with their full phenotypic description. There were 13 studies reporting on ≥3 severe ventriculomegaly cases, encompassing 117 severe ventriculomegaly cases that were included in the synthetic analysis. Of all the included cases, 45% (95% confidence interval, 30-60) had positive pathogenic/likely pathogenic exome sequencing results. The highest yield was for nonisolated cases (presence of extracranial anomalies; 54%; 95% confidence interval, 38-69), followed by severe ventriculomegaly with other cranial anomalies (38%; 95% confidence interval, 22-57) and isolated severe ventriculomegaly (35%; 95% confidence interval, 18-58). CONCLUSION There is an apparent incremental diagnostic yield of prenatal exome sequencing following negative chromosomal microarray analysis results in bilateral severe ventriculomegaly. Although the greatest yield was found in cases of nonisolated severe ventriculomegaly, consideration should also be given to performing exome sequencing in cases of isolated severe ventriculomegaly as the only brain anomaly identified on prenatal imaging.
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Affiliation(s)
- Hiba J Mustafa
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Indiana University School of Medicine, Indianapolis, IN (Dr Mustafa); Fetal Center at Riley Children's Health, Indiana University Health, Indianapolis, IN (Dr Mustafa).
| | - Enaja V Sambatur
- Research Division, Houston Center for Maternal Fetal Medicine, Houston, TX (Ms Sambatur)
| | - Julie P Barbera
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (Ms Barbera)
| | - Giorgio Pagani
- Maternal Fetal Medicine Unit, Department of Obstetrics and Gynecology, ASST Papa Giovanni XXIII, Bergamo, Italy (Dr Pagani)
| | - Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel (Dr Yaron); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel (Dr Yaron)
| | - Caitlin D Baptiste
- Division of Women's Genetics, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY (Drs Baptiste and Wapner)
| | - Ronald J Wapner
- Division of Women's Genetics, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY (Drs Baptiste and Wapner)
| | - Asma Khalil
- Fetal Medicine Unit, St George's Hospital, St George's University of London, London, United Kingdom (Dr Khalil); Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, United Kingdom (Dr Khalil)
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10
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Puri D, Barry BJ, Engle EC. TUBB3 and KIF21A in neurodevelopment and disease. Front Neurosci 2023; 17:1226181. [PMID: 37600020 PMCID: PMC10436312 DOI: 10.3389/fnins.2023.1226181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Neuronal migration and axon growth and guidance require precise control of microtubule dynamics and microtubule-based cargo transport. TUBB3 encodes the neuronal-specific β-tubulin isotype III, TUBB3, a component of neuronal microtubules expressed throughout the life of central and peripheral neurons. Human pathogenic TUBB3 missense variants result in altered TUBB3 function and cause errors either in the growth and guidance of cranial and, to a lesser extent, central axons, or in cortical neuronal migration and organization, and rarely in both. Moreover, human pathogenic missense variants in KIF21A, which encodes an anterograde kinesin motor protein that interacts directly with microtubules, alter KIF21A function and cause errors in cranial axon growth and guidance that can phenocopy TUBB3 variants. Here, we review reported TUBB3 and KIF21A variants, resulting phenotypes, and corresponding functional studies of both wildtype and mutant proteins. We summarize the evidence that, in vitro and in mouse models, loss-of-function and missense variants can alter microtubule dynamics and microtubule-kinesin interactions. Lastly, we highlight additional studies that might contribute to our understanding of the relationship between specific tubulin isotypes and specific kinesin motor proteins in health and disease.
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Affiliation(s)
- Dharmendra Puri
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Brenda J. Barry
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Elizabeth C. Engle
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
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11
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Jolly A, Du H, Borel C, Chen N, Zhao S, Grochowski CM, Duan R, Fatih JM, Dawood M, Salvi S, Jhangiani SN, Muzny DM, Koch A, Rouskas K, Glentis S, Deligeoroglou E, Bacopoulou F, Wise CA, Dietrich JE, Van den Veyver IB, Dimas AS, Brucker S, Sutton VR, Gibbs RA, Antonarakis SE, Wu N, Coban-Akdemir ZH, Zhu L, Posey JE, Lupski JR. Rare variant enrichment analysis supports GREB1L as a contributory driver gene in the etiology of Mayer-Rokitansky-Küster-Hauser syndrome. HGG ADVANCES 2023; 4:100188. [PMID: 37124138 PMCID: PMC10130500 DOI: 10.1016/j.xhgg.2023.100188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by aplasia of the female reproductive tract; the syndrome can include renal anomalies, absence or dysgenesis, and skeletal anomalies. While functional models have elucidated several candidate genes, only WNT4 (MIM: 603490) variants have been definitively associated with a subtype of MRKH with hyperandrogenism (MIM: 158330). DNA from 148 clinically diagnosed MRKH probands across 144 unrelated families and available family members from North America, Europe, and South America were exome sequenced (ES) and by family-based genomics analyzed for rare likely deleterious variants. A replication cohort consisting of 442 Han Chinese individuals with MRKH was used to further reproduce GREB1L findings in diverse genetic backgrounds. Proband and OMIM phenotypes annotated using the Human Phenotype Ontology were analyzed to quantitatively delineate the phenotypic spectrum associated with GREB1L variant alleles found in our MRKH cohort and those previously published. This study reports 18 novel GREB1L variant alleles, 16 within a multiethnic MRKH cohort and two within a congenital scoliosis cohort. Cohort-wide analyses for a burden of rare variants within a single gene identified likely damaging variants in GREB1L (MIM: 617782), a known disease gene for renal hypoplasia and uterine abnormalities (MIM: 617805), in 16 of 590 MRKH probands. GREB1L variant alleles, including a CNV null allele, were found in 8 MRKH type 1 probands and 8 MRKH type II probands. This study used quantitative phenotypic analyses in a worldwide multiethnic cohort to identify and strengthen the association of GREB1L to isolated uterine agenesis (MRKH type I) and syndromic MRKH type II.
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Affiliation(s)
- Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | | | - Na Chen
- Department of Obstetrics and Gynaecology, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases and Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Sejal Salvi
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - André Koch
- University of Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | - Konstantinos Rouskas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Efthymios Deligeoroglou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Greece
| | - Flora Bacopoulou
- Center for Adolescent Medicine and UNESCO Chair on Adolescent Health Care, First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Greece
| | - Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- McDermott Center for Human Growth and Development, Department of Pediatrics and Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jennifer E. Dietrich
- Department of Obstetrics and Gynecology, Houston, TX, USA
- Department of Pediatrics, BCM, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Ignatia B. Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Obstetrics and Gynecology, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Antigone S. Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center Al. Fleming, Vari, Athens 16672, Greece
| | - Sara Brucker
- University of Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Stylianos E. Antonarakis
- University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, 1205 Geneva, Switzerland
- Medigenome, the Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases and Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zeynep H. Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Lan Zhu
- Department of Obstetrics and Gynaecology, Beijing 100730, China
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine (BCM), Houston, TX, USA
- Department of Pediatrics, BCM, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
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12
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Tantry MSA, Santhakumar K. Insights on the Role of α- and β-Tubulin Isotypes in Early Brain Development. Mol Neurobiol 2023; 60:3803-3823. [PMID: 36943622 DOI: 10.1007/s12035-023-03302-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/05/2023] [Indexed: 03/23/2023]
Abstract
Tubulins are the highly conserved subunit of microtubules which involve in various fundamental functions including brain development. Microtubules help in neuronal proliferation, migration, differentiation, cargo transport along the axons, synapse formation, and many more. Tubulin gene family consisting of multiple isotypes, their differential expression and varied post translational modifications create a whole new level of complexity and diversity in accomplishing manifold neuronal functions. The studies on the relation between tubulin genes and brain development opened a new avenue to understand the role of each tubulin isotype in neurodevelopment. Mutations in tubulin genes are reported to cause brain development defects especially cortical malformations, referred as tubulinopathies. There is an increased need to understand the molecular correlation between various tubulin mutations and the associated brain pathology. Recently, mutations in tubulin isotypes (TUBA1A, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB3, and TUBG1) have been linked to cause various neurodevelopmental defects like lissencephaly, microcephaly, cortical dysplasia, polymicrogyria, schizencephaly, subcortical band heterotopia, periventricular heterotopia, corpus callosum agenesis, and cerebellar hypoplasia. This review summarizes on the microtubule dynamics, their role in neurodevelopment, tubulin isotypes, post translational modifications, and the role of tubulin mutations in causing specific neurodevelopmental defects. A comprehensive list containing all the reported tubulin pathogenic variants associated with brain developmental defects has been prepared to give a bird's eye view on the broad range of tubulin functions.
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Affiliation(s)
- M S Ananthakrishna Tantry
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603203, India
| | - Kirankumar Santhakumar
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603203, India.
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13
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Shah YB, Lin P, Chen S, Zheng A, Alcaraz W, Towne MC, Gabriel C, Bhoj EJ, Lambert MP, Olson TS, Frank DM, Ellis CA, Babushok DV. Inherited bone marrow failure with macrothrombocytopenia due to germline tubulin beta class I (TUBB) variant. Br J Haematol 2023; 200:222-228. [PMID: 36207145 PMCID: PMC10989998 DOI: 10.1111/bjh.18491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/30/2022] [Accepted: 09/19/2022] [Indexed: 01/14/2023]
Abstract
Germline mutations in tubulin beta class I (TUBB), which encodes one of the β-tubulin isoforms, were previously associated with neurological and cutaneous abnormalities. Here, we describe the first case of inherited bone marrow (BM) failure, including marked thrombocytopenia, morphological abnormalities, and cortical dysplasia, associated with a de novo p.D249V variant in TUBB. Mutant TUBB had abnormal cellular localisation in transfected cells. Following interferon/ribavirin therapy administered for transfusion-acquired hepatitis C, severe pancytopenia and BM aplasia ensued, which was unresponsive to immunosuppression. Acquired chromosome arm 6p loss of heterozygosity was identified, leading to somatic loss of the mutant TUBB allele.
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Affiliation(s)
- Yash B. Shah
- Comprehensive Bone Marrow Failure Center, Children’s Hospital of Philadelphia, Philadelphia, PA, US
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ping Lin
- Comprehensive Bone Marrow Failure Center, Children’s Hospital of Philadelphia, Philadelphia, PA, US
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Stone Chen
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Alan Zheng
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Courtney Gabriel
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth J. Bhoj
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michele P. Lambert
- Division of Hematology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Timothy S. Olson
- Comprehensive Bone Marrow Failure Center, Children’s Hospital of Philadelphia, Philadelphia, PA, US
- Division of Oncology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dale M. Frank
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Colin A. Ellis
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Daria V. Babushok
- Comprehensive Bone Marrow Failure Center, Children’s Hospital of Philadelphia, Philadelphia, PA, US
- Division of Hematology-Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
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14
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Application of Prenatal Whole Exome Sequencing for Structural Congenital Anomalies-Experience from a Local Prenatal Diagnostic Laboratory. Healthcare (Basel) 2022; 10:healthcare10122521. [PMID: 36554045 PMCID: PMC9778831 DOI: 10.3390/healthcare10122521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Fetal structural congenital abnormalities (SCAs) complicate 2-3% of all pregnancies. Whole-exome sequencing (WES) has been increasingly adopted prenatally when karyotyping and chromosomal microarray do not yield a diagnosis. This is a retrospective cohort study of 104 fetuses with SCAs identified on antenatal ultrasound in Hong Kong, where whole exome sequencing is performed. Molecular diagnosis was obtained in 25 of the 104 fetuses (24%). The highest diagnostic rate was found in fetuses with multiple SCAs (29.2%), particularly those with involvement of the cardiac and musculoskeletal systems. Variants of uncertain significance were detected in 8 out of the 104 fetuses (7.7%). Our study shows the utility of WES in the prenatal setting, and the extended use of the technology would be recommended in addition to conventional genetic workup.
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15
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Chen N, Song S, Bao X, Zhu L. Update on Mayer-Rokitansky-Küster-Hauser syndrome. Front Med 2022; 16:859-872. [PMID: 36562950 DOI: 10.1007/s11684-022-0969-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/12/2022] [Indexed: 12/24/2022]
Abstract
This review presents an update of Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome on its etiologic, clinical, diagnostic, psychological, therapeutic, and reproductive aspects. The etiology of MRKH syndrome remains unclear due to its intrinsic heterogeneity. Nongenetic and genetic causes that may interact during the embryonic development have been proposed with no definitive etiopathogenesis identified. The proportion of concomitant extragenital malformations varies in different studies, and the discrepancies may be explained by ethnic differences. In addition to physical examination and pelvic ultrasound, the performance of pelvic magnetic resonance imaging is crucial in detecting the presence of rudimentary uterine endometrium. MRKH syndrome has long-lasting psychological effects on patients, resulting in low esteem, poor coping strategies, depression, and anxiety symptoms. Providing psychological counseling and peer support to diagnosed patients is recommended. Proper and timely psychological intervention could significantly improve a patient's outcome. Various nonsurgical and surgical methods have been suggested for treatment of MRKH syndrome. Due to the high success rate and minimal risk of complications, vaginal dilation has been proven to be the first-line therapy. Vaginoplasty is the second-line option for patients experiencing dilation failure. Uterine transplantation and gestational surrogacy are options for women with MRKH syndrome to achieve biological motherhood.
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Affiliation(s)
- Na Chen
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shuang Song
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xinmiao Bao
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Peking Union Medical College, M.D. Program, Beijing, 100730, China
| | - Lan Zhu
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
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16
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Wu S, Wang X, Dai S, Zhang G, Zhou J, Shen Y. A novel missense mutation in GREB1L identified in a three-generation family with renal hypodysplasia/aplasia-3. Orphanet J Rare Dis 2022; 17:413. [PMID: 36371238 PMCID: PMC9652819 DOI: 10.1186/s13023-022-02553-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/11/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Renal hypodysplasia/aplasia-3 (RHDA3), as the most severe end of the spectrum of congenital anomalies of the kidney and urinary tract, is mainly caused by mutations in GREB1L. However, the mutations in GREB1L identified to date only explain a limited proportion of RHDA3 cases, and the mechanism of GREB1L mutations causing RHDA3 is unclear. RESULTS According to whole-exome sequencing, a three-generation family suffering from RHDA3 was investigated with a novel missense mutation in GREB1L, c.4507C>T. All three-generation patients suffered from unilateral absent kidney. This missense mutation resulted in sharp downregulation of mRNA and protein expression, which might lead to RHDA3. Mechanistically, through RNA-sequencing, it was found that the mRNA levels of PAX2 and PTH1R, which are key molecules involved in the development of the kidney, were significantly downregulated by knocking out GREB1L in vitro. CONCLUSIONS This novel missense mutation in GREB1L can be helpful in the genetic diagnosis of RHDA3, and the discovery of the potential mechanism that GREB1L mutations involved in RHDA3 pathogenesis can promote the adoption of optimal treatment measures and the development of personalized medicine directly targeting these effects.
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Affiliation(s)
- Sixian Wu
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xiang Wang
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Siyu Dai
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Guohui Zhang
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Jiaojiao Zhou
- grid.412901.f0000 0004 1770 1022Division of Ultrasound, West China Hospital of Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Ying Shen
- grid.13291.380000 0001 0807 1581Joint Laboratory of Reproductive Medicine, Gynaecology and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
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Adadey SM, Aboagye ET, Esoh K, Acharya A, Bharadwaj T, Lin NS, Amenga-Etego L, Awandare GA, Schrauwen I, Leal SM, Wonkam A. A novel autosomal dominant GREB1L variant associated with non-syndromic hearing impairment in Ghana. BMC Med Genomics 2022; 15:237. [PMID: 36357908 PMCID: PMC9648021 DOI: 10.1186/s12920-022-01391-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/08/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Childhood hearing impairment (HI) is genetically heterogeneous with many implicated genes, however, only a few of these genes are reported in African populations. METHODS This study used exome and Sanger sequencing to resolve the possible genetic cause of non-syndromic HI in a Ghanaian family. RESULTS We identified a novel variant c.3041G > A: p.(Gly1014Glu) in GREB1L (DFNA80) in the index case. The GREB1L: p.(Gly1014Glu) variant had a CADD score of 26.5 and was absent from human genomic databases such as TopMed and gnomAD. In silico homology protein modeling approaches displayed major structural differences between the wildtype and mutant proteins. Additionally, the variant was predicted to probably affect the secondary protein structure that may impact its function. Publicly available expression data shows a higher expression of Greb1L in the inner ear of mice during development and a reduced expression in adulthood, underscoring its importance in the development of the inner ear structures. CONCLUSION This report on an African individual supports the association of GREB1L variant with non-syndromic HI and extended the evidence of the implication of GREB1L variants in HI in diverse populations.
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Affiliation(s)
- Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Kevin Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Anushree Acharya
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Thashi Bharadwaj
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Nicole S Lin
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, LG 54, Accra, Ghana
| | - Isabelle Schrauwen
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Suzanne M Leal
- Department of Neurology, Center for Statistical Genetics, Sergievsky Center, Columbia University Medical Centre, New York, NY, 10032, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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Fu F, Li R, Yu Q, Wang D, Deng Q, Li L, Lei T, Chen G, Nie Z, Yang X, Han J, Pan M, Zhen L, Zhang Y, Jing X, Li F, Li F, Zhang L, Yi C, Li Y, Lu Y, Zhou H, Cheng K, Li J, Xiang L, Zhang J, Tang S, Fang P, Li D, Liao C. Application of exome sequencing for prenatal diagnosis of fetal structural anomalies: clinical experience and lessons learned from a cohort of 1618 fetuses. Genome Med 2022; 14:123. [PMID: 36307859 PMCID: PMC9615232 DOI: 10.1186/s13073-022-01130-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/19/2022] [Indexed: 11/29/2022] Open
Abstract
Background Exome sequencing (ES) is becoming more widely available in prenatal diagnosis. However, data on its clinical utility and integration into clinical management remain limited in practice. Herein, we report our experience implementing prenatal ES (pES) in a large cohort of fetuses with anomalies detected by ultrasonography using a hospital-based in-house multidisciplinary team (MDT) facilitated by a three-step genotype-driven followed by phenotype-driven analysis framework. Methods We performed pES in 1618 fetal cases with positive ultrasound findings but negative for karyotyping and chromosome microarray analysis between January 2014 and October 2021, including both retrospective (n=565) and prospective (n=1053) cohorts. The diagnostic efficiency and its correlation to organ systems involved, phenotypic spectrum, and the clinical impacts of pES results on pregnancy outcomes were analyzed. Results A genotype-driven followed by phenotype-driven three-step approach was carried out in all trio pES. Step 1, a genotype-driven analysis resulted in a diagnostic rate of 11.6% (187/1618). Step 2, a phenotype-driven comprehensive analysis yielded additional diagnostic findings for another 28 cases (1.7%; 28/1618). In the final step 3, data reanalyses based on new phenotypes and/or clinical requests found molecular diagnosis in 14 additional cases (0.9%; 14/1618). Altogether, 229 fetal cases (14.2%) received a molecular diagnosis, with a higher positive rate in the retrospective than the prospective cohort (17.3% vs. 12.4%, p<0.01). The diagnostic rates were highest in fetuses with skeletal anomalies (30.4%) and multiple organ involvements (25.9%), and lowest in fetuses with chest anomalies (0%). In addition, incidental and secondary findings with childhood-onset disorders were detected in 11 (0.7%) cases. Furthermore, we described the prenatal phenotypes for the first time for 27 gene-associated conditions (20.0%, 27/135) upon a systematic analysis of the diagnosed cases and expanded the phenotype spectrum for 26 (19.3%) genes where limited fetal phenotypic information was available. In the prospective cohort, the combined prenatal ultrasound and pES results had significantly impacted the clinical decisions (61.5%, 648/1053). Conclusions The genotype-driven approach could identify about 81.7% positive cases (11.6% of the total cohort) with the initial limited fetal phenotype information considered. The following two steps of phenotype-driven analysis and data reanalyses helped us find the causative variants in an additional 2.6% of the entire cohort (18.3% of all positive findings). Our extensive phenotype analysis on a large number of molecularly confirmed prenatal cases had greatly enriched our current knowledge on fetal phenotype-genotype correlation, which may guide more focused prenatal ultrasound in the future. This is by far the largest pES cohort study that combines a robust trio sequence data analysis, systematic phenotype-genotype correlation, and well-established MDT in a single prenatal clinical setting. This work underlines the value of pES as an essential component in prenatal diagnosis in guiding medical management and parental decision making. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01130-x.
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Attard TJ, Welburn JPI, Marsh JA. Understanding molecular mechanisms and predicting phenotypic effects of pathogenic tubulin mutations. PLoS Comput Biol 2022; 18:e1010611. [PMID: 36206299 PMCID: PMC9581425 DOI: 10.1371/journal.pcbi.1010611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/19/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
Cells rely heavily on microtubules for several processes, including cell division and molecular trafficking. Mutations in the different tubulin-α and -β proteins that comprise microtubules have been associated with various diseases and are often dominant, sporadic and congenital. While the earliest reported tubulin mutations affect neurodevelopment, mutations are also associated with other disorders such as bleeding disorders and infertility. We performed a systematic survey of tubulin mutations across all isotypes in order to improve our understanding of how they cause disease, and increase our ability to predict their phenotypic effects. Both protein structural analyses and computational variant effect predictors were very limited in their utility for differentiating between pathogenic and benign mutations. This was even worse for those genes associated with non-neurodevelopmental disorders. We selected tubulin-α and -β disease mutations that were most poorly predicted for experimental characterisation. These mutants co-localise to the mitotic spindle in HeLa cells, suggesting they may exert dominant-negative effects by altering microtubule properties. Our results show that tubulin mutations represent a blind spot for current computational approaches, being much more poorly predicted than mutations in most human disease genes. We suggest that this is likely due to their strong association with dominant-negative and gain-of-function mechanisms.
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Affiliation(s)
- Thomas J. Attard
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Julie P. I. Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
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20
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Claus LR, Snoek R, Knoers NVAM, van Eerde AM. Review of genetic testing in kidney disease patients: Diagnostic yield of single nucleotide variants and copy number variations evaluated across and within kidney phenotype groups. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:358-376. [PMID: 36161467 PMCID: PMC9828643 DOI: 10.1002/ajmg.c.31995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/02/2022] [Accepted: 08/18/2022] [Indexed: 01/29/2023]
Abstract
Genetic kidney disease comprises a diverse group of disorders. These can roughly be divided in the phenotype groups congenital anomalies of the kidney and urinary tract, ciliopathies, glomerulopathies, stone disorders, tubulointerstitial kidney disease, and tubulopathies. Many etiologies can lead to chronic kidney disease that can progress to end-stage kidney disease. Despite each individual disease being rare, together these genetic disorders account for a large proportion of kidney disease cases. With the introduction of massively parallel sequencing, genetic testing has become more accessible, but a comprehensive analysis of the diagnostic yield is lacking. This review gives an overview of the diagnostic yield of genetic testing across and within the full range of kidney disease phenotypes through a systematic literature search that resulted in 115 included articles. Patient, test, and cohort characteristics that can influence the diagnostic yield are highlighted. Detection of copy number variations and their contribution to the diagnostic yield is described for all phenotype groups. Also, the impact of a genetic diagnosis for a patient and family members, which can be diagnostic, therapeutic, and prognostic, is shown through the included articles. This review will allow clinicians to estimate an a priori probability of finding a genetic cause for the kidney disease in their patients.
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Affiliation(s)
- Laura R. Claus
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Rozemarijn Snoek
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Nine V. A. M. Knoers
- Department of GeneticsUniversity Medical Center GroningenGroningenThe Netherlands
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21
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Yaron Y, Ofen Glassner V, Mory A, Zunz Henig N, Kurolap A, Bar Shira A, Brabbing Goldstein D, Marom D, Ben Sira L, Baris Feldman H, Malinger G, Krajden Haratz K, Reches A. Exome sequencing as first-tier test for fetuses with severe central nervous system structural anomalies. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 60:59-67. [PMID: 35229910 PMCID: PMC9328397 DOI: 10.1002/uog.24885] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 05/08/2023]
Abstract
OBJECTIVE Prenatally detected central nervous system (CNS) anomalies present a diagnostic challenge. In this study, we compared the diagnostic yield of exome sequencing (ES) and chromosomal microarray analysis (CMA) in fetuses with a major CNS anomaly. METHODS This was a retrospective study of 114 cases referred for genetic evaluation following termination of pregnancy (TOP) due to a major CNS anomaly detected on prenatal ultrasound. All fetuses were first analyzed by CMA. All CMA-negative cases were offered ES. CMA-positive cases were reanalyzed using ES to assess its ability to detect copy-number variants (CNVs). RESULTS CMA identified a pathogenic or likely pathogenic (P/LP) CNV in 11/114 (10%) cases. Eighty-six CMA-negative cases were analyzed using ES, which detected P/LP sequence variants in 38/86 (44%). Among recurrent cases (i.e. cases with a previously affected pregnancy), the incidence of P/LP sequence variants was non-significantly higher compared with non-recurrent ones (12/19 (63%) vs 26/67 (39%); P = 0.06). Among the 38 cases with an ES diagnosis, 20 (53%) were inherited and carried a significant risk of recurrence. Reanalysis of 10 CMA-positive cases by ES demonstrated that the bioinformatics pipeline used for sequence variant analysis also detected all P/LP CNVs, as well as three previously known non-causative CNVs. CONCLUSIONS In our study, ES provided a high diagnostic yield (> 50%) in fetuses with severe CNS structural anomalies, which may have been partly due to the highly selected case series that included post-TOP cases from a specialist referral center. These data suggest that ES may be considered as a first-tier test for the prenatal diagnosis of major fetal CNS anomalies, detecting both P/LP sequence variants and CNVs. This is of particular importance given the time constraints of an ongoing pregnancy and the risk of recurrence in future pregnancies. © 2022 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- Y. Yaron
- Prenatal Genetic Diagnosis UnitGenetics Institute, Tel Aviv Sourasky Medical CenterTel AvivIsrael
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - V. Ofen Glassner
- Prenatal Genetic Diagnosis UnitGenetics Institute, Tel Aviv Sourasky Medical CenterTel AvivIsrael
| | - A. Mory
- Prenatal Genetic Diagnosis UnitGenetics Institute, Tel Aviv Sourasky Medical CenterTel AvivIsrael
| | - N. Zunz Henig
- Prenatal Genetic Diagnosis UnitGenetics Institute, Tel Aviv Sourasky Medical CenterTel AvivIsrael
| | - A. Kurolap
- Prenatal Genetic Diagnosis UnitGenetics Institute, Tel Aviv Sourasky Medical CenterTel AvivIsrael
| | - A. Bar Shira
- Prenatal Genetic Diagnosis UnitGenetics Institute, Tel Aviv Sourasky Medical CenterTel AvivIsrael
| | - D. Brabbing Goldstein
- Prenatal Genetic Diagnosis UnitGenetics Institute, Tel Aviv Sourasky Medical CenterTel AvivIsrael
- Division of Obstetric Ultrasound, Lis Maternity HospitalTel Aviv Sourasky Medical CenterTel AvivIsrael
| | - D. Marom
- Prenatal Genetic Diagnosis UnitGenetics Institute, Tel Aviv Sourasky Medical CenterTel AvivIsrael
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - L. Ben Sira
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- Radiology DepartmentTel Aviv Sourasky Medical CenterTel AvivIsrael
| | - H. Baris Feldman
- Prenatal Genetic Diagnosis UnitGenetics Institute, Tel Aviv Sourasky Medical CenterTel AvivIsrael
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - G. Malinger
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- Division of Obstetric Ultrasound, Lis Maternity HospitalTel Aviv Sourasky Medical CenterTel AvivIsrael
| | - K. Krajden Haratz
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- Division of Obstetric Ultrasound, Lis Maternity HospitalTel Aviv Sourasky Medical CenterTel AvivIsrael
| | - A. Reches
- Prenatal Genetic Diagnosis UnitGenetics Institute, Tel Aviv Sourasky Medical CenterTel AvivIsrael
- Division of Obstetric Ultrasound, Lis Maternity HospitalTel Aviv Sourasky Medical CenterTel AvivIsrael
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22
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Mellis R, Oprych K, Scotchman E, Hill M, Chitty LS. Diagnostic yield of exome sequencing for prenatal diagnosis of fetal structural anomalies: A systematic review and meta-analysis. Prenat Diagn 2022; 42:662-685. [PMID: 35170059 PMCID: PMC9325531 DOI: 10.1002/pd.6115] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/10/2022]
Abstract
Objectives We conducted a systematic review and meta‐analysis to determine the diagnostic yield of exome sequencing (ES) for prenatal diagnosis of fetal structural anomalies, where karyotype/chromosomal microarray (CMA) is normal. Methods Following electronic searches of four databases, we included studies with ≥10 structurally abnormal fetuses undergoing ES or whole genome sequencing. The incremental diagnostic yield of ES over CMA/karyotype was calculated and pooled in a meta‐analysis. Sub‐group analyses investigated effects of case selection and fetal phenotype on diagnostic yield. Results We identified 72 reports from 66 studies, representing 4350 fetuses. The pooled incremental yield of ES was 31% (95% confidence interval (CI) 26%–36%, p < 0.0001). Diagnostic yield was significantly higher for cases pre‐selected for likelihood of monogenic aetiology compared to unselected cases (42% vs. 15%, p < 0.0001). Diagnostic yield differed significantly between phenotypic sub‐groups, ranging from 53% (95% CI 42%–63%, p < 0.0001) for isolated skeletal abnormalities, to 2% (95% CI 0%–5%, p = 0.04) for isolated increased nuchal translucency. Conclusion Prenatal ES provides a diagnosis in an additional 31% of structurally abnormal fetuses when CMA/karyotype is non‐diagnostic. The expected diagnostic yield depends on the body system(s) affected and can be optimised by pre‐selection of cases following multi‐disciplinary review to determine that a monogenic cause is likely.
What's already known about this topic?
Prenatal exome sequencing (ES) increases genetic diagnoses in fetuses with structural abnormalities and a normal karyotype and chromosomal microarray. Published diagnostic yields from ES are varied and may be influenced by study size, case selection and fetal phenotype.
What does this study add?
This study provides a comprehensive systematic review of the literature to date and investigates the diagnostic yield of ES for a range of isolated system anomalies, to support clinical decision‐making on how to offer prenatal ES.
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Affiliation(s)
- Rhiannon Mellis
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | | | - Elizabeth Scotchman
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Melissa Hill
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Lyn S Chitty
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
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Loss of DSTYK activates Wnt/β-catenin signaling and glycolysis in lung adenocarcinoma. Cell Death Dis 2021; 12:1122. [PMID: 34853310 PMCID: PMC8636471 DOI: 10.1038/s41419-021-04385-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 08/03/2021] [Accepted: 09/16/2021] [Indexed: 11/23/2022]
Abstract
Aberrant activation of Wnt/β-catenin signaling and dysregulation of metabolism have been frequently observed in lung cancer. However, the molecular mechanism by which Wnt/β-catenin signaling is regulated and the link between Wnt/β-catenin signaling and cancer metabolism are not fully understood. In this study, we showed that the loss of dual serine/threonine tyrosine protein kinase (DSTYK) led to the activation of Wnt/β-catenin signaling and upregulation of its target gene, lactate dehydrogenase (LDHA), and thus the elevation of lactate. DSTYK phosphorylated the N-terminal domain of β-catenin and inhibited Wnt/β-catenin signaling, which led to the inhibition of cell growth, colony formation and tumorigenesis in a lung adenocarcinoma mouse model. DSTYK was downregulated in lung cancer tissues, and its expression was positively correlated with the survival of patients with lung adenocarcinoma. Taken together, these results demonstrate that the loss of DSTYK activates Wnt/β-catenin/LDHA signaling to promote the tumorigenesis of lung cancer and that DSTYK may be a therapeutic target.
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25
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Mone F, Eberhardt RY, Hurles ME, Mcmullan DJ, Maher ER, Lord J, Chitty LS, Dempsey E, Homfray T, Giordano JL, Wapner RJ, Sun L, Sparks TN, Norton ME, Kilby MD. Fetal hydrops and the Incremental yield of Next-generation sequencing over standard prenatal Diagnostic testing (FIND) study: prospective cohort study and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:509-518. [PMID: 33847422 PMCID: PMC8487902 DOI: 10.1002/uog.23652] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 05/30/2023]
Abstract
OBJECTIVE To determine the incremental yield of exome sequencing (ES) over chromosomal microarray analysis (CMA) or karyotyping in prenatally diagnosed non-immune hydrops fetalis (NIHF). METHODS A prospective cohort study (comprising an extended group of the Prenatal Assessment of Genomes and Exomes (PAGE) study) was performed which included 28 cases of prenatally diagnosed NIHF undergoing trio ES following negative CMA or karyotyping. These cases were combined with data from a systematic review of the literature. MEDLINE, EMBASE, CINAHL and ClinicalTrials.gov databases were searched electronically (January 2000 to October 2020) for studies reporting on the incremental yield of ES over CMA or karyotyping in fetuses with prenatally detected NIHF. Inclusion criteria for the systematic review were: (i) at least two cases of NIHF undergoing sequencing; (ii) testing initiated based on prenatal ultrasound-based phenotype; and (iii) negative CMA or karyotyping result. The incremental diagnostic yield of ES was assessed in: (i) all cases of NIHF; (ii) isolated NIHF; (iii) NIHF associated with an additional fetal structural anomaly; and (iv) NIHF according to severity (i.e. two vs three or more cavities affected). RESULTS In the extended PAGE study cohort, the additional diagnostic yield of ES over CMA or karyotyping was 25.0% (7/28) in all NIHF cases, 21.4% (3/14) in those with isolated NIHF and 28.6% (4/14) in those with non-isolated NIHF. In the meta-analysis, the pooled incremental yield based on 21 studies (306 cases) was 29% (95% CI, 24-34%; P < 0.00001; I2 = 0%) in all NIHF, 21% (95% CI, 13-30%; P < 0.00001; I2 = 0%) in isolated NIHF and 39% (95% CI, 30-49%; P < 0.00001; I2 = 1%) in NIHF associated with an additional fetal structural anomaly. In the latter group, congenital limb contractures were the most prevalent additional structural anomaly associated with a causative pathogenic variant, occurring in 17.3% (19/110) of cases. The incremental yield did not differ significantly according to hydrops severity. The most common genetic disorders identified were RASopathies, occurring in 30.3% (27/89) of cases with a causative pathogenic variant, most frequently due to a PTPN11 variant (44.4%; 12/27). The predominant inheritance pattern in causative pathogenic variants was autosomal dominant in monoallelic disease genes (57.3%; 51/89), with most being de novo (86.3%; 44/51). CONCLUSIONS Use of prenatal next-generation sequencing in both isolated and non-isolated NIHF should be considered in the development of clinical pathways. Given the wide range of potential syndromic diagnoses and heterogeneity in the prenatal phenotype of NIHF, exome or whole-genome sequencing may prove to be a more appropriate testing approach than a targeted gene panel testing strategy. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- F Mone
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | | | - D J Mcmullan
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - E R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - J Lord
- Wellcome Sanger Institute, Hinxton, UK
| | - L S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - E Dempsey
- Molecular and Clinical Sciences, St George's University of London, London, UK
| | - T Homfray
- SW Thames Regional Genetics Department, St George's University Hospitals NHS Foundation Trust, London, UK
| | - J L Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - R J Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - L Sun
- Fetal Medicine Unit and Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital of Tongji University, Shanghai, China
| | - T N Sparks
- Center for Maternal-Fetal Precision Medicine, Division of Maternal-Fetal Medicine, University of California, San Francisco, CA, USA
| | - M E Norton
- Center for Maternal-Fetal Precision Medicine, Division of Maternal-Fetal Medicine, University of California, San Francisco, CA, USA
| | - M D Kilby
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
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Qiao F, Wang Y, Zhang C, Zhou R, Wu Y, Wang C, Meng L, Mao P, Cheng Q, Luo C, Hu P, Xu Z. Comprehensive evaluation of genetic variants using chromosomal microarray analysis and exome sequencing in fetuses with congenital heart defect. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:377-387. [PMID: 33142350 DOI: 10.1002/uog.23532] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To evaluate comprehensively, using chromosomal microarray analysis (CMA) and exome sequencing (ES), the prevalence of chromosomal abnormalities and sequence variants in unselected fetuses with congenital heart defect (CHD) and to evaluate the potential diagnostic yields of CMA and ES for different CHD subgroups. METHODS This was a study of 360 unselected singleton fetuses with CHD detected by echocardiography, referred to our department for genetic testing between February 2018 and December 2019. We performed CMA, as a routine test for aneuploidy and copy number variations (CNV), and then, in cases without aneuploidy or pathogenic CNV on CMA, we performed ES. RESULTS Overall, positive genetic diagnoses were made in 84 (23.3%) fetuses: chromosomal abnormalities were detected by CMA in 60 (16.7%) and sequence variants were detected by ES in a further 24 (6.7%) cases. The detection rate of pathogenic and likely pathogenic genetic variants in fetuses with non-isolated CHD (32/83, 38.6%) was significantly higher than that in fetuses with isolated CHD (52/277, 18.8%) (P < 0.001), this difference being due mainly to the difference in frequency of aneuploidy between the two groups. The prevalence of a genetic defect was highest in fetuses with an atrioventricular septal defect (36.8%), ventricular septal defect with or without atrial septal defect (28.4%), conotruncal defect (22.2%) or right ventricular outflow tract obstruction (20.0%). We also identified two novel missense mutations (c.2447G>C, p.Arg816Pro; c.1171C>T, p.Arg391Cys) and a new phenotype caused by variants in PLD1. CONCLUSIONS Chromosomal abnormalities were identified in 16.7% and sequence variants in a further 6.7% of fetuses with CHD. ES should be offered to all pregnant women with a CHD fetus without chromosomal abnormality or pathogenic CNV identified by CMA, regardless of whether the CHD is isolated. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- F Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Y Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - R Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Y Wu
- Department of Ultrasound, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - L Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - P Mao
- Personnel Division, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Q Cheng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Luo
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - P Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Z Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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Papamichail M, Manolakos E, Papoulidis I, Siomou E, Eleftheriades A, Marinakis I, Tzanakis K, Sartsidis A, Vlahos NF, Eleftheriades M. Prenatal diagnosis of Baraitser - Winter syndrome using exome sequencing: Clinical report and review of literature. Eur J Med Genet 2021; 64:104318. [PMID: 34450357 DOI: 10.1016/j.ejmg.2021.104318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 10/20/2022]
Abstract
Baraitser - Winter Cerebrofrontofacial Syndrome (BWCFF) is a rare disorder characterized by facial dysmorphism and mental retardation of varying grades. The clinical phenotype of BWCFF indicates variable phenotypic expression involving various congenital malformations such as cardiac, renal and musculoskeletal abnormalities. Nevertheless, the prenatal presentation of BWCFF is rarely described, making prenatal diagnosis challenging. This report describes a prenatal diagnosis of BWCFF syndrome to date; a case of a fetus with intrauterine growth restriction, increased nuchal fold, bilateral hydronerphosis, rocker bottom foot and clubfoot detected on Anomaly Scan is outlined. Molecular karyotype failed to detect any abnormality. Assessment with Next Generation Sequencing was then performed, revealing a heterozygous de novo mutation in ACTB gene setting the diagnosis of BWCFF.
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Affiliation(s)
- Maria Papamichail
- Postgraduate Programme "Maternal Fetal Medicine" Medical SchoolNational & Kapodistrian University of Athens, Greece.
| | - Emmanouil Manolakos
- Access To Genome (ATG), Clinical Laboratory Genetics, Athens-Thessaloniki-Belgrade, Greece
| | - Ioannis Papoulidis
- Access To Genome (ATG), Clinical Laboratory Genetics, Athens-Thessaloniki-Belgrade, Greece
| | - Elisavet Siomou
- Access To Genome (ATG), Clinical Laboratory Genetics, Athens-Thessaloniki-Belgrade, Greece
| | | | | | | | - Anastasios Sartsidis
- Access To Genome (ATG), Clinical Laboratory Genetics, Athens-Thessaloniki-Belgrade, Greece
| | - Nikolaos F Vlahos
- 2nd Department of Obstetrics and Gynecology, Aretaieio Hospital Medical School, National & Kapodistrian University of Athens, Greece
| | - Makarios Eleftheriades
- 2nd Department of Obstetrics and Gynecology, Aretaieio Hospital Medical School, National & Kapodistrian University of Athens, Greece.
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FAM20C Overview: Classic and Novel Targets, Pathogenic Variants and Raine Syndrome Phenotypes. Int J Mol Sci 2021; 22:ijms22158039. [PMID: 34360805 PMCID: PMC8348777 DOI: 10.3390/ijms22158039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 12/24/2022] Open
Abstract
FAM20C is a gene coding for a protein kinase that targets S-X-E/pS motifs on different phosphoproteins belonging to diverse tissues. Pathogenic variants of FAM20C are responsible for Raine syndrome (RS), initially described as a lethal and congenital osteosclerotic dysplasia characterized by generalized atherosclerosis with periosteal bone formation, characteristic facial dysmorphisms and intracerebral calcifications. The aim of this review is to give an overview of targets and variants of FAM20C as well as RS aspects. We performed a wide phenotypic review focusing on clinical aspects and differences between all lethal (LRS) and non-lethal (NLRS) reported cases, besides the FAM20C pathogenic variant description for each. As new targets of FAM20C kinase have been identified, we reviewed FAM20C targets and their functions in bone and other tissues, with emphasis on novel targets not previously considered. We found the classic lethal and milder non-lethal phenotypes. The milder phenotype is defined by a large spectrum ranging from osteonecrosis to osteosclerosis with additional congenital defects or intellectual disability in some cases. We discuss our current understanding of FAM20C deficiency, its mechanism in RS through classic FAM20C targets in bone tissue and its potential biological relevance through novel targets in non-bone tissues.
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Watanabe K, Nakashima M, Kumada S, Mashimo H, Enokizono M, Yamada K, Kato M, Saitsu H. Identification of two novel de novo TUBB variants in cases with brain malformations: case reports and literature review. J Hum Genet 2021; 66:1193-1197. [PMID: 34211110 DOI: 10.1038/s10038-021-00956-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/09/2022]
Abstract
Heterozygous variants in TUBB encoding one of β-tubulin isotypes are known to cause two overlapping developmental brain disorders, complex cortical dysplasia with other brain malformations (CDCBM) and congenital symmetric circumferential skin creases (CSCSC). To date, six cases of CSCSC and eight cases of CDCBM caused by nine heterozygous variants have been reported. Here we report two cases with novel de novo missense TUBB variants (NM_178014.4:c.863A>G, p.(Glu288Gly) and c.869C>T, p.(Thr290Ile)). Case 1 presented brain malformations consistent with tubulinopathies including abnormalities in cortex, basal ganglia, corpus callosum, brain stem, and cerebellum along with other systemic features such as coloboma, facial dysmorphisms, vesicoureteral reflux, hypoplastic kidney, and cutis laxa-like mild skin loosening. Another case presented abnormalities of the corpus callosum, brain stem, and cerebellum along with facial dysmorphisms. We reviewed previous literature and suggest the diversity of clinical findings of TUBB-related disorders.
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Affiliation(s)
- Kazuki Watanabe
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
| | - Satoko Kumada
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Hideaki Mashimo
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Mikako Enokizono
- Department of Radiology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Keitaro Yamada
- Department of Pediatric Neurology, Aichi Developmental Disability Center Central Hospital, Kasugai, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
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Yu Y, Wang Z, Zheng Q, Li J. GREB1L overexpression correlates with prognosis and immune cell infiltration in lung adenocarcinoma. Sci Rep 2021; 11:13281. [PMID: 34168239 PMCID: PMC8225624 DOI: 10.1038/s41598-021-92695-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
GREB1L is a protein-coding gene that is an important paralog of GREB1. However, its effects in lung adenocarcinoma (LUAD) have not been determined. Thus, we evaluated the prognostic value of GREB1L in LUAD using bioinformatics approaches. In particular, we evaluated the relationship between GREB1L and LUAD using a wide range of databases and analysis tools, including TCGA, GEO, HPA, TIMER, cBioPortal, and MethSurv. Compared with its expression in normal lung tissues, GREB1L expression was significantly increased in LUAD tissues. A univariate Cox analysis showed that high GREB1L expression levels were correlated with a poor OS in LUAD. Additionally, GREB1L expression was independently associated with OS through a multivariate Cox analysis. GSEA analysis revealed enrichment in cell cycle, immune regulation, and methylation. Moreover, high GREB1L expression was associated with poor survival. We also found that the methylation and genetic alteration level was associated with prognosis in patients with LUAD. Finally, an analysis of immune infiltration showed that GREB1L is correlated with immune cell infiltration, PD-1, and PD-L1. In summary, these results indicate that GREB1L is a potential molecular marker for poor prognosis in LUAD and provide additional insight for the development of therapies and prognostic markers.
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Affiliation(s)
- Yilin Yu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Zhiping Wang
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Qunhao Zheng
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Jiancheng Li
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China.
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Dworschak GC, Reutter HM, Ludwig M. Currarino syndrome: a comprehensive genetic review of a rare congenital disorder. Orphanet J Rare Dis 2021; 16:167. [PMID: 33836786 PMCID: PMC8034116 DOI: 10.1186/s13023-021-01799-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/30/2021] [Indexed: 11/10/2022] Open
Abstract
Background The triad of a presacral mass, sacral agenesis and an anorectal anomaly constitutes the rare Currarino syndrome (CS), which is caused by dorsal–ventral patterning defects during embryonic development. The major causative CS gene is MNX1, encoding a homeobox protein. Main body In the majority of patients, CS occurs as an autosomal dominant trait; however, a female predominance observed, implies that CS may underlie an additional mode(s) of inheritance. Often, the diagnosis of CS is established solely by clinical findings, impacting a detailed analysis of the disease. Our combined data, evaluating more than 60 studies reporting patients with CS-associated mutations, revealed a slightly higher incidence rate in females with a female-to-male ratio of 1.39:1. Overall, MNX1 mutation analysis was successful in only 57.4% of all CS patients investigated, with no mutation detected in 7.7% of the familial and 68% of the sporadic patients. Our studies failed to detect the presence of an expressed MNX1 isoform that might explain at least some of these mutation-negative cases. Conclusion Aside from MNX1, other genes or regulatory regions may contribute to CS and we discuss several cytogenetic studies and whole-exome sequencing data that have implicated further loci/genes in its etiology. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01799-0.
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Affiliation(s)
- Gabriel C Dworschak
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany. .,Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, 53115, Bonn, Germany. .,Department of Pediatrics, University Hospital Bonn, 53127, Bonn, Germany.
| | - Heiko M Reutter
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.,Department of Neonatology and Pediatric Intensive Care, University Hospital Bonn, 53127, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, 53127, Bonn, Germany
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Abstract
PURPOSE OF REVIEW The current review seeks to provide a comprehensive update on the revolutionary technology of whole exome sequencing (WES) which has been used to interrogate abnormal foetal phenotypes since the last few years, and is changing the paradigms of prenatal diagnosis, facilitating accurate genetic diagnosis and optimal management of pregnancies affected with foetal abnormalities, as well enabling delineation of novel Mendelian disorders. RECENT FINDINGS WES has contributed to identification of more than 1000 Mendelian genes and made rapid strides into clinical diagnostics in recent years. Diagnostic yield of WES in postnatal cohorts has ranged from 25 to 50%, and this test is now a first tier investigation for various clinical presentations. Various abnormal perinatal phenotypes have also been investigated using WES since 2014, with diagnostic yields ranging from 8.5 to 80%. Studies in foetal phenotypes have been challenging and guidelines in this cohort are still evolving. SUMMARY WES has proven to be a disrupting technology, enabling genetic diagnosis for pregnancies complicated by previously unexplained foetal abnormalities, and revealing a significant contribution of single gene disorders in these, thereby changing clinical diagnostic paradigms. The application of this technology in perinatal cohorts is also providing interesting insights into single gene defects presenting as previously unknown genetic syndromes, hence contributing to expansion of Mendelian genetics to encompass various foetal phenotypes.
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The ABCs of the atypical Fam20 secretory pathway kinases. J Biol Chem 2021; 296:100267. [PMID: 33759783 PMCID: PMC7948968 DOI: 10.1016/j.jbc.2021.100267] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
The study of extracellular phosphorylation was initiated in late 19th century when the secreted milk protein, casein, and egg-yolk protein, phosvitin, were shown to be phosphorylated. However, it took more than a century to identify Fam20C, which phosphorylates both casein and phosvitin under physiological conditions. This kinase, along with its family members Fam20A and Fam20B, defined a new family with altered amino acid sequences highly atypical from the canonical 540 kinases comprising the kinome. Fam20B is a glycan kinase that phosphorylates xylose residues and triggers peptidoglycan biosynthesis, a role conserved from sponges to human. The protein kinase, Fam20C, conserved from nematodes to humans, phosphorylates well over 100 substrates in the secretory pathway with overall functions postulated to encompass endoplasmic reticulum homeostasis, nutrition, cardiac function, coagulation, and biomineralization. The preferred phosphorylation motif of Fam20C is SxE/pS, and structural studies revealed that related member Fam20A allosterically activates Fam20C by forming a heterodimeric/tetrameric complex. Fam20A, a pseudokinase, is observed only in vertebrates. Loss-of-function genetic alterations in the Fam20 family lead to human diseases such as amelogenesis imperfecta, nephrocalcinosis, lethal and nonlethal forms of Raine syndrome with major skeletal defects, and altered phosphate homeostasis. Together, these three members of the Fam20 family modulate a diverse network of secretory pathway components playing crucial roles in health and disease. The overarching theme of this review is to highlight the progress that has been made in the emerging field of extracellular phosphorylation and the key roles secretory pathway kinases play in an ever-expanding number of cellular processes.
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Guadagnolo D, Mastromoro G, Di Palma F, Pizzuti A, Marchionni E. Prenatal Exome Sequencing: Background, Current Practice and Future Perspectives-A Systematic Review. Diagnostics (Basel) 2021; 11:diagnostics11020224. [PMID: 33540854 PMCID: PMC7913004 DOI: 10.3390/diagnostics11020224] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 12/16/2022] Open
Abstract
The introduction of Next Generation Sequencing (NGS) technologies has exerted a significant impact on prenatal diagnosis. Prenatal Exome Sequencing (pES) is performed with increasing frequency in fetuses with structural anomalies and negative chromosomal analysis. The actual diagnostic value varies extensively, and the role of incidental/secondary or inconclusive findings and negative results has not been fully ascertained. We performed a systematic literature review to evaluate the diagnostic yield, as well as inconclusive and negative-result rates of pES. Papers were divided in two groups. The former includes fetuses presenting structural anomalies, regardless the involved organ; the latter focuses on specific class anomalies. Available findings on non-informative or negative results were gathered as well. In the first group, the weighted average diagnostic yield resulted 19%, and inconclusive finding rate 12%. In the second group, the percentages were extremely variable due to differences in sample sizes and inclusion criteria, which constitute major determinants of pES efficiency. Diagnostic pES availability and its application have a pivotal role in prenatal diagnosis, though more homogeneity in access criteria and a consensus on clinical management of controversial information management is envisageable to reach widespread use in the near future.
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Affiliation(s)
- Daniele Guadagnolo
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Francesca Di Palma
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Antonio Pizzuti
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Clinical Genomics Unit, IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy
| | - Enrica Marchionni
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Correspondence:
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Lasić V, Kosović I, Jurić M, Racetin A, Čurčić J, Šolić I, Lozić M, Filipović N, Šoljić V, Martinović V, Saraga-Babić M, Vukojević K. GREB1L, CRELD2 and ITGA10 expression in the human developmental and postnatal kidneys: an immunohistochemical study. Acta Histochem 2021; 123:151679. [PMID: 33460985 DOI: 10.1016/j.acthis.2021.151679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/19/2020] [Accepted: 01/01/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Aim of our study is to provide an insight into the genetic expression landscape of GREB1L, ITGA10 and CRELD2 which are important in human genitourinary tract development which might help elucidate the critical stages for the onset of kidney anomalies. METHODS Morphological parameters were analyzed using immunohistochemistry on human foetal (13-38 w) and postnatal (1.5 and 7.5y) human kidney samples. RESULTS GREB1L marker had a strong intensity and the highest rate in proximal tubules (PTC) of 1.5 years' kidney (90.25%). In the distal tubules (DCT) there were statistically significant differences in 13 w, 15 w, 16 w, 21 w, 38 w and 7.5y regarding 1.5y (Kruskal-Wallis test, p < 0.001). There was significantly more GREB1L in the glomeruli at 21 w and 38 w in regard to all other stages (Kruskal-Wallis test, p < 0.01). ITGA10 staining intensity was strongest in PCT with the highest rate in 13 w (92.75%), while the lowest rate was found in glomeruli and DCT (Kruskal-Wallis test, p < 0.001). CRELD2 had the strongest staining intensity in PCT with the highest rate in 13 w and 1.5y (92.25%) and lowest in the glomeruli of 7.5 years (24.3 %). In DCT there were statistically significant differences in CRELD2 positive cells in 13 w, 15 w, 16 w, 21 w, 38 w and 7.5y regarding 1.5y (Kruskal-Wallis test, p < 0.01). ITGA10 and CRELD2 co-localised in the postnatal period in DCT. CONCLUSION High kidney expressions of GREB1L, ITGA10 and CRELD2 even in the postnatal period implicate their importance not only for the onset of CAKUT in the case of their mutation but also for maintenance of kidney homeostasis.
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Beyond diagnostic yield: prenatal exome sequencing results in maternal, neonatal, and familial clinical management changes. Genet Med 2021; 23:909-917. [PMID: 33442022 PMCID: PMC7804210 DOI: 10.1038/s41436-020-01067-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/30/2022] Open
Abstract
Purpose Previous studies have reported that prenatal exome sequencing (pES) can detect monogenic diseases in fetuses with congenital anomalies with diagnostic yields ranging from 6% to 81%, but there are few reports of its clinical utility. Methods We conducted a retrospective chart review of patients who had pES to determine whether results led to clinical management changes. Results Of 20 patients, 8 (40%) received a definitive diagnosis. Seven patients (35%) had medical management changes based on the pES results, including alterations to their delivery plan and neonatal management (such as use of targeted medications, subspecialty referrals, additional imaging and/or procedures). All patients who received a definitive diagnosis and one who received a likely pathogenic variant (n = 9; 45%) received specific counseling about recurrence risk and the medical/developmental prognosis for the baby. In five (25%) cases, the result facilitated a diagnosis in parents and/or siblings. Conclusion pES results can have significant impacts on clinical management, some of which would not be possible if testing is deferred until after birth. To maximize the clinical utility, pES should be prioritized in cases where multiple care options are available and the imaging findings alone are not sufficient to guide parental decision-making, or where postnatal testing will not be feasible.
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Mone F, Eberhardt RY, Morris RK, Hurles ME, McMullan DJ, Maher ER, Lord J, Chitty LS, Giordano JL, Wapner RJ, Kilby MD. COngenital heart disease and the Diagnostic yield with Exome sequencing (CODE) study: prospective cohort study and systematic review. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 57:43-51. [PMID: 32388881 DOI: 10.1002/uog.22072] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/26/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To determine the incremental yield of antenatal exome sequencing (ES) over chromosomal microarray analysis (CMA) or conventional karyotyping in prenatally diagnosed congenital heart disease (CHD). METHODS A prospective cohort study of 197 trios undergoing ES following CMA or karyotyping owing to CHD identified prenatally and a systematic review of the literature were performed. MEDLINE, EMBASE, CINAHL and ClinicalTrials.gov (January 2000 to October 2019) databases were searched electronically for studies reporting on the diagnostic yield of ES in prenatally diagnosed CHD. Selected studies included those with more than three cases, with initiation of testing based upon prenatal phenotype only and that included cases in which CMA or karyotyping was negative. The incremental diagnostic yield of ES was assessed in: (1) all cases of CHD; (2) isolated CHD; (3) CHD associated with extracardiac anomaly (ECA); and (4) CHD according to phenotypic subgroup. RESULTS In our cohort, ES had an additional diagnostic yield in all CHD, isolated CHD and CHD associated with ECA of 12.7% (25/197), 11.5% (14/122) and 14.7% (11/75), respectively (P = 0.81). The corresponding pooled incremental yields from 18 studies (encompassing 636 CHD cases) included in the systematic review were 21% (95% CI, 15-27%), 11% (95% CI, 7-15%) and 37% (95% CI, 18-56%), respectively. The results did not differ significantly when subanalysis was limited to studies including more than 20 cases, except for CHD associated with ECA, in which the incremental yield was greater (49% (95% CI, 17-80%)). In cases of CHD associated with ECA in the primary analysis, the most common extracardiac anomalies associated with a pathogenic variant were those affecting the genitourinary system (23/52 (44.2%)). The greatest incremental yield was in cardiac shunt lesions (41% (95% CI, 19-63%)), followed by right-sided lesions (26% (95% CI, 9-43%)). In the majority (68/96 (70.8%)) of instances, pathogenic variants occurred de novo and in autosomal dominant (monoallelic) disease genes. The most common (19/96 (19.8%)) monogenic syndrome identified was Kabuki syndrome. CONCLUSIONS There is an apparent incremental yield of prenatal ES in CHD. While the greatest yield is in CHD associated with ECA, consideration could also be given to performing ES in the presence of an isolated cardiac abnormality. A policy of routine application of ES would require the adoption of robust bioinformatic, clinical and ethical pathways. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- F Mone
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - R K Morris
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - D J McMullan
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - E R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - J Lord
- Wellcome Sanger Institute, Hinxton, UK
| | - L S Chitty
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust and UCL Great Ormond Street Institute of Child Health, London, UK
| | - J L Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - R J Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - M D Kilby
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
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Diderich KEM, Romijn K, Joosten M, Govaerts LCP, Polak M, Bruggenwirth HT, Wilke M, van Slegtenhorst MA, van Bever Y, Brooks AS, Mancini GMS, van de Laar IMBH, Kromosoeto JNR, Knapen MFCM, Go ATJI, Van Opstal D, Hoefsloot LH, Galjaard RJH, Srebniak MI. The potential diagnostic yield of whole exome sequencing in pregnancies complicated by fetal ultrasound anomalies. Acta Obstet Gynecol Scand 2020; 100:1106-1115. [PMID: 33249554 PMCID: PMC8247008 DOI: 10.1111/aogs.14053] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/30/2020] [Accepted: 11/22/2020] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The aim of this retrospective cohort study was to determine the potential diagnostic yield of prenatal whole exome sequencing in fetuses with structural anomalies on expert ultrasound scans and normal chromosomal microarray results. MATERIAL AND METHODS In the period 2013-2016, 391 pregnant women with fetal ultrasound anomalies who received normal chromosomal microarray results, were referred for additional genetic counseling and opted for additional molecular testing pre- and/or postnatally. Most of the couples received only a targeted molecular test and in 159 cases (40.7%) whole exome sequencing (broad gene panels or open exome) was performed. The results of these molecular tests were evaluated retrospectively, regardless of the time of the genetic diagnosis (prenatal or postnatal). RESULTS In 76 of 391 fetuses (19.4%, 95% CI 15.8%-23.6%) molecular testing provided a genetic diagnosis with identification of (likely) pathogenic variants. In the majority of cases (91.1%, 73/76) the (likely) pathogenic variant would be detected by prenatal whole exome sequencing analysis. CONCLUSIONS Our retrospective cohort study shows that prenatal whole exome sequencing, if offered by a clinical geneticist, in addition to chromosomal microarray, would notably increase the diagnostic yield in fetuses with ultrasound anomalies and would allow early diagnosis of a genetic disorder irrespective of the (incomplete) fetal phenotype.
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Affiliation(s)
- Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Kathleen Romijn
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Marike Polak
- Department of Psychology, Education & Child Studies (DPECS), Erasmus University Rotterdam, Rotterdam, the Netherlands
| | | | - Martina Wilke
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Yolande van Bever
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Joan N R Kromosoeto
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Maarten F C M Knapen
- Department of Obstetrics and Prenatal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands.,Foundation Prenatal Screening Southwest Region of the Netherlands, Rotterdam, The Netherlands
| | - Attie T J I Go
- Department of Obstetrics and Prenatal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
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Li D, Shen KM, Zackai EH, Bhoj EJ. Clinical variability of TUBB-associated disorders: Diagnosis through reanalysis. Am J Med Genet A 2020; 182:3035-3039. [PMID: 33016642 DOI: 10.1002/ajmg.a.61897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 11/06/2022]
Abstract
A range of clinical findings have been associated with heterozygous mutations in the Beta Tubulin (TUBB) gene, including microcephaly, structural brain abnormalities, intellectual disability, and skin creases. We report a 5-year-old male who presented for evaluation of cleft palate, cardiac defects, growth retardation, hemivertebrae causing scoliosis, and preauricular skin tags. Previous clinical exome sequencing of this patient was nondiagnostic, but reanalysis in the research setting identified a de novo missense c. 925C>G p.(Arg309Gly) mutation in TUBB. This mutation was not found in population allele frequency databases, and was classified to be likely pathogenic. This patient shares some phenotypic characteristics with previous reported patients of TUBB mutations of the two TUBB-related phenotypes: "Cortical dysplasia, complex, with other brain malformations 6" [MIM 615771] and "Circumferential Skin Creases Kunze type (CSC-KT)" [MIM 156610], but has no excess skin creases or structural brain anomalies. We also report previously undescribed features, including transposition of the great arteries and vertebral fusion, thus representing phenotype expansion of TUBB-associated disorders.
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Affiliation(s)
- Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kaitlyn M Shen
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elizabeth J Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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40
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El-Dessouky SH, Abdel-Hamid MS, Abdel-Ghafar SF, Aboulghar MM, Gaafar HM, Fouad M, Ahmed AH, Abdel-Salam GMH. Raine syndrome: Prenatal diagnosis based on recognizable fetal facial features and characteristic intracranial calcification. Prenat Diagn 2020; 40:1578-1597. [PMID: 32833257 DOI: 10.1002/pd.5818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 01/21/2023]
Abstract
OBJECTIVE The purpose of this study was to elucidate the facial morphology and the pattern of internal malformations in three fetuses with RS born to first cousins of Egyptian decent. METHODS The fetal ultrasonography findings were highly suggestive of RS leading to targeted Sanger sequencing of FAM20C and postnatal assessment. RESULTS The prenatal ultrasound findings of osteosclerotic skull, exorbitism, hypoplastic nose, midface hypoplasia, small mouth with down-curved corners, and a distinct and recognizable pattern of intracranial calcification were identified in three fetuses with RS. The calcifications were evident specifically around the corpus callosum and/or ventricular walls. Ectopic renal and hepatic calcifications, pulmonary hypoplasia, mild rhizomelic shortening of the upper limbs, intrauterine fractures, and cerebellar hypoplasia were also noted. Molecular analysis identified three novel homozygous variants, two frameshift: [c.456delC (p.Gly153Alafs*34)] in exon 1 and [c.905delT (Phe302Serfs*35)] in exon 4 and one nonsense mutation in exon 10, [c.1557C>G(p.Tyrs519*)]. The three variants were segregated with the phenotype. This is the first description of a phenotype associated with homozygous truncating variants of FAM20C. CONCLUSION RS has characteristic prenatal ultrasound findings which can improve the prenatal identification of this condition and help in guiding the molecular diagnosis and counseling.
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Affiliation(s)
- Sara H El-Dessouky
- Department of Prenatal Diagnosis & Fetal Medicine, Division of Human Genetics and Genome Research, National Research Centre, Cairo, Egypt
| | - Mohamed S Abdel-Hamid
- Department of Medical & Molecular Genetics, Division of Human Genetics and Genome Research, National Research Centre, Cairo, Egypt
| | - Sherif F Abdel-Ghafar
- Department of Medical & Molecular Genetics, Division of Human Genetics and Genome Research, National Research Centre, Cairo, Egypt
| | | | | | - Mona Fouad
- Fetal Medicine Unit, Cairo University, Cairo, Egypt
| | - Adel H Ahmed
- Fetal Medicine Unit, Cairo University, Cairo, Egypt
| | - Ghada M H Abdel-Salam
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, National Research Centre, Cairo, Egypt
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41
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El-Dessouky SH, Issa MY, Aboulghar MM, Gaafar HM, Elarab AE, Ateya MI, Omar HH, Beetz C, Zaki MS. Prenatal delineation of a distinct lethal fetal syndrome caused by a homozygous truncating KIDINS220 variant. Am J Med Genet A 2020; 182:2867-2876. [PMID: 32909676 DOI: 10.1002/ajmg.a.61858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/19/2020] [Accepted: 08/22/2020] [Indexed: 02/06/2023]
Abstract
Kinase D-interacting substrate of 220 kDa (KIDINS220) is a transmembrane protein playing integral role in growth mediating pathways in the nervous and cardiovascular systems. KIDINS220 heterozygous truncating variants that affect the protein's C-terminus have been associated with a phenotype, so far described only in few unrelated children, including spastic paraplegia, intellectual disability, nystagmus, and obesity. More recently, a homozygous, more N-terminal truncating variant in KIDINS220 gene was suggested to be associated with enlarged cerebral ventricles and limb contractures in three fetuses from a consanguineous family. We confirm the latter finding by presenting the first detailed prenatal identification of a fetal phenotype associated with novel homozygous deleterious frameshift variant in KIDINS220 gene in a consanguineous healthy Egyptian couple. History of unexplained seven miscarriages and a similar stillbirth were recorded. Prenatal ultrasonography revealed limb contractions and ventriculomegaly; in addition to previously unreported cerebellar anomalies, cardiac anomalies and hydrops fetalis. These findings represent an expansion of clinical and molecular spectrum associated with KIDINS220 variants and broaden our understanding of genotype-phenotype relationships in lethal congenital contractures syndromes and associated severe abnormal embryological development. More generally, our study adds KIDINS220 to the rare group of genes which may cause disease by either of two distinct mutational mechanisms.
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Affiliation(s)
- Sara H El-Dessouky
- Prenatal Diagnosis and Fetal Medicine Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Mahmoud Y Issa
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Mona M Aboulghar
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Cairo University, Cairo, Egypt
| | - Hassan M Gaafar
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Cairo University, Cairo, Egypt
| | - Ahmed Ezz Elarab
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Cairo University, Cairo, Egypt
| | - Mohamed I Ateya
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Cairo University, Cairo, Egypt
| | - Heba H Omar
- Diagnostic and Research Department, Centogene AG, Rostock, Germany
| | - Christian Beetz
- Diagnostic and Research Department, Centogene AG, Rostock, Germany
| | - Maha Saad Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
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42
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Application of exome sequencing for prenatal diagnosis: a rapid scoping review. Genet Med 2020; 22:1925-1934. [PMID: 32747765 DOI: 10.1038/s41436-020-0918-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/20/2020] [Indexed: 01/03/2023] Open
Abstract
Genetic diagnosis provides important information for prenatal decision-making and management. Promising results from exome sequencing (ES) for genetic diagnosis in fetuses with structural anomalies are emerging. The objective of this scoping review was to identify what is known about the use of ES for genetic testing in prenatal cases with known or suspected genetic disease. A rapid scoping review was conducted over a six-week timeframe of English-language peer-reviewed studies. Search strategies for major databases (e.g., Medline) and gray literature were developed, and peer reviewed by information specialists. Identified studies were categorized and charted using tables and diagrams. Twenty-four publications were included from seven countries published between 2014 and 2019. Most commonly reported outcomes were diagnostic yields, which varied widely from 5% to 57%, and prenatal phenotype. Few studies reported clinical outcomes related to impact, decision-making, and clinical utility. Qualitative studies (n = 6) provided useful insights into patient and health-care provider experiences with ES. Findings suggest prenatal ES is beneficial, but more research is needed to better understand the clinical utility, circumstances for ideal use, feasibility, and costs of offering rapid ES as a routine option for prenatal genetic testing.
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43
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Wang A, Ji B, Wu F, Zhao X. Clinical Exome Sequencing Identifies a Novel Mutation of the GREB1L Gene in a Chinese Family with Renal Agenesis. Genet Test Mol Biomarkers 2020; 24:520-526. [PMID: 32598191 DOI: 10.1089/gtmb.2020.0036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Renal agenesis (RA) is one of the most severe congenital anomalies of the kidney and urinary tract; it is known to be highly genetically heterogeneous. The purpose of this study was to explore the clinical significance of genetic diagnostics in a Chinese RA family. Methods: Five members of an RA family and 100 healthy people were recruited. Clinical exome sequencing was conducted to explore the underlying genetic cause in the affected family. Results: Exome sequencing identified a novel missense mutation (c.2333T>A, p.Val778Asp) in the GREB1L gene. This GREB1L variant was not detected in controls and was predicted to be highly damaging to the physiological function of the GREB1L protein. Conclusion: We identified a novel c.2333T>A variant in the GREB1L gene that extends the mutational spectrum associated with renal agenesis.
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Affiliation(s)
- Ancong Wang
- Department of Reproductive Medicine, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
- Department of Obstetrics and Gynecology, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
| | - Baoju Ji
- Department of Clinical Laboratory, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
| | - Fengxia Wu
- Department of Anatomy, School of Basic Medical Sciences, Shandong University, Jinan, Shandong Province, P.R. China
| | - Xiangyu Zhao
- Department of Clinical Laboratory, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
- Department of Medical Genetics, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
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44
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Autosomal Dominantly Inherited GREB1L Variants in Individuals with Profound Sensorineural Hearing Impairment. Genes (Basel) 2020; 11:genes11060687. [PMID: 32585897 PMCID: PMC7349314 DOI: 10.3390/genes11060687] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/16/2020] [Accepted: 06/20/2020] [Indexed: 01/15/2023] Open
Abstract
Congenital hearing impairment is a sensory disorder that is genetically highly heterogeneous. By performing exome sequencing in two families with congenital nonsyndromic profound sensorineural hearing loss (SNHL), we identified autosomal dominantly inherited missense variants [p.(Asn283Ser); p.(Thr116Ile)] in GREB1L, a neural crest regulatory molecule. The p.(Thr116Ile) variant was also associated with bilateral cochlear aplasia and cochlear nerve aplasia upon temporal bone imaging, an ultra-rare phenotype previously seen in patients with de novo GREB1L variants. An important role of GREB1L in normal ear development has also been demonstrated by greb1l-/- zebrafish, which show an abnormal sensory epithelia innervation. Last, we performed a review of all disease-associated variation described in GREB1L, as it has also been implicated in renal, bladder and genital malformations. We show that the spectrum of features associated with GREB1L is broad, variable and with a high level of reduced penetrance, which is typically characteristic of neurocristopathies. So far, seven GREB1L variants (14%) have been associated with ear-related abnormalities. In conclusion, these results show that autosomal dominantly inherited variants in GREB1L cause profound SNHL. Furthermore, we provide an overview of the phenotypic spectrum associated with GREB1L variants and strengthen the evidence of the involvement of GREB1L in human hearing.
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45
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Hampshire K, Martin PM, Carlston C, Slavotinek A. Baraitser-Winter cerebrofrontofacial syndrome: Report of two adult siblings. Am J Med Genet A 2020; 182:1923-1932. [PMID: 32506774 DOI: 10.1002/ajmg.a.61637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/21/2020] [Accepted: 04/25/2020] [Indexed: 11/07/2022]
Abstract
Baraitser-Winter cerebrofrontofacial syndrome (BWCS) is a rare, autosomal dominant condition that is characterized by intellectual disability, distinctive craniofacial features, structural brain abnormalities, seizures, microcephaly, hearing loss, and ocular colobomas. The first three cases were described in 1988 by Baraitser and Winter and included two siblings and an unrelated third patient. Subsequently, causative missense variants in the ACTB and ACTG1 genes were identified, with de novo occurrence in patients with the condition. Herein, we describe two adult siblings who were born to unaffected parents and who were diagnosed with BWCS in their fourth and sixth decade of life following exome sequencing performed for intellectual disability. We review the literature reports of adult patients with BWCS to document the clinical features and phenotypic variability that can occur later in life. This is the first molecularly confirmed report of germline mosaicism in BWCS and one of only a few reports to describe two BWCS patients belonging to the same family.
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Affiliation(s)
- Karly Hampshire
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Colleen Carlston
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
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46
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Jacquinet A, Boujemla B, Fasquelle C, Thiry J, Josse C, Lumaka A, Brischoux-Boucher E, Dubourg C, David V, Pasquier L, Lehman A, Morcel K, Guerrier D, Bours V. GREB1L variants in familial and sporadic hereditary urogenital adysplasia and Mayer-Rokitansky-Kuster-Hauser syndrome. Clin Genet 2020; 98:126-137. [PMID: 32378186 DOI: 10.1111/cge.13769] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/22/2020] [Accepted: 05/01/2020] [Indexed: 12/20/2022]
Abstract
Congenital uterine anomalies (CUA) may have major impacts on the health and social well-being of affected individuals. Their expressivity is variable, with the most severe end of the spectrum being the absence of any fully or unilaterally developed uterus (aplastic uterus), which is a major feature in Mayer-Rokitansky-Kuster-Hauser syndrome (MRKH). So far, etiologies of CUA remain largely unknown. As reports of familial occurrences argue for strong genetic contributors in some cases, we performed whole exome sequencing in nine multiplex families with recurrence of uterine and kidney malformations, a condition called hereditary urogenital adysplasia. Heterozygous likely causative variants in the gene GREB1L were identified in four of these families, confirming GREB1L as an important gene for proper uterine and kidney development. The apparent mode of inheritance was autosomal dominant with incomplete penetrance. The four families included fetuses with uterovaginal aplasia and bilateral renal agenesis, highlighting the importance to investigate GREB1L in such phenotypes. Subsequent sequencing of the gene in a cohort of 68 individuals with MRKH syndrome or uterine malformation (mostly sporadic cases) identified six additional variants of unknown significance. We therefore conclude that heterozygous GREB1L variants contribute to MRKH syndrome and this probably requires additional genetic or environmental factors for full penetrance.
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Affiliation(s)
- Adeline Jacquinet
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium.,Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Bouchra Boujemla
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Corinne Fasquelle
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium
| | - Jerôme Thiry
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Claire Josse
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium.,Medical Oncology, Centre Hospitalier Universitaire CHU Liege, Liège, Belgium
| | - Aimé Lumaka
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Christèle Dubourg
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France.,Department of Molecular Genetics and Genomics, Université de Rennes, CHU Rennes, Rennes, France
| | - Véronique David
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France.,Department of Molecular Genetics and Genomics, Université de Rennes, CHU Rennes, Rennes, France
| | - Laurent Pasquier
- Department of Medical Genetics, CLAD Ouest, Université de Rennes, CHU Rennes, Rennes, France
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, BC Children's Hospital and BC Women's Hospital, Vancouver, British Columbia, Canada
| | - Karine Morcel
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France
| | - Daniel Guerrier
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France
| | - Vincent Bours
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium.,Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
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Lemire GT, Beauregard-Lacroix É, Campeau PM, Parent S, Roy-Beaudry M, Soglio DD, Grignon A, Rypens F, Wavrant S, Laberge AM, Delrue MA. Retrospective analysis of fetal vertebral defects: Associated anomalies, etiologies, and outcome. Am J Med Genet A 2019; 182:664-672. [PMID: 31880412 DOI: 10.1002/ajmg.a.61468] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/13/2019] [Accepted: 12/16/2019] [Indexed: 01/04/2023]
Abstract
Our objectives were to describe fetal cases of vertebral defects (VD), assess the diagnostic yield of fetal chromosomal analysis for VD and determine which investigations should be performed when evaluating fetal VD. We performed a retrospective chart review for fetuses with VD seen between 2006 and 2015. Cases were identified from CHU Sainte-Justine's prenatal clinic visits, postmortem fetal skeletal surveys, and medical records. Cases with neural tube defects were excluded. Sixty-six fetuses with VD were identified at a mean gestational age of 20 weeks. Forty-seven (71.2%) had associated antenatal anomalies, most commonly genitourinary, skeletal/limb, and cardiac anomalies. Thirteen mothers (19.7%) had pregestational diabetes (95% CI [10.1%-29.3%]). Fifty-three cases had chromosomal analysis. Three had abnormal results (5.6%): trisomy 13, trisomy 22, and 9q33.1q34.11 deletion. Thirty-four (51.5%) pregnancies were terminated, one led to intrauterine fetal demise and 31 (46.9%) continued to term. Of 27 children who survived the neonatal period, 21 had congenital scoliosis and 3 had spondylocostal dysostosis. Seven had developmental delay. In conclusion, prenatal evaluation of fetuses with VD should include detailed morphological assessment (including fetal echocardiogram), maternal diabetes screening, and chromosomal microarray if non-isolated. Our findings provide guidance about management and counseling after a diagnosis of fetal VD.
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Affiliation(s)
- Gabrielle T Lemire
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Éliane Beauregard-Lacroix
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Philippe M Campeau
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Stefan Parent
- Department of Surgery, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Marjolaine Roy-Beaudry
- Department of Surgery, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Dorothée Dal Soglio
- Department of Pathology, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Andrée Grignon
- Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Department of Medical Imaging, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Françoise Rypens
- Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Department of Medical Imaging, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Sandrine Wavrant
- Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Maternal-Fetal Medicine, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Anne-Marie Laberge
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Marie-Ange Delrue
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.,Integrated Prenatal Diagnosis Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
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48
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Aggarwal S, Vineeth VS, Das Bhowmik A, Tandon A, Kulkarni A, Narayanan DL, Bhattacherjee A, Dalal A. Exome sequencing for perinatal phenotypes: The significance of deep phenotyping. Prenat Diagn 2019; 40:260-273. [PMID: 31742715 DOI: 10.1002/pd.5616] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To ascertain the performance of exome sequencing (ES) technology for determining the etiological basis of abnormal perinatal phenotypes and to study the impact of comprehensive phenotyping on variant prioritization. METHODS A carefully selected cohort of 32/204 fetuses with abnormal perinatal phenotypes following postmortem/postnatal deep phenotyping underwent ES to identify a causative variant for the fetal phenotype. A retrospective comparative analysis of the prenatal versus postmortem/postnatal phenotype-based variant prioritization was performed with aid of Phenolyzer software. A review of selected literature reports was done to examine the completeness of phenotypic information for cases in those reports and how it impacted the performance of fetal ES. RESULTS In 18/32 (56%) fetuses, a pathogenic/likely pathogenic variant was identified. This included novel genotype-phenotype associations, expanded prenatal phenotypes of known Mendelian disorders and dual Mendelian diagnoses. The retrospective analysis revealed that the putative diagnostic variant could not be identified on basis of prenatal findings alone in 15/22 (68%) cases, indicating the importance of comprehensive postmortem/postnatal phenotype information. Literature review was supportive of these findings but could not be conclusive due to marked heterogeneity of involved studies. CONCLUSION Comprehensive phenotyping is essential for improving diagnostic performance and facilitating identification of novel genotype-phenotype associations in perinatal cohorts undergoing ES.
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Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Aneek Das Bhowmik
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwani Tandon
- Department of Pathology, All India Institute of Medical Sciences, Bhopal, India
| | | | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Amrita Bhattacherjee
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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49
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Talati AN, Webster CM, Vora NL. Prenatal genetic considerations of congenital anomalies of the kidney and urinary tract (CAKUT). Prenat Diagn 2019; 39:679-692. [PMID: 31343747 DOI: 10.1002/pd.5536] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/16/2019] [Accepted: 07/20/2019] [Indexed: 12/20/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) constitute 20% of all congenital malformations occurring in one in 500 live births. Worldwide, CAKUT are responsible for 40% to 50% of pediatric and 7% of adult end-stage renal disease. Pathogenic variants in genes causing CAKUT include monogenic diseases such as polycystic kidney disease and ciliopathies, as well as syndromes that include isolated kidney disease in conjunction with other abnormalities. Prenatal diagnosis most often occurs using ultrasonography; however, further genetic diagnosis may be made using a variety of testing strategies. Family history and pathologic examination can also provide information to improve the ability to make a prenatal diagnosis of CAKUT. Here, we provide a comprehensive overview of genetic considerations in the prenatal diagnosis of CAKUT disorders. Specifically, we discuss monogenic causes of CAKUT, associated ultrasound characteristics, and considerations for genetic diagnosis, antenatal care, and postnatal care.
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Affiliation(s)
- Asha N Talati
- Department of Obstetrics and Gynecology, DRAFT, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Carolyn M Webster
- Department of Obstetrics and Gynecology, DRAFT, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, DRAFT, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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50
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Hung CY, Rodriguez M, Roberts A, Bauer M, Mihalek I, Bodamer O. A novel FAM20C mutation causes a rare form of neonatal lethal Raine syndrome. Am J Med Genet A 2019; 179:1866-1871. [PMID: 31297960 DOI: 10.1002/ajmg.a.61291] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/08/2019] [Accepted: 06/23/2019] [Indexed: 02/06/2023]
Abstract
Raine syndrome is a rare, autosomal recessive, osteosclerotic bone dysplasia due to pathogenic variants in FAM20C. The clinical phenotype is characterized by generalized osteosclerosis affecting all bones, cerebral calcifications, and craniofacial dysmorphism. Most cases present during the neonatal period with early lethality due to pulmonary hypoplasia and respiratory compromise while only few affected individuals have been reported to survive into adulthood. FAM20C is a ubiquitously expressed protein kinase that contains five functional domains including a catalytic domain, a binding pocket for FAM20A and three distinct N-glycosylation sites. We report a newborn infant with a history of prenatal onset fractures, generalized osteosclerosis, and craniofacial dysmorphism and early lethality. The clinical presentation was highly suggestive of Raine syndrome. A homozygous, novel missense variant in exon 5 of FAM20C (c.1007T>G; p.Met336Arg) was identified by targeted Sanger sequencing. Following in silico analysis and mapping of the variant on a three-dimensional (3D) model of FAM20C it is predicted to be deleterious and to affect N-glycosylation, protein folding, and subsequent secretion of FAM20C. In addition, we reviewed all published FAM20C mutations and observed that most pathogenic variants affect functional regions within the protein establishing evidence for an emerging genotype-phenotype correlation.
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Affiliation(s)
- Christina Y Hung
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Mario Rodriguez
- Hussmann Institute of Genomics, University of Miami, Miami, Florida
| | - Abra Roberts
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Mislen Bauer
- Division of Clinical Genetics and Metabolism, Nicklas Children's Hospital, Miami, Florida
| | - Ivana Mihalek
- Department of Molecular Medicine and Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Olaf Bodamer
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
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