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Togi S, Ura H, Niida Y. Qualitative and quantitative analysis of MED12 c.887G>A causing both missense and splicing variants in X-linked Ohdo syndrome. Am J Med Genet A 2024; 194:e63628. [PMID: 38655688 DOI: 10.1002/ajmg.a.63628] [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: 12/05/2023] [Revised: 03/24/2024] [Accepted: 03/29/2024] [Indexed: 04/26/2024]
Abstract
The phenotypes associated with MED12 pathogenic variants are diverse. Male patients usually have missense variants, but the effects of base substitutions on mRNA splicing have not been investigated. Here, we report a Japanese brother with intellectual disability, characteristic facial appearance with blepharophimosis, cleft palate, Fallot tetralogy, vesicoureteral reflux, and deafness. A known missense pathogenic variant was detected in MED12, NM_005120.3:c.887G>A p.(Arg296Gln), and X-linked Ohdo syndrome was diagnosed in combination with their phenotype. mRNA splicing of MED12 was evaluated qualitatively and quantitatively using long-range PCR-based targeted RNA sequencing (reverse transcribed long amplicon sequencing), and it was shown that this missense variant simultaneously causes aberrant splicing of the 42-bp in-frame deletion in exon 7, r.847_888del, which accounts for approximately 30% of the mRNAs in both siblings. The X chromosome inactivation study showed that the X chromosome carrying the mutant allele was 100% inactivated in the carrier mothers. mRNA level analysis is essential for the accurate interpretation of the effects of variants. In this case, the MED12 protein function may be reduced by more than just an amino acid substitution, resulting in the patients with the most severe phenotype of MED12-related syndrome in males.
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Affiliation(s)
- Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
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2
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Kao EC, Mizerik EA, Bacino CA, Dai H, Vossaert L, Scott DA. MED12 Loss-of-Function Variants as a Cause of Congenital Diaphragmatic Hernia in Females With Hardikar Syndrome and Nonspecific Intellectual Disability. Am J Med Genet A 2024:e63868. [PMID: 39215511 DOI: 10.1002/ajmg.a.63868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/09/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Mediator complex subunit 12 (MED12) is required for the assembly of the kinase module of Mediator, a regulatory complex that controls the formation of the RNA polymerase II-mediated preinitiation complex. MED12-related disorders display unique gender-specific genotype-phenotype associations and include X-linked recessive Opitz-Kaveggia syndrome, Lujan-Fryns syndrome, Ohdo syndrome, and nonspecific intellectual disability in males predominantly carrying missense variants, and X-linked dominant Hardikar syndrome and nonspecific intellectual disability in females known to predominantly carry de novo nonsense/frameshift and nonsense/missense variants, respectively. MED12 was previously identified as a low-penetrance candidate gene for non-isolated congenital diaphragmatic hernia (CDH+). At the time, however, there was insufficient evidence to confirm this association. In a clinical database search, we identified 18 individuals who were molecularly diagnosed with MED12-related disorders by exome or genome sequencing, including eight missense, four frameshift, two nonsense, and one splice variant. Nine of these variants have not been previously reported. Two females with nonspecific intellectual disability were found to carry a de novo frameshift variant, indicating that potentially truncating variants causing nonspecific intellectual disability are not limited to nonsense variants. Notably, CDH was reported in three out of seven females with Hardikar syndrome or nonspecific intellectual disability but was not reported in males with MED12-related disorders. These results suggest that pathogenic MED12 variants are a cause of CDH+ in females with Hardikar syndrome and nonspecific intellectual disability.
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Affiliation(s)
- Eric C Kao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics, Houston, Texas, USA
| | - Elizabeth A Mizerik
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics, Houston, Texas, USA
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics, Houston, Texas, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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3
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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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4
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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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Makhamreh MM, Shivashankar K, Araji S, Critchlow E, O'Brien BM, Wodoslawsky S, Berger SI, Al-Kouatly HB. RASopathies are the most common set of monogenic syndromes identified by exome sequencing for nonimmune hydrops fetalis: A systematic review and meta-analysis. Am J Med Genet A 2024; 194:e63494. [PMID: 38156365 DOI: 10.1002/ajmg.a.63494] [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: 02/19/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023]
Abstract
RASopathies are a group of malformation syndromes known to lead to nonimmune hydrops fetalis (NIHF) in severe presentations. Pathogenic variants can be de novo or parentally inherited. Despite being a known frequent presentation, the fraction of monogenic NIHF cases due to RASopathies is limited in the literature. Also, the specific parental contribution of RASopathies to NIHF is not well described. Our objective was to review pooled exome sequencing (ES) diagnostic yield of RASopathies for NIHF and to determine the parental contribution of RASopathy to NIHF. We performed a systematic review of prenatal ES studies from January 1, 2000 to August 1, 2022. Thirty-six studies met inclusion criteria. Cases with RASopathy gene variants were reviewed. NIHF cases were further classified as isolated or non-isolated. Thirty-six ES studies including 46 pregnancies with NIHF and a diagnosed RASopathy were reviewed. Forty-four diagnostic variants and 2 variants of uncertain significance in 12 RASopathy genes were identified. Expanding on what was previously published, a total of 506 NIHF cases were extracted with 191 cases yielding a positive diagnosis by ES. The overall rate of RASopathy diagnosis in clinically diagnosed NIHF cases was 9% (44/506). The rate of RASopathy diagnosis among NIHF cases with positive genetic diagnosis by ES was 23% (44/191). Of the 46 cases identified, 13 (28%) variants were parentally inherited; specifically, 5/13 (38%) maternal, 3/13 (23%) paternal, 2/13 (15%) biparental, and 3/13 (23%) unspecified. Majority of NIHF cases 29/46 (63%) were isolated. Among NIHF cases with positive ES diagnoses, RASopathy diagnostic yield by ES was 23%. NIHF secondary to RASopathies was parentally inherited in 28% of cases. Most cases of NIHF due to RASopathy were isolated, with no prenatal detection of associated anomalies.
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Affiliation(s)
- Mona M Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Kavya Shivashankar
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Sarah Araji
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Mississippi, Jackson, Mississippi, USA
| | - Elizabeth Critchlow
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Barbara M O'Brien
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Seth I Berger
- Center for Genetic Medicine Research and Rare Disease Institute, Children's National Medical Center, Washington, DC, USA
| | - Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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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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7
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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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8
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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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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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Gupta S, Mathur P, Mishra AK, Medicherla KM, Bandapalli OR, Suravajhala P. Whole Exome-Trio Analysis Reveals Rare Variants Associated with Congenital Pouch Colon. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10050902. [PMID: 37238450 DOI: 10.3390/children10050902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Anorectal malformations (ARM) are individually common, but Congenital Pouch Colon (CPC) is a rare anorectal anomaly that causes a dilated pouch and communication with the genitourinary tract. In this work, we attempted to identify de novo heterozygous missense variants, and further discovered variants of unknown significance (VUS) which could provide insights into CPC manifestation. From whole exome sequencing (WES) performed earlier, the trio exomes were analyzed from those who were admitted to J.K. Lon Hospital, SMS Medical College, Jaipur, India, between 2011 and 2017. The proband exomes were compared with the unaffected sibling/family members, and we sought to ask whether any variants of significant interest were associated with the CPC manifestation. The WES data from a total of 64 samples including 16 affected neonates (11 male and 5 female) with their parents and unaffected siblings were used for the study. We examined the role of rare allelic variation associated with CPC in a 16 proband/parent trio family, comparing the mutations to those of their unaffected parents/siblings. We also performed RNA-Seq as a pilot to find whether or not the genes harboring these mutations were differentially expressed. Our study revealed extremely rare variants, viz., TAF1B, MUC5B and FRG1, which were further validated for disease-causing mutations associated with CPC, further closing the gaps of surgery by bringing intervention in therapies.
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Affiliation(s)
- Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, Jaipur 303002, India
| | - Praveen Mathur
- Department of Pediatric Surgery, SMS Medical College and Hospital, JLN Marg, Jaipur 302004, India
| | | | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Department of Bioengineering, Birla Institute of Technology, Mesra, Jaipur Campus, 27-Malaviya Industrial, Area, Jaipur 302017, India
| | | | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita University, Vallikavu, Clappana P.O. Box 690525, Kerala, India
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11
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A deep intronic TCTN2 variant activating a cryptic exon predicted by SpliceRover in a patient with Joubert syndrome. J Hum Genet 2023:10.1038/s10038-023-01143-3. [PMID: 36894704 DOI: 10.1038/s10038-023-01143-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/26/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
The recent introduction of genome sequencing in genetic analysis has led to the identification of pathogenic variants located in deep introns. Recently, several new tools have emerged to predict the impact of variants on splicing. Here, we present a Japanese boy of Joubert syndrome with biallelic TCTN2 variants. Exome sequencing identified only a heterozygous maternal nonsense TCTN2 variant (NM_024809.5:c.916C >T, p.(Gln306Ter)). Subsequent genome sequencing identified a deep intronic variant (c.1033+423G>A) inherited from his father. The machine learning algorithms SpliceAI, Squirls, and Pangolin were unable to predict alterations in splicing by the c.1033+423G>A variant. SpliceRover, a tool for splice site prediction using FASTA sequence, was able to detect a cryptic exon which was 85-bp away from the variant and within the inverted Alu sequence while SpliceRover scores for these splice sites showed slight increase (donor) or decrease (acceptor) between the reference and mutant sequences. RNA sequencing and RT-PCR using urinary cells confirmed inclusion of the cryptic exon. The patient showed major symptoms of TCTN2-related disorders such as developmental delay, dysmorphic facial features and polydactyly. He also showed uncommon features such as retinal dystrophy, exotropia, abnormal pattern of respiration, and periventricular heterotopia, confirming these as one of features of TCTN2-related disorders. Our study highlights usefulness of genome sequencing and RNA sequencing using urinary cells for molecular diagnosis of genetic disorders and suggests that database of cryptic splice sites predicted in introns by SpliceRover using the reference sequences can be helpful in extracting candidate variants from large numbers of intronic variants in genome sequencing.
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12
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Al-Kouatly HB, Shivashankar K, Mossayebi MH, Makhamreh M, Critchlow E, Gao Z, Fasehun LK, Alkuraya FS, Ryan EE, Hegde M, Wodoslawsky S, Hughes J, Berger SI. Diagnostic yield from prenatal exome sequencing for non-immune hydrops fetalis: A systematic review and meta-analysis. Clin Genet 2023; 103:503-512. [PMID: 36757664 DOI: 10.1111/cge.14309] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Non-immune hydrops fetalis (NIHF) has multiple genetic etiologies diagnosable by exome sequencing (ES). We evaluated the yield of prenatal ES for NIHF, and the contribution of additional clinical findings and history. Systematic review was performed with PROSPERO tag 232951 using CINAHL, PubMed, and Ovid MEDLINE from January 1, 2000 through December 1, 2021. Selected studies performed ES to augment standard prenatal diagnostic approaches. Cases meeting a strict NIHF phenotype were tabulated with structured data imputed from papers or requested from authors. Genetic variants and diagnostic outcomes were harmonized across studies using current ACMG and ClinGen variant classification guidelines. Thirty-one studies reporting 445 NIHF cases had a 37% (95% CI: 32%-41%) diagnostic rate. There was no significant difference between isolated NIHF and NIHF with fetal malformations or between recurrent and simplex cases. Diagnostic rate was higher for consanguineous than non-consanguineous cases. Disease categories included RASopathies (24%), neuromuscular (21%), metabolic (17%), lymphatic (13%), other syndromes (9%), cardiovascular (5%), hematologic (2%), skeletal (2%), and other categories (7%). Inheritance patterns included recessive (55%), dominant (41%), and X-linked (4%). ES should be considered in the diagnostic workup of NIHF with and without associated ultrasound findings regardless of history of recurrence or consanguinity.
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Affiliation(s)
- Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Kavya Shivashankar
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Matthew H Mossayebi
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Mona Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Elizabeth Critchlow
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Zimeng Gao
- Department of Obstetrics and Gynecology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Luther-King Fasehun
- Department of Epidemiology and Biostatistics, College of Public Health, Temple University, Philadelphia, Pennsylvania, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Erin E Ryan
- Genomic Data / Genetic Counseling, GeneDx, Gaithersburg, Maryland, USA
| | - Madhuri Hegde
- Global Lab Services, PerkinElmer Genomics, Atlanta, Georgia, USA
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Joel Hughes
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
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13
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Zhu X, Gao Z, Wang Y, Huang W, Li Q, Jiao Z, Liu N, Kong X. Utility of trio-based prenatal exome sequencing incorporating splice-site and mitochondrial genome assessment in pregnancies with fetal ultrasound anomalies: prospective cohort study. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 60:780-792. [PMID: 35726512 DOI: 10.1002/uog.24974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To evaluate the utility of trio-based prenatal exome sequencing (pES), incorporating splice-site and mitochondrial genome assessment, in the prenatal diagnosis of fetuses with ultrasound anomalies and normal copy-number variant sequencing (CNV-seq) results. METHODS This was a prospective study of 90 ongoing pregnancies with ultrasound anomalies that underwent trio-based pES after receiving normal CNV-seq results, from September 2020 to November 2021, in a single center in China. By using pES with a panel encompassing exome coding and splicing regions as well as mitochondrial genome for fetuses and parents, we identified the underlying genetic causes of fetal anomalies, incidental fetal findings and parental carrier status. Information on pregnancy outcome and the impact of pES findings on parental decision-making was collected. RESULTS Of the 90 pregnancies included, 28 (31.1%) received a diagnostic result that could explain the fetal ultrasound anomalies. The highest diagnostic yield was noted for brain abnormalities (3/6 (50.0%)), followed by hydrops (4/9 (44.4%)) and skeletal abnormalities (13/34 (38.2%)). Collectively, 34 variants of 20 genes were detected in the 28 diagnosed cases, with 55.9% (19/34) occurring de novo. Variants of uncertain significance (VUS) associated with fetal phenotypes were detected in six (6.7%) fetuses. Interestingly, fetal (n = 4) and parental (n = 3) incidental findings (IFs) were detected in seven (7.8%) cases. These included two fetuses carrying a de-novo likely pathogenic (LP) variant of the CIC and FBXO11 genes, respectively, associated with neurodevelopmental disorders, and one fetus with a LP variant in a mitochondrial gene. The remaining fetus presented with unilateral renal dysplasia and was incidentally found to carry a pathogenic PKD1 gene variant resulting in adult-onset polycystic kidney, which was later confirmed to be inherited from the mother. In addition, parental heterozygous variants associated with autosomal recessive diseases were detected in three families, including one with additional fetal diagnostic findings. Diagnostic results or fetal IFs contributed to parental decision-making about termination of the pregnancy in 26 families (26/72 (36.1%)), while negative pES results or identification of VUS encouraged 40 families (40/72 (55.6%)) to continue their pregnancy, which ended in a live birth in all cases. CONCLUSION Trio-based pES can provide additional genetic information for pregnancies with fetal ultrasound anomalies without a CNV-seq diagnosis. The incidental findings and parental carrier status reported by trio-based pES with splice-site and mitochondrial genome analysis extend its clinical application, but careful genetic counseling is warranted. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- X Zhu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Z Gao
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Y Wang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - W Huang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Q Li
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Z Jiao
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - N Liu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - X Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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14
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Bukowska-Olech E, Glista F, Dinwiddie A, Pepler A, Jamsheer A. Rare multiple congenital anomalies-hypotonia-seizures syndrome type 1 (MCAHS1) - the clinical and molecular summary. Eur J Med Genet 2022; 66:104668. [PMID: 36384198 DOI: 10.1016/j.ejmg.2022.104668] [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: 08/27/2022] [Revised: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 11/15/2022]
Abstract
Multiple congenital anomalies-hypotonia-seizures syndrome type 1 (MCAHS1) is a rare autosomal recessive genetic disease belonging to glycosylphosphatidylinositols biosynthesis defects (GPIBD), a group of recessive disorders characterized by intellectual disability, hypotonia, and seizures. Glycosylphosphatidylinositols (GPIs) are glycolipids that anchor and remodel cell proteins. These processes are highly conserved and fundamental in the metabolism of all eukaryotes, including humans. Here, we have reported a male patient presenting with hypotonia, intellectual disability, and epilepsy, who underwent whole exome sequencing (WES). The analysis revealed the presence of two deleterious variants in PIGN that encodes GPI ethanolamine phosphate transferase-1 - one novel (c.1247_1251delAAGTG; p.Glu416Glyfs*22), and one that has been previously reported in the medical literature (c.1434+5G>A) resulting in MCAHS1. The detailed clinical assessment followed by the medical literature review also pointed out transient macrosomia and unreported in MCAHS1 advanced bone age and postnatal tall stature. These symptoms suggest that MCAHS1 shares a phenotypic overlap with disorders associated with overgrowth. To conclude, our case report and summary of the medical literature may be helpful for clinicians and geneticists who diagnose patients presenting with hypotonia accompanied by tall stature, advanced bone age, and transient macrosomia.
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Affiliation(s)
| | - Filip Glista
- Poznan University of Medical Sciences, Department of Medical Genetics, Poznan, Poland
| | | | | | - Aleksander Jamsheer
- Poznan University of Medical Sciences, Department of Medical Genetics, Poznan, Poland; Centers for Medical Genetics GENESIS, Poznan, Poland.
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15
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Chandler NJ, Scotchman E, Mellis R, Ramachandran V, Roberts R, Chitty LS. Lessons learnt from prenatal exome sequencing. Prenat Diagn 2022; 42:831-844. [PMID: 35506549 PMCID: PMC9325487 DOI: 10.1002/pd.6165] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/21/2022] [Accepted: 05/01/2022] [Indexed: 12/27/2022]
Abstract
Background Prenatal exome sequencing (ES) for monogenic disorders in fetuses with structural anomalies increases diagnostic yield. In England there is a national trio ES service delivered from two laboratories. To minimise incidental findings and reduce the number of variants investigated, analysis uses a panel of 1205 genes where pathogenic variants may cause abnormalities presenting prenatally. Here we review our laboratory's early experience developing and delivering ES to identify challenges in interpretation and reporting and inform service development. Methods A retrospective laboratory records review from 01.04.2020 to 31.05.2021. Results Twenty‐four of 116 completed cases were identified as challenging including 13 resulting in difficulties in analysis and reporting, nine where trio inheritance filtering would have missed the diagnosis, and two with no prenatal diagnosis; one due to inadequate pipeline sensitivity, the other because the gene was not on the panel. Two cases with copy number variants identified were not detectable by microarray. Conclusions Variant interpretation requires close communication between referring clinicians, with occasional additional examination of the fetus or parents and communication of evolving phenotypes. Inheritance filtering misses ∼5% of diagnoses. Panel analysis reduces but does not exclude incidental findings. Regular review of published literature is required to identify new reports that may aid classification.
What's already known about this topic?
Prenatal exome sequencing (ES) for monogenic disorders in fetuses with structural anomalies is known to increase diagnostic yield Diagnostic prenatal ES services are being embedded into clinical practice internationally
What does this study add?
This study identifies challenges encountered running a diagnostic prenatal ES service including those in variant interpretation and reporting, incidental findings and ethical issues It demonstrates that solely relying on trio inheritance filtering will miss ∼5% of diagnoses Close communication between scientists and referring clinicians is essential to identify evolving phenotypes Regular review of published literature is required to identify new reports that may alter variant classification
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Affiliation(s)
- Natalie J Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rhiannon Mellis
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Vijaya Ramachandran
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rowenna Roberts
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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16
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Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
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17
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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: 92] [Impact Index Per Article: 46.0] [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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18
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Prenatal Exome Sequencing in Recurrent Fetal Structural Anomalies: Systematic Review and Meta-Analysis. J Clin Med 2021; 10:jcm10204739. [PMID: 34682862 PMCID: PMC8538791 DOI: 10.3390/jcm10204739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/04/2021] [Accepted: 10/13/2021] [Indexed: 01/14/2023] Open
Abstract
To determine the diagnostic yield of exome sequencing (ES), a microarray analysis was carried out of fetuses with recurrent fetal structural anomalies (with similar anomalies in consecutive pregnancies). This is a systematic review conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) criteria. The selected studies describing ES in fetuses with recurrent fetal malformation were assessed using the Standards for Reporting of Diagnostic Accuracy Studies (STARD) criteria for risk of bias. Incidence was used as the pooled effect size by single-proportion analysis using random-effects modeling (weighted by inverse of variance). We identified nine studies on ES diagnostic yield that included 140 fetuses with recurrent structural anomalies. A pathogenic or likely pathogenic variant was found in 57 fetuses, resulting in a 40% (95%CI: 26% to 54%) incremental performance pool of ES. As expected, the vast majority (86%: 36/42) of the newly identified diseases had a recessive inheritance pattern, and among these, 42% (15/36) of variants were found in homozygosity. Meckel syndrome was the monogenic disease most frequently found, although the genes involved were diverse. The ES diagnostic yield in pregnancies with recurrent fetal structural anomalies was 40% (57/140). Homozygous disease-causing variants were found in 36% (15/57) of the newly identified monogenic disorders.
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19
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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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20
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Castleman JS, Wall E, Allen S, Williams D, Doyle S, Kilby MD. The prenatal exome - a door to prenatal diagnostics? Expert Rev Mol Diagn 2021; 21:465-474. [PMID: 33877000 DOI: 10.1080/14737159.2021.1920398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Prenatal exome sequencing (ES) allows parents the opportunity to obtain arapid molecular diagnosis of monogenic etiology when their fetus is found to have structural anomalies detected on prenatal ultrasound. Such information can improve antenatal and neonatal counseling, decision-making and management, and expand reproductive options in subsequent pregnancies.Areas covered: This review appraises the evidence, from acomprehensive search of bibliographic databases, for the introduction of ES into the fetal medicine care pathway when investigating congenital malformations. The perspectives of clinical geneticists, clinical scientists, fetal medicine specialists, and patients are explored in relation to the novel investigation and the benefits and challenges of its use in ongoing pregnancies with particular reference to UK medical practice.Expert opinion: ES provides agenetic diagnosis for more than 1 in 10 fetuses with structural differences on ultrasound and normal conventional tests (karyotype or chromosomal microarray) in carefully selected cases. The diagnostic rate increases for certain phenotypes and can range between 6% and 80% where conventional cytogenetics have not detected adiagnosis. Expert oversight is required to ensure that patients receive high-quality, evidence-based care and accurate counseling, supported by amultidisciplinary team familiar with the test and its implications.
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Affiliation(s)
- James S Castleman
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Elizabeth Wall
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Edgbaston. Birmingham, UK
| | - Denise Williams
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Samantha Doyle
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Mark 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 and Dental Sciences, University of Birmingham, Birmingham, UK
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21
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van de Plassche SR, de Brouwer APM. MED12-Related (Neuro)Developmental Disorders: A Question of Causality. Genes (Basel) 2021; 12:663. [PMID: 33925166 PMCID: PMC8146938 DOI: 10.3390/genes12050663] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022] Open
Abstract
MED12 is a member of the Mediator complex that is involved in the regulation of transcription. Missense variants in MED12 cause FG syndrome, Lujan-Fryns syndrome, and Ohdo syndrome, as well as non-syndromic intellectual disability (ID) in hemizygous males. Recently, female patients with de novo missense variants and de novo protein truncating variants in MED12 were described, resulting in a clinical spectrum centered around ID and Hardikar syndrome without ID. The missense variants are found throughout MED12, whether they are inherited in hemizygous males or de novo in females. They can result in syndromic or nonsyndromic ID. The de novo nonsense variants resulting in Hardikar syndrome that is characterized by facial clefting, pigmentary retinopathy, biliary anomalies, and intestinal malrotation, are found more N-terminally, whereas the more C-terminally positioned variants are de novo protein truncating variants that cause a severe, syndromic phenotype consisting of ID, facial dysmorphism, short stature, skeletal abnormalities, feeding difficulties, and variable other abnormalities. This broad range of distinct phenotypes calls for a method to distinguish between pathogenic and non-pathogenic variants in MED12. We propose an isogenic iNeuron model to establish the unique gene expression patterns that are associated with the specific MED12 variants. The discovery of these patterns would help in future diagnostics and determine the causality of the MED12 variants.
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Affiliation(s)
| | - Arjan P. M. de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
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22
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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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23
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Sukenik-Halevy R, Ruhrman-Shahar N, Orenstein N, Gonzaga-Jauregui C, Shuldiner AR, Magal N, Hagari O, Azulay N, Lidzbarsky GA, Bazak L, Basel-Salmon L. The diagnostic efficacy of exome data analysis using fixed neurodevelopmental gene lists: Implications for prenatal setting. Prenat Diagn 2021; 41:701-707. [PMID: 33686681 DOI: 10.1002/pd.5929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/16/2021] [Accepted: 02/28/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Laboratories performing prenatal exome sequencing (ES) frequently limit analysis to predetermined gene lists. We used a diagnostic postnatal ES cohort to assess how many of the genes diagnosed are not included in a number of select fixed lists used for prenatal diagnosis. METHODS Of 601 postnatal ES tests, pathogenic variants related to neurodevelopmental disorders were detected in 138 probands. We evaluated if causative genes were present in the following: (1) Developmental Disorders Genotype-Phenotype database list, (2) a commercial laboratory list for prenatal ES, (3) the PanelApp fetal anomalies panel, and (4) a published list used for prenatal diagnosis by ES (Prenatal Assessment of Genomes and Exomes study). RESULTS The percentages of cases where the diagnosed gene was not included in the selected four lists were; 11.6%, 17.24%, 23.2%, and 10.9%, respectively. In 13/138 (9.4%) cases, the causative gene was not included in any of the lists; in 4/13 (∼30%) cases noninclusion was explained by a relatively recent discovery of gene-phenotype association. CONCLUSIONS A significant number of genes related to neurocognitive phenotypes are not included in some of the lists used for prenatal ES data interpretation. These are not only genes related to recently discovered disorders, but also genes with well-established gene-phenotype.
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Affiliation(s)
- Rivka Sukenik-Halevy
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noa Ruhrman-Shahar
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel
| | - Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | | | | | - Nurit Magal
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel
| | - Ofir Hagari
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel
| | - Noy Azulay
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel
| | - Gabriel A Lidzbarsky
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel
| | - Lily Bazak
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel
| | - Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
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24
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Abstract
PURPOSE OF REVIEW Human reproduction is remarkably inefficient; with pregnancy loss occurring in 10-30% of clinically recognized pregnancies. Of those, 3-5% of couples experience recurrent pregnancy loss (RPL), more than 50% of who never receive an underlying diagnosis. Herein, we review evidence that genetic changes, including pathogenic variant(s) in highly penetrant genes, may provide an explanation for a proportion of couples with pregnancy loss. RECENT FINDINGS Genetic abnormalities that may predispose to pregnancy loss include chromosomal aneuploidy, copy number variants, single-gene changes and others. Although previously limited by the need for hypothesis-driven assessment, advancement of various molecular technologies have sheparded in the opportunity to identify molecular cause of highly heterogeneous conditions, including RPL. The identification of causative genetic aberrations associated with RPL demonstrates a promising area of further research. SUMMARY The journey of human development from a single-cell zygote to a term infant is complex process. Early research into copy number variants and highly penetrant single-gene changes may provide diagnosis for a proportion of couples with RPL as well as inform genes critical for early human development.
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Affiliation(s)
- Christina G Tise
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, California, USA
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25
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Litz Philipsborn S, Hartmajer S, Shtorch Asor A, Vinovezky M, Regev M, Singer A, Reinstein E. A founder mutation in TCTN2 causes Meckel-Gruber syndrome type 8 among Jews of Ethiopian and Yemenite origin. Am J Med Genet A 2021; 185:1610-1613. [PMID: 33590725 DOI: 10.1002/ajmg.a.62119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/18/2021] [Accepted: 01/24/2021] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | - Mika Vinovezky
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba, Israel
| | - Miriam Regev
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Israel
| | - Amihood Singer
- Community Genetics, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Eyal Reinstein
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba, Israel.,Sackler School of Medicine, Tel Aviv University, Israel
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26
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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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27
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Dempsey E, Haworth A, Ive L, Dubis R, Savage H, Serra E, Kenny J, Elmslie F, Greco E, Thilaganathan B, Mansour S, Homfray T, Drury S. A report on the impact of rapid prenatal exome sequencing on the clinical management of 52 ongoing pregnancies: a retrospective review. BJOG 2021; 128:1012-1019. [PMID: 32981126 DOI: 10.1111/1471-0528.16546] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Studies have shown that prenatal exome sequencing (PES) improves diagnostic yield in cases of fetal structural malformation. We have retrospectively analysed PES cases from two of the largest fetal medicine centres in the UK to determine the impact of results on management of a pregnancy. DESIGN A retrospective review of clinical case notes. SETTING Two tertiary fetal medicine centres. POPULATION Pregnancies with fetal structural abnormalities referred to clinical genetics via a multidisciplinary team. METHODS We retrospectively reviewed the notes of all patients who had undergone PES. DNA samples were obtained via chorionic villus sampling or amniocentesis. Variants were filtered using patient-specific panels and interpreted using American College of Medical Genetics guidelines. RESULTS A molecular diagnosis was made in 42% (18/43) ongoing pregnancies; of this group, there was a significant management implication in 44% (8/18). A positive result contributed to the decision to terminate a pregnancy in 16% (7/43) of cases. A negative result had a significant impact on management in two cases by affirming the decision to continue pregnancy. CONCLUSIONS We demonstrate that the results of PES can inform pregnancy management. Challenges include variant interpretation with limited phenotype information. These results emphasise the importance of the MDT and collecting phenotype and variant data. As this testing is soon to be widely available, we should look to move beyond diagnostic yield as a measure of the value of PES. TWEETABLE ABSTRACT Prenatal exome sequencing can aid decision-making in pregnancy management; review ahead of routine implementation in NHS.
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Affiliation(s)
- E Dempsey
- South West Thames Regional Genetics Service, London, UK.,School of Biological and Molecular Sciences, St George's University of London, London, UK
| | - A Haworth
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - L Ive
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - R Dubis
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - H Savage
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - E Serra
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - J Kenny
- South West Thames Regional Genetics Service, London, UK
| | - F Elmslie
- South West Thames Regional Genetics Service, London, UK
| | - E Greco
- Harris Birthright Centre, King's College London, London, UK.,Barts Health NHS Trust, London, UK
| | - B Thilaganathan
- Fetal Medicine Centre, St George's Hospital, London, UK.,Vascular Biology Unit, St George's University of London, London, UK
| | - S Mansour
- South West Thames Regional Genetics Service, London, UK.,School of Biological and Molecular Sciences, St George's University of London, London, UK
| | - T Homfray
- South West Thames Regional Genetics Service, London, UK
| | - S Drury
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
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28
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Abstract
Many genetic disorders are detectable in the prenatal period, and the capacity to identify them has increased remarkably as molecular genetic testing techniques continue to improve and become incorporated into clinical practice. The indications for prenatal genetic testing vary widely, including follow-up of an anomaly found by routine ultrasound or maternal aneuploidy screening, a family history of genetic disease, advanced maternal or paternal age, or evaluation of a low-risk pregnancy due to parental concern. The interpretation of genetic variants identified in the prenatal period poses unique challenges due to the lack of ability for deep phenotyping as well as the option to make critical decisions regarding pregnancy continuation and perinatal management. In this review, we address the various modalities currently available and commonly used for genetic testing, including preimplantation genetic testing of embryos, cell-free DNA testing, and diagnostic procedures such as chorionic villous sampling, amniocentesis, or percutaneous umbilical blood sampling, from which samples may be sent for a wide variety of genetic tests. We discuss the difference between these modalities for the genetic diagnosis of a fetus, their strengths and weaknesses, and strategies for their optimal use in order to direct perinatal care.
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29
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Rohanizadegan M, Tracy S, Galarreta CI, Poorvu T, Buchmiller TL, Bird LM, Estroff JA, Tan WH. Genetic diagnoses and associated anomalies in fetuses prenatally diagnosed with esophageal atresia. Am J Med Genet A 2020; 182:1890-1895. [PMID: 32573094 DOI: 10.1002/ajmg.a.61639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/12/2020] [Accepted: 05/04/2020] [Indexed: 12/28/2022]
Abstract
Esophageal atresia (EA) is a congenital anomaly occurring in 2.3 per 10,000 live births. Due to advances in prenatal imaging, EA is more readily diagnosed, but data on the associated genetic diagnoses, other anomalies, and postnatal outcome for fetuses diagnosed prenatally with EA are scarce. We collected data from two academic medical centers (n = 61). Our data included fetuses with suspected EA on prenatal imaging that was confirmed postnatally and had at least one genetic test. In our cohort of 61 cases, 29 (49%) were born prematurely and 19% of those born alive died in the first 9 years of life. The most commonly associated birth defects were cardiac anomalies (67%) and spine anomalies (50%). A diagnosis was made in 61% of the cases; the most common diagnoses were vertebral defects, anal atresia, cardiac anomalies, tracheoesophageal fistula with esophageal atresia, radial or renal dysplasia, and limb anomalies association (43%, although 12% met only 2 of the criteria), trisomy 21 (5%), and CHARGE syndrome (5%). Our findings suggest that most fetuses with prenatally diagnosed EA have one or more additional major anomaly that warrants a more comprehensive clinical genetics evaluation. Fetuses diagnosed prenatally appear to represent a cohort with a worse outcome.
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Affiliation(s)
- Mersedeh Rohanizadegan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah Tracy
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carolina I Galarreta
- Department of Pediatrics, University of California, San Diego, California, USA
- Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, California, USA
| | - Tabitha Poorvu
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Maternal Fetal Care Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Terry L Buchmiller
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Maternal Fetal Care Center, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California, San Diego, California, USA
- Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, California, USA
| | - Judy A Estroff
- Maternal Fetal Care Center, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Wen-Hann Tan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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30
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Li R, Wang J, Wang L, Lu Y, Wang C. Two novel mutations of COL1A1 in fetal genetic skeletal dysplasia of Chinese. Mol Genet Genomic Med 2020; 8:e1105. [PMID: 31898422 PMCID: PMC7057086 DOI: 10.1002/mgg3.1105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/23/2019] [Accepted: 12/10/2019] [Indexed: 12/18/2022] Open
Abstract
Background Skeletal disorders, which have great genotypic and phenotypic varieties, are a considerable challenge to differentiate these diseases and provide a definitive prenatal diagnosis or pre‐implantation. The present study aims to identify the causative mutation in two unrelated outbred Han–Chinese families. Method Two short‐limb fetuses were referred to our hospital. Genomic DNA was extracted from the amniotic fluid of the short‐limb fetuses and from peripheral blood of their parents. To identify the causative gene, next‐generation‐based target capture sequencing was performed on these two fetuses, followed by Sanger Sequencing in unrelated healthy controls. Segregation analysis of the candidate variant was performed in parents by using Sanger sequencing. The mutations were analyzed by SIFT, PolyPhen and Provean. Results We found that fetal genetic skeletal dysplasia was confirmed according to the correlations between genetic mutations and phenotypes in two Chinese families. Targeted next generation sequencing was performed to screen causative mutations in patients. Two novel heterozygous mutations COL1A1 c.1706 G > C (p. G569A) and c.3307 G > A (p. G1103S) were respectively identified. The results suggested that COL1A1 novel mutations were in highly conserved glycine residues present in the Gly‐X‐Y sequence repeats of the triple helical region of the collagen type I α chain, which was responsible for Osteogenesis Imperfecta. The presence of the missense mutation was also confirmed with the Sanger sequence. These two mutations were predicted to be pathogenic by SIFT, PolyPhen and Provean. Conclusion Our findings showed that the mutations of COL1A1 may play important roles in fetal genetic skeletal dysplasia in Chinese patients. Exome sequencing enhances the accurate diagnosis in utero then provides appropriate genetic counseling.
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Affiliation(s)
- Ruibing Li
- Department of Obstetrics and Gynecology, the First Medical Center, Chinese PLA General Hospital, Beijing, China.,Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jianan Wang
- Department of Obstetrics and Gynecology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Longxia Wang
- Department of Ultrasonography, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yanping Lu
- Department of Obstetrics and Gynecology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Chengbin Wang
- Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China
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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: 20] [Impact Index Per Article: 4.0] [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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