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Koenigbauer JT, Fangmann L, Reinhardt C, Weichert A, Henrich W, Saskia B, Gabriel HP. Spectrum of congenital anomalies of the kidney and urinary tract (CAKUT) including renal parenchymal malformations during fetal life and the implementation of prenatal exome sequencing (WES). Arch Gynecol Obstet 2024; 309:2613-2622. [PMID: 37535131 PMCID: PMC11147883 DOI: 10.1007/s00404-023-07165-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/16/2023] [Indexed: 08/04/2023]
Abstract
OBJECTIVES AND BACKGROUND Congenital malformations of the kidney and urinary tract (CAKUT) have a prevalence of 4-60 in 10,000 livebirths and constitute for 40-50% of all end stage pediatric kidney disease. CAKUT can have a genetic background due to monogenetic inherited disease, such as PKD or ciliopathies. They can also be found in combination with extra-renal findings as part of a syndrome. Upon detection of genitourinary malformations during the fetal anomaly scan the question arises if further genetic testing is required. The purpose of this study was to determine the phenotypic presentation of CAKUT cases and the results of exome analysis (WES). METHODS This is a retrospective analysis of 63 fetal cases with a diagnosis of CAKUT or DSD at a single center between August 2018 and December 2022. RESULTS A total of 63 cases (5.6%) out of 1123 matched CAKUT phenotypes including renal parenchyma malformations. In 15 out of 63 WES analysis a pathogenic variant was detected (23.8%). In fetuses with isolated CAKUT the rate of detecting a pathogenic variant on exome sequencing was five out of 44 (11.4%). Ten out of 19 fetuses (52.6%) that displayed extra-renal findings in combination with CAKUT were diagnosed with a pathogenic variant. CONCLUSIONS WES provides an increase in diagnosing pathogenic variants in cases of prenatally detected CAKUT. Especially in fetuses with extra-renal malformations, WES facilitates a gain in information on the fetal genotype to enhance prenatal counselling and management.
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Affiliation(s)
- Josefine Theresia Koenigbauer
- Department of Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany.
- Prenatal Diagnosis Bergmannstrasse, Bergmannstrasse 102, Berlin, Germany.
| | - Laura Fangmann
- Department of Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Charlotte Reinhardt
- Department of Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Alexander Weichert
- Prenatal Diagnosis Bergmannstrasse, Bergmannstrasse 102, Berlin, Germany
| | - Wolfgang Henrich
- Department of Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
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2
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Qin Y, Yao Y, Liu N, Wang B, Liu L, Li H, Gao T, Xu R, Wang X, Zhang F, Song J. Prenatal whole-exome sequencing for fetal structural anomalies: a retrospective analysis of 145 Chinese cases. BMC Med Genomics 2023; 16:262. [PMID: 37880672 PMCID: PMC10601195 DOI: 10.1186/s12920-023-01697-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) significantly improves the diagnosis of the etiology of fetal structural anomalies. This study aims to evaluate the diagnostic value of prenatal WES and to investigate the pathogenic variants in structurally abnormal fetuses. METHODS We recruited 144 fetuses with structural anomalies between 14 and 2020 and 15 December 2021 in the study. Genetic screening was performed by WES combined with karyotyping and chromosomal microarray analysis. The molecular diagnostic yield of prenatal WES for each type of fetal structural anomaly and the identified pathogenic genes and mutations were reported. RESULTS In this study, we retrospectively analyzed the clinical and genetic data of 145 structurally anomalous fetuses. These cases were classified into 9 phenotypic classes based on antenatal ultrasound findings. Thirty-eight pathogenic variants in 24 genes were identified in 35 of the 145 cases, including 14 novel variants in 13 genes (EP300, MYH3, TSC2, MMP9, CPLANE1, INVS, COL1A1, EYA1, TTC21B, MKS1, COL11A2, PDHA1 and L1CAM). Five additional pathogenic variants were classified as incidental findings. Our study showed that the overall diagnosis rate of WES was 28.1% (27/96) in the parent-fetus trio cases and 16.3% (8/49) in the proband-only cases. Fetuses with musculoskeletal anomalies had the highest diagnostic yield (51.4%, 19/37). In addition, FGFR3 and COL1A1 were the most common pathogenic genes. CONCLUSIONS Our work expands the mutation spectrum of the genes associated with fetal structural anomalies and provides valuable information for future parental genetic counselling and pregnancy management of the structurally anomalous fetuses.
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Affiliation(s)
- Yayun Qin
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Yanyi Yao
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Nian Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Bo Wang
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Lijun Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Hui Li
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Tangxinzi Gao
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Runhong Xu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Xiaoyan Wang
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Fanglian Zhang
- Honghu Hospital of Traditional Chinese Medicine, Jingzhou, 433200, Hubei Province, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China.
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3
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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: 0.5] [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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Enhancing Molecular Testing for Effective Delivery of Actionable Gene Diagnostics. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120745. [PMID: 36550951 PMCID: PMC9774983 DOI: 10.3390/bioengineering9120745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022]
Abstract
There is a deep need to navigate within our genomic data to find, understand and pave the way for disease-specific treatments, as the clinical diagnostic journey provides only limited guidance. The human genome is enclosed in every nucleated cell, and yet at the single-cell resolution many unanswered questions remain, as most of the sequencing techniques use a bulk approach. Therefore, heterogeneity, mosaicism and many complex structural variants remain partially uncovered. As a conceptual approach, nanopore-based sequencing holds the promise of being a single-molecule-based, long-read and high-resolution technique, with the ability of uncovering the nucleic acid sequence and methylation almost in real time. A key limiting factor of current clinical genetics is the deciphering of key disease-causing genomic sequences. As the technological revolution is expanding regarding genetic data, the interpretation of genotype-phenotype correlations should be made with fine caution, as more and more evidence points toward the presence of more than one pathogenic variant acting together as a result of intergenic interplay in the background of a certain phenotype observed in a patient. This is in conjunction with the observation that many inheritable disorders manifest in a phenotypic spectrum, even in an intra-familial way. In the present review, we summarized the relevant data on nanopore sequencing regarding clinical genomics as well as highlighted the importance and content of pre-test and post-test genetic counselling, yielding a complex approach to phenotype-driven molecular diagnosis. This should significantly lower the time-to-right diagnosis as well lower the time required to complete a currently incomplete genotype-phenotype axis, which will boost the chance of establishing a new actionable diagnosis followed by therapeutical approach.
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Characteristic features of electroencephalogram in a pediatric patient with GRIN1 encephalopathy. BRAIN DISORDERS 2022. [DOI: 10.1016/j.dscb.2022.100056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Suzuki T, Osaka H, Miyake N, Fujita A, Uchiyama Y, Seyama R, Koshimizu E, Miyatake S, Mizuguchi T, Takeda S, Matsumoto N. Distal 2q duplication in a patient with intellectual disability. Hum Genome Var 2022; 9:39. [PMID: 36357380 PMCID: PMC9649592 DOI: 10.1038/s41439-022-00215-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 11/11/2022] Open
Abstract
We report on a patient with a distal 16.4-Mb duplication at 2q36.3-qter, who presented with severe intellectual disability, microcephaly, brachycephaly, prominent forehead, hypertelorism, prominent eyes, thin upper lip, and progenia. Copy number analysis using whole exome data detected a distal 2q duplication. This is the first report describing a distal 2q duplication at the molecular level.
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Affiliation(s)
- Toshifumi Suzuki
- grid.258269.20000 0004 1762 2738Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, 113-8421 Japan ,Department of Obstetrics and Gynecology, Keiai Hospital, Saitama, 354-0017 Japan
| | - Hitoshi Osaka
- grid.410804.90000000123090000Department of Pediatrics, Jichi Medical University, Shimotsuke, 329-0498 Japan
| | - Noriko Miyake
- grid.45203.300000 0004 0489 0290Department of Human Genetics, Research Institute National Center for Global Health and Medicine, Tokyo, Japan
| | - Atsushi Fujita
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Yuri Uchiyama
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan ,grid.470126.60000 0004 1767 0473Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004 Japan
| | - Rie Seyama
- grid.258269.20000 0004 1762 2738Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, 113-8421 Japan ,grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Eriko Koshimizu
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Satoko Miyatake
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan ,grid.470126.60000 0004 1767 0473Clinical Genetics Department, Yokohama City University Hospital, Yokohama, 236-0004 Japan
| | - Takeshi Mizuguchi
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Satoru Takeda
- grid.258269.20000 0004 1762 2738Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, 113-8421 Japan ,Aiiku Research Institute for Maternal, Child Health and Welfare, Tokyo, Japan
| | - Naomichi Matsumoto
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
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7
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Cao Y, Chau M, Zheng Y, Zhao YL, Kwan A, Hui A, Lam YH, Tan T, Tse WT, Wong L, Leung TY, Dong Z, Choy KW. Exploring the diagnostic utility of genome sequencing for fetal congenital heart defects. Prenat Diagn 2022; 42:862-872. [PMID: 35441720 DOI: 10.1002/pd.6151] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVE The diagnostic yield for congenital heart defects (CHD) with routine genetic testing is around 10-20% when considering the pathogenic CNVs or aneuploidies as positive findings. This is a pilot study to investigate the utility of genome sequencing (GS) for prenatal diagnosis of CHD. METHODS Genome sequencing (GS, 30X) was performed on 13 trios with CHD for which karyotyping and/or chromosomal microarray results were non-diagnostic. RESULTS Trio GS provided a diagnosis for 4/13 (30.8%) fetuses with complex CHDs and other structural anomalies. Findings included pathogenic or likely pathogenic variants in DNAH5, COL4A1, PTPN11, and KRAS. Of nine cases without a possibly genetic etiology by GS, we had follow-up on eight. For five of them (60%), the parents chose to keep the pregnancy. A balanced translocation [46,XX,t(14;22)(q32.33;q13.31)mat] was detected in a trio with biallelic DNAH5 mutations, which together explained the recurrent fetal situs inversus and dextrocardia that was presumably due to de novo Phelan-McDermid syndrome. A secondary finding of a BRCA2 variant and carrier status of HBB, USH2A, HBA1/HBA2 were detected in the trio. CONCLUSIONS GS expands the diagnostic scope of mutation types over conventional testing, revealing the genetic etiology for fetal heart anomalies. Patients without a known genetic abnormality indicated by GS likely opted to keep pregnancy especially if the heart issue could be repaired. We provide evidence to support the application of GS for fetuses with CHD. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Y Cao
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Laboratory Genetics and Genomics, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mhk Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Laboratory Genetics and Genomics, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Y Zheng
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Y L Zhao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ahw Kwan
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Asy Hui
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Y H Lam
- OB GYN ULTRASOUND, Henley Building, 5 Queen's Road C, Central, Hong Kong SAR, China
| | - Tyt Tan
- Tony Tan Women and Fetal Clinic, Mount Alvernia Hospital, Singapore
| | - W T Tse
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - L Wong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - T Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Laboratory Genetics and Genomics, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong SAR, China
| | - Z Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Laboratory Genetics and Genomics, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - K W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Laboratory Genetics and Genomics, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong SAR, China
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Lei Y, Meng Y, Guo X, Ning K, Bian Y, Li L, Hu Z, Anashkina AA, Jiang Q, Dong Y, Zhu X. Overview of structural variation calling: Simulation, identification, and visualization. Comput Biol Med 2022; 145:105534. [DOI: 10.1016/j.compbiomed.2022.105534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/09/2022] [Accepted: 04/14/2022] [Indexed: 12/11/2022]
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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: 3.7] [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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10
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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: 120] [Impact Index Per Article: 40.0] [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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11
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Long-term course of early onset developmental and epileptic encephalopathy associated with 2q24.3 microduplication. Epilepsy Behav Rep 2022; 19:100547. [PMID: 35733834 PMCID: PMC9207545 DOI: 10.1016/j.ebr.2022.100547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
2q24.3 is a region containing a cluster of genes for multiple voltage-gated sodium channels and CNVs in the region cause developmental and epileptic encephalopathy. DEE associated with 2q24.3 duplication have been reported to show early-onset epilepsy, resistant to antiseizure drugs, and severe developmental delay. Drug-resistant epilepsy due to 2q24.3 duplication can be seizure free after infancy. Our case was considered pyridoxine dependent but identifying duplication of 2q24.3 led to the discontinuation of unnecessary medication.
Copy number variations (CNVs) have been related to developmental and epileptic encephalopathy (DEE). The 2q24.3 region includes a cluster of genes for voltage-gated sodium channels (SCN) and CNVs in this region cause DEE. However, the long-term course of DEE with a 2q24.3 duplication has not been described. A 20-year-old female developed epileptic encephalopathy in early infancy that was resistant to various antiseizure medications. Her seizures disappeared after starting vitamin B6 therapy. Therefore, her epilepsy was considered pyridoxine-dependent epilepsy. At 16 years old, whole exome sequencing revealed a 2q24.3 microduplication including SCN1A, SCN2A, SCN3A, SCN7A, and SCN9A. Quantitative PCR detected an increased copy number of 1.3 Mb on 2q24.3 involving these genes, but no gene mutation accounting for pyridoxine-dependent epilepsy. Considering that with this duplication she was reported to be seizure-free after infancy, she was able to be off antiseizure medications including vitamin B6. Our case involvingdrug-resistant epilepsy in early infancy had no recurrent seizures during long-term follow up. Detecting CNVs using whole exome sequencing data was useful to identify a 2q24.3 duplication unassociated with pyridoxine-dependent epilepsy, leading to cessation of unnecessary medications.
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12
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Kameyama S, Mizuguchi T, Fukuda H, Moey LH, Keng WT, Okamoto N, Tsuchida N, Uchiyama Y, Koshimizu E, Hamanaka K, Fujita A, Miyatake S, Matsumoto N. Biallelic null variants in ZNF142 cause global developmental delay with familial epilepsy and dysmorphic features. J Hum Genet 2021; 67:169-173. [PMID: 34531528 DOI: 10.1038/s10038-021-00978-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 11/09/2022]
Abstract
Biallelic variants in ZNF142 at 2q35, which encodes zinc-finger protein 142, cause neurodevelopmental disorder with seizures or dystonia. We identified compound heterozygous null variants in ZNF142, NM_001105537.4:c.[1252C>T];[1274-2A>G],p.[Arg418*];[Glu426*], in Malaysian siblings suffering from global developmental delay with epilepsy and dysmorphism. cDNA analysis showed the marked reduction of ZNF142 transcript level through nonsense-mediated mRNA decay by these novel biallelic variants. The affected siblings present with global developmental delay and epilepsy in common, which were previously described, as well as dysmorphism, which was not recognized. It is important to collect patients with ZNF142 abnormality to define its phenotypic spectrum.
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Affiliation(s)
- Shinichi Kameyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Lip Hen Moey
- Department of Genetics, Penang General Hospital, George Town, Penang, Malaysia
| | - Wee Teik Keng
- Department of Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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13
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Intellectual disability and microcephaly associated with a novel CHAMP1 mutation. Hum Genome Var 2021; 8:34. [PMID: 34404773 PMCID: PMC8371100 DOI: 10.1038/s41439-021-00165-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 11/09/2022] Open
Abstract
Mutations in a number of genes related to chromosomal segregation reportedly cause developmental disorders, e.g., chromosome alignment-maintaining phosphoprotein 1 (CHAMP1). We report on an 8-year-old Japanese girl who presented with a developmental disorder and microcephaly and carries a novel nonsense mutation in CHAMP1. Therefore, CHAMP1 mutation should be considered as a differential diagnosis of global developmental delay and microcephaly.
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14
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Okazaki T, Yamada H, Matsuura K, Kasagi N, Miyake N, Matsumoto N, Adachi K, Nanba E, Maegaki Y. Clinical course of epilepsy and white matter abnormality linked to a novel DYRK1A variant. Hum Genome Var 2021; 8:26. [PMID: 34253714 PMCID: PMC8275604 DOI: 10.1038/s41439-021-00157-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/30/2021] [Accepted: 06/11/2021] [Indexed: 11/09/2022] Open
Abstract
Epilepsy and white matter abnormality have been reported in DYRK1A-related intellectual disability syndrome; however, the clinical course has yet to be elucidated. Here, we report the clinical course of an 18-year-old male with a novel heterozygous DYRK1A variant (NM_001396.4: c.957C>G, p.Tyr319*); based on previous reports, epilepsy with this syndrome tends to be well controlled. Follow-up MRIs of the patient’s lesion revealed slightly reduced signal intensity compared to the first image.
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Affiliation(s)
- Tetsuya Okazaki
- Division of Clinical Genetics, Tottori University Hospital, Yonago, Japan.
| | - Hiroyuki Yamada
- Division of Child Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kaori Matsuura
- Division of Clinical Genetics, Tottori University Hospital, Yonago, Japan
| | - Noriko Kasagi
- Division of Clinical Genetics, Tottori University Hospital, Yonago, Japan.,Department of Fundamental Nursing, School of Health Science, Tottori University Faculty of Medicine, Yonago, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kaori Adachi
- Research Initiative Center, Organization for Research Initiative and Promotion, Tottori University, Yonago, Japan
| | - Eiji Nanba
- Division of Clinical Genetics, Tottori University Hospital, Yonago, Japan.,Research Strategy Division, Organization for Research Initiative and Promotion, Tottori University, Yonago, Japan
| | - Yoshihiro Maegaki
- Division of Child Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Yonago, Japan
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15
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Itai T, Miyatake S, Tsuchida N, Saida K, Narahara S, Tsuyusaki Y, Castro MAA, Kim CA, Okamoto N, Uchiyama Y, Koshimizu E, Hamanaka K, Fujita A, Mizuguchi T, Matsumoto N. Novel CLTC variants cause new brain and kidney phenotypes. J Hum Genet 2021; 67:1-7. [PMID: 34230591 DOI: 10.1038/s10038-021-00957-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/12/2021] [Accepted: 06/21/2021] [Indexed: 11/09/2022]
Abstract
Heterozygous variants in CLTC, which encode the clathrin heavy chain protein, cause neurodevelopmental delay of varying severity, and often accompanied by dysmorphic features, seizures, hypotonia, and ataxia. To date, 28 affected individuals with CLTC variants have been reported, although their phenotypes have not been fully elucidated. Here, we report three novel de novo CLTC (NM_001288653.1) variants in three individuals with previously unreported clinical symptoms: c.3662_3664del:p.(Leu1221del) in individual 1, c.2878T>C:p.(Trp960Arg) in individual 2, and c.2430+1G>T:p.(Glu769_Lys810del) in individual 3. Consistent with previous reports, individuals with missense or small in-frame variants were more severely affected. Unreported symptoms included a brain defect (cystic lesions along the lateral ventricles of the brain in individuals 1 and 3), kidney findings (high-echogenic kidneys in individual 1 and agenesis of the left kidney and right vesicoureteral reflux in individual 3), respiratory abnormality (recurrent pneumonia in individual 1), and abnormal hematological findings (anemia in individual 1 and pancytopenia in individual 3). Of note, individual 1 even exhibited prenatal abnormality (fetal growth restriction, cystic brain lesions, high-echogenic kidneys, and a heart defect), suggesting that CLTC variants should be considered when abnormal prenatal findings in multiple organs are detected.
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Affiliation(s)
- Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Sho Narahara
- Department of Pediatrics, Anjo Kosei Hospital, Anjo, Aichi, Japan
| | - Yu Tsuyusaki
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Kanagawa, Japan
| | - Matheus Augusto Araujo Castro
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Chong Ae Kim
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.
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16
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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: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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