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Zemet R, Van den Veyver IB. Impact of prenatal genomics on clinical genetics practice. Best Pract Res Clin Obstet Gynaecol 2024; 97:102545. [PMID: 39265228 DOI: 10.1016/j.bpobgyn.2024.102545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/18/2024] [Accepted: 09/02/2024] [Indexed: 09/14/2024]
Abstract
Genetic testing for prenatal diagnosis in the pre-genomic era primarily focused on detecting common fetal aneuploidies, using methods that combine maternal factors and imaging findings. The genomic era, ushered in by the emergence of new technologies like chromosomal microarray analysis and next-generation sequencing, has transformed prenatal diagnosis. These new tools enable screening and testing for a broad spectrum of genetic conditions, from chromosomal to monogenic disorders, and significantly enhance diagnostic precision and efficacy. This chapter reviews the transition from traditional karyotyping to comprehensive sequencing-based genomic analyses. We discuss both the clinical utility and the challenges of integrating prenatal exome and genome sequencing into prenatal care and underscore the need for ethical frameworks, improved prenatal phenotypic characterization, and global collaboration to further advance the field.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Division of Prenatal and Reproductive Genetics, Baylor College of Medicine, Houston, TX, USA.
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2
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Basel-Salmon L, Brabbing-Goldstein D. Fetal whole genome sequencing as a clinical diagnostic tool: Advantages, limitations and pitfalls. Best Pract Res Clin Obstet Gynaecol 2024; 97:102549. [PMID: 39259994 DOI: 10.1016/j.bpobgyn.2024.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/25/2024] [Accepted: 09/02/2024] [Indexed: 09/13/2024]
Abstract
Genome-wide sequencing, which includes exome sequencing and genome sequencing, has revolutionized the diagnostics of genetic disorders in both postnatal and prenatal settings. Compared to exome sequencing, genome sequencing enables the detection of many additional types of genomic variants, although this depends on the bioinformatics pipelines used. Variant classification might vary among laboratories. In the prenatal setting, variant classification may change if new fetal phenotypic features emerge as the pregnancy progresses. There is still a need to evaluate the incremental diagnostic yield of genome sequencing compared to exome sequencing in the prenatal setting. This article reviews the advantages and limitations of genome sequencing, with an emphasis on fetal diagnostics.
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Affiliation(s)
- Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva 4941492, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Felsenstein Medical Research Center, Petach Tikva, 4920235, Israel.
| | - Dana Brabbing-Goldstein
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva 4941492, Israel; Ultrasound Unit, The Helen Schneider Women's Hospital, Rabin Medical Center - Beilinson Hospital, Petach Tikva 4941492, Israel
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Boucherie C, Alkailani M, Jossin Y, Ruiz-Reig N, Mahdi A, Aldaalis A, Aittaleb M, Tissir F. Auts2 enhances neurogenesis and promotes expansion of the cerebral cortex. J Adv Res 2024:S2090-1232(24)00296-0. [PMID: 39013538 DOI: 10.1016/j.jare.2024.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/28/2023] [Accepted: 07/13/2024] [Indexed: 07/18/2024] Open
Abstract
INTRODUCTION The AUTS2 gene is associated with various neurodevelopmental and psychiatric disorders and has been suggested to play a role in acquiring human-specific traits. Functional analyses of Auts2 knockout mice have focused on postmitotic neurons, and the reported phenotypes do not faithfully recapitulate the whole spectrum of AUTS2-related human diseases. OBJECTIVE The objective of the study is to assess the role of AUTS2 in the biology of neural progenitor cells, cortical neurogenesis and expansion; and understand how its deregulation leads to neurological disorders. METHODS We screened the literature and conducted a time point analysis of AUTS2 expression during cortical development. We used in utero electroporation to acutely modulate the expression level of AUTS2 in the developing cerebral cortex in vivo, and thoroughly characterized cortical neurogenesis and morphogenesis using immunofluorescence, cell tracing and sorting, transcriptomic profiling, and gene ontology enrichment analyses. RESULTS In addition to its expression in postmitotic neurons, we showed that AUTS2 is also expressed in neural progenitor cells at the peak of neurogenesis. Upregulation of AUTS2 dramatically altered the differentiation program and fate determination of cortical progenitors. Notably, it increased the number of basal progenitors and neurons and changed the expression of hundreds of genes, among which 444 have not been implicated in mouse brain development or function. CONCLUSION The study provides evidence that AUTS2 is expressed in germinal zones and plays a key role in fate decision of neural progenitor cells with impact on corticogenesis. It also presents comprehensive lists of AUTS2 target genes thus advancing the molecular mechanisms underlying AUTS2-associated diseases and the evolutionary expansion of the cerebral cortex.
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Affiliation(s)
- Cédric Boucherie
- Université Catholique de Louvain, Institute of Neuroscience, Developmental Neurobiology, Avenue Mounier 73, Box B1.73.16, Brussels, Belgium
| | - Maisa Alkailani
- Hamad Bin Khalifa University, College of Health and Life Sciences, Doha, Qatar
| | - Yves Jossin
- Université Catholique de Louvain, Institute of Neuroscience, Developmental Neurobiology, Avenue Mounier 73, Box B1.73.16, Brussels, Belgium
| | - Nuria Ruiz-Reig
- Université Catholique de Louvain, Institute of Neuroscience, Developmental Neurobiology, Avenue Mounier 73, Box B1.73.16, Brussels, Belgium
| | - Asma Mahdi
- Hamad Bin Khalifa University, College of Health and Life Sciences, Doha, Qatar
| | - Arwa Aldaalis
- Hamad Bin Khalifa University, College of Health and Life Sciences, Doha, Qatar
| | - Mohamed Aittaleb
- Hamad Bin Khalifa University, College of Health and Life Sciences, Doha, Qatar
| | - Fadel Tissir
- Université Catholique de Louvain, Institute of Neuroscience, Developmental Neurobiology, Avenue Mounier 73, Box B1.73.16, Brussels, Belgium; Hamad Bin Khalifa University, College of Health and Life Sciences, Doha, Qatar.
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Cacheiro P, Lawson S, Van den Veyver IB, Marengo G, Zocche D, Murray SA, Duyzend M, Robinson PN, Smedley D. Lethal phenotypes in Mendelian disorders. Genet Med 2024; 26:101141. [PMID: 38629401 PMCID: PMC11232373 DOI: 10.1016/j.gim.2024.101141] [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: 02/05/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
PURPOSE Existing resources that characterize the essentiality status of genes are based on either proliferation assessment in human cell lines, viability evaluation in mouse knockouts, or constraint metrics derived from human population sequencing studies. Several repositories document phenotypic annotations for rare disorders; however, there is a lack of comprehensive reporting on lethal phenotypes. METHODS We queried Online Mendelian Inheritance in Man for terms related to lethality and classified all Mendelian genes according to the earliest age of death recorded for the associated disorders, from prenatal death to no reports of premature death. We characterized the genes across these lethality categories, examined the evidence on viability from mouse models and explored how this information could be used for novel gene discovery. RESULTS We developed the Lethal Phenotypes Portal to showcase this curated catalog of human essential genes. Differences in the mode of inheritance, physiological systems affected, and disease class were found for genes in different lethality categories, as well as discrepancies between the lethal phenotypes observed in mouse and human. CONCLUSION We anticipate that this resource will aid clinicians in the diagnosis of early lethal conditions and assist researchers in investigating the properties that make these genes essential for human development.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Samantha Lawson
- ITS Research, Queen Mary University of London, London, United Kingdom
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | - Gabriel Marengo
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park and St Mark's Hospitals, London, United Kingdom
| | | | - Michael Duyzend
- Massachusetts General Hospital, Boston, MA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Peter N Robinson
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom.
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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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Marchetto A, Leidescher S, van Hoi T, Hirschberger N, Vogel F, Köhler S, Bedei IA, Axt-Fliedner R, Shoukier M, Keil C. Prenatal Diagnosis of Fryns Syndrome through Identification of Two Novel Splice Variants in the PIGN Gene-A Case Series. Life (Basel) 2024; 14:628. [PMID: 38792648 PMCID: PMC11122441 DOI: 10.3390/life14050628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Fryns syndrome (FS) is a multiple congenital anomaly syndrome with different multisystemic malformations. These include congenital diaphragmatic hernia, pulmonary hypoplasia, and craniofacial dysmorphic features in combination with malformations of the central nervous system such as agenesis of the corpus callosum, cerebellar hypoplasia, and enlarged ventricles. We present a non-consanguineous northern European family with two recurrent cases of FS: a boy with multiple congenital malformations who died at the age of 2.5 months and a female fetus with a complex developmental disorder with similar features in a following pregnancy. Quad whole exome analysis revealed two likely splicing-affecting disease-causing mutations in the PIGN gene: a synonymous mutation c.2619G>A, p.(Leu873=) in the last nucleotide of exon 29 and a 30 bp-deletion c.996_1023+2del (NM_176787.5) protruding into intron 12, with both mutations in trans configuration in the affected patients. Exon skipping resulting from these two variants was confirmed via RNA sequencing. Our molecular and clinical findings identified compound heterozygosity for two novel splice-affecting variants as the underlying pathomechanism for the development of FS in two patients.
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Affiliation(s)
- Aruna Marchetto
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Susanne Leidescher
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Theresia van Hoi
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Niklas Hirschberger
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Florian Vogel
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Siegmund Köhler
- Department of Prenatal Medicine and Fetal Therapy, Philipps University, 35043 Marburg, Germany;
| | - Ivonne Alexandra Bedei
- Department of Prenatal Medicine and Fetal Therapy, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Roland Axt-Fliedner
- Department of Prenatal Medicine and Fetal Therapy, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Moneef Shoukier
- Eurofins Humangenetik und Pränatal-Medizin MVZ GmbH, 80639 Munich, Germany (M.S.)
| | - Corinna Keil
- Department of Prenatal Medicine and Fetal Therapy, Philipps University, 35043 Marburg, Germany;
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Wang L, Bu T, Wu X, Li L, Sun F, Cheng CY. Motor proteins, spermatogenesis and testis function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:381-445. [PMID: 38960481 DOI: 10.1016/bs.apcsb.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The role of motor proteins in supporting intracellular transports of vesicles and organelles in mammalian cells has been known for decades. On the other hand, the function of motor proteins that support spermatogenesis is also well established since the deletion of motor protein genes leads to subfertility and/or infertility. Furthermore, mutations and genetic variations of motor protein genes affect fertility in men, but also a wide range of developmental defects in humans including multiple organs besides the testis. In this review, we seek to provide a summary of microtubule and actin-dependent motor proteins based on earlier and recent findings in the field. Since these two cytoskeletons are polarized structures, different motor proteins are being used to transport cargoes to different ends of these cytoskeletons. However, their involvement in germ cell transport across the blood-testis barrier (BTB) and the epithelium of the seminiferous tubules remains relatively unknown. It is based on recent findings in the field, we have provided a hypothetical model by which motor proteins are being used to support germ cell transport across the BTB and the seminiferous epithelium during the epithelial cycle of spermatogenesis. In our discussion, we have highlighted the areas of research that deserve attention to bridge the gap of research in relating the function of motor proteins to spermatogenesis.
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Affiliation(s)
- Lingling Wang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China; Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Tiao Bu
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Xiaolong Wu
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Linxi Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Fei Sun
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - C Yan Cheng
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China; Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China.
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8
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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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Kirschen GW, Blakemore K, Al-Kouatly HB, Fridkis G, Baschat A, Gearhart J, Jelin AC. The genetic etiologies of bilateral renal agenesis. Prenat Diagn 2024; 44:205-221. [PMID: 38180355 DOI: 10.1002/pd.6516] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
OBJECTIVE The goal of this study was to review and analyze the medical literature for cases of prenatal and/or postnatally diagnosed bilateral renal agenesis (BRA) and create a comprehensive summary of the genetic etiologies known to be associated with this condition. METHODS A literature search was conducted as a scoping review employing Online Mendeliain Inheritance in Man, PubMed, and Cochrane to identify cases of BRA with known underlying genetic (chromosomal vs. single gene) etiologies and those described in syndromes without any known genetic etiology. The cases were further categorized as isolated versus non-isolated, describing additional findings reported prenatally, postnatally, and postmortem. Inheritance pattern was also documented when appropriate in addition to the reported timing of diagnosis and sex. RESULTS We identified six cytogenetic abnormalities and 21 genes responsible for 20 single gene disorders associated with BRA. Five genes have been reported to associate with BRA without other renal anomalies; sixteen others associate with both BRA as well as unilateral renal agenesis. Six clinically recognized syndromes/associations were identified with an unknown underlying genetic etiology. Genetic etiologies of BRA are often phenotypically expressed as other urogenital anomalies as well as complex multi-system syndromes. CONCLUSION Multiple genetic etiologies of BRA have been described, including cytogenetic abnormalities and monogenic syndromes. The current era of the utilization of exome and genome-wide sequencing is likely to significantly expand our understanding of the underlying genetic architecture of BRA.
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Affiliation(s)
- Gregory W Kirschen
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Karin Blakemore
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Jefferson Health, Philadelphia, New York, USA
| | - Gila Fridkis
- Physician Affiliate Group of New York, P.C. (PAGNY), Department of Pediatrics, Metropolitan Hospital Center, New York, New York, USA
| | - Ahmet Baschat
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - John Gearhart
- Department of Urology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Angie C Jelin
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, The Johns Hopkins Hospital, Baltimore, Maryland, USA
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10
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Li L, Ran J. Regulation of ciliary homeostasis by intraflagellar transport-independent kinesins. Cell Death Dis 2024; 15:47. [PMID: 38218748 PMCID: PMC10787775 DOI: 10.1038/s41419-024-06428-9] [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: 10/01/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
Cilia are highly conserved eukaryotic organelles that protrude from the cell surface and are involved in sensory perception, motility, and signaling. Their proper assembly and function rely on the bidirectional intraflagellar transport (IFT) system, which involves motor proteins, including antegrade kinesins and retrograde dynein. Although the role of IFT-mediated transport in cilia has been extensively studied, recent research has highlighted the contribution of IFT-independent kinesins in ciliary processes. The coordinated activities and interplay between IFT kinesins and IFT-independent kinesins are crucial for maintaining ciliary homeostasis. In this comprehensive review, we aim to delve into the specific contributions and mechanisms of action of the IFT-independent kinesins in cilia. By shedding light on their involvement, we hope to gain a more holistic perspective on ciliogenesis and ciliopathies.
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Affiliation(s)
- Lin Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Jie Ran
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, 250014, China.
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11
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Cacheiro P, Lawson S, Van den Veyver IB, Marengo G, Zocche D, Murray SA, Duyzend M, Robinson PN, Smedley D. Lethal phenotypes in Mendelian disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.12.24301168. [PMID: 38260283 PMCID: PMC10802756 DOI: 10.1101/2024.01.12.24301168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Essential genes are those whose function is required for cell proliferation and/or organism survival. A gene's intolerance to loss-of-function can be allocated within a spectrum, as opposed to being considered a binary feature, since this function might be essential at different stages of development, genetic backgrounds or other contexts. Existing resources that collect and characterise the essentiality status of genes are based on either proliferation assessment in human cell lines, embryonic and postnatal viability evaluation in different model organisms, and gene metrics such as intolerance to variation scores derived from human population sequencing studies. There are also several repositories available that document phenotypic annotations for rare disorders in humans such as the Online Mendelian Inheritance in Man (OMIM) and the Human Phenotype Ontology (HPO) knowledgebases. This raises the prospect of being able to use clinical data, including lethality as the most severe phenotypic manifestation, to further our characterisation of gene essentiality. Here we queried OMIM for terms related to lethality and classified all Mendelian genes into categories, according to the earliest age of death recorded for the associated disorders, from prenatal death to no reports of premature death. To showcase this curated catalogue of human essential genes, we developed the Lethal Phenotypes Portal (https://lethalphenotypes.research.its.qmul.ac.uk), where we also explore the relationships between these lethality categories, constraint metrics and viability in cell lines and mouse. Further analysis of the genes in these categories reveals differences in the mode of inheritance of the associated disorders, physiological systems affected and disease class. We highlight how the phenotypic similarity between genes in the same lethality category combined with gene family/group information can be used for novel disease gene discovery. Finally, we explore the overlaps and discrepancies between the lethal phenotypes observed in mouse and human and discuss potential explanations that include differences in transcriptional regulation, functional compensation and molecular disease mechanisms. We anticipate that this resource will aid clinicians in the diagnosis of early lethal conditions and assist researchers in investigating the properties that make these genes essential for human development.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Ignatia B. Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Gabriel Marengo
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park & St Mark’s Hospitals, London, UK
| | | | | | - Peter N. Robinson
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK
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12
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Crenshaw MM, Thompson L, Piqué DG, Micke K, Saenz M, Baker PR. Congenital diaphragmatic hernia in siblings with PIGA-related congenital disorder of glycosylation. Am J Med Genet A 2023; 191:2860-2867. [PMID: 37589195 DOI: 10.1002/ajmg.a.63373] [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: 12/18/2022] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023]
Abstract
There are over 150 proteins involved in glycosylphosphatidylinositol (GPI)-anchored protein biosynthesis, a class within the larger category of congenital disorders of glycosylation (CDG). Pathogenic variants identified in phosphatidylinositol glycan class A protein (PIGA) are associated with X-linked PIGA-CDG, a GPI-anchor defect. The disease has primarily been characterized by hypotonia, epilepsy, and global developmental delay; however, only 89 known cases are reported, so the phenotypic spectrum has likely not yet been fully delineated. Congenital diaphragmatic hernia (CDH) has been reported in patients with various GPI-anchor related defects but has only been described in one prior individual with PIGA-CDG. Here, we describe the second and third reported cases of CDH in two brothers with PIGA-CDG caused by a pathogenic missense variant in PIGA: c.355C > T, p.R119W. Chromosomal microarray and whole exome sequencing did not reveal another plausible explanation for the CDH. We relate our patients' clinical features to the single previously reported individual with CDH and PIGA-CDG. We then compare this case series with the subset of individuals with CDH and other GPI-anchor defects. These findings suggest that CDH should be considered in the phenotypic disease spectrum of PIGA-CDG.
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Affiliation(s)
- Molly M Crenshaw
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine (CU-SOM), Aurora, Colorado, USA
| | - Lauren Thompson
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine (CU-SOM), Aurora, Colorado, USA
| | - Daniel G Piqué
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine (CU-SOM), Aurora, Colorado, USA
| | - Kestutis Micke
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine (CU-SOM), Aurora, Colorado, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, CU-SOM, Aurora, Colorado, USA
| | - Margarita Saenz
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine (CU-SOM), Aurora, Colorado, USA
| | - Peter R Baker
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine (CU-SOM), Aurora, Colorado, USA
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13
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Moradi B, Ariaei A, Heidari-Foroozan M, Banihashemian M, Ghorani H, Rashidi-Nezhad A, Kazemi MA, Taheri MS. Diagnostic yield of prenatal exome sequencing in the genetic screening of fetuses with brain anomalies detected by MRI and ultrasonography: A systematic review and meta-analysis. BJOG 2023. [PMID: 37932235 DOI: 10.1111/1471-0528.17710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 10/03/2023] [Accepted: 10/22/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Brain anomalies (BAs) have been the focus of research, as they have a high impact on fetal health but therapeutic and diagnostic approaches are limited. OBJECTIVES In this study, the application and efficiency of exome sequencing (ES) in detecting different cases of BAs in fetuses were evaluated and compared with chromosomal microarray analysis (CMA). SEARCH STRATEGY To conduct this study, three databases including PubMed, Web of Science and Embase were utilised with the keywords 'prenatal', 'diagnoses', 'brain anomalies' and 'exome sequencing'. SELECTION CRITERIA Studies were included based on the STARD checklist, for which the ES and CMA diagnostic yields were calculated. DATA COLLECTION AND ANALYSIS Meta-analysis was performed on the included studies using a random-effects model and subgroup analysis to define the risk difference between them. MAIN RESULTS We included 11 studies representing 779 fetuses that implemented ES along with imaging techniques. The pooled ES diagnostic yield in fetuses with BAs detected through magnetic resonance imaging (MRI) and ultrasonography was 26.53%, compared with 3.46% for CMA. The risk difference between ES and CMA for complex BAs was 0.36 [95% confidence interval (CI) 0.24-0.47], which was higher than for single BAs (0.22; 95% CI 0.18-0.25]. CONCLUSIONS ES is a useful method with a significantly higher diagnostic yield than CMA for genetic assessment of fetuses with complex BAs detected by imaging techniques. Moreover, ES could be applied to suspected fetuses with related family histories to predict congenital diseases with high efficiency.
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Affiliation(s)
- Behnaz Moradi
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiology, Yas Complex Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Armin Ariaei
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Student Research Committee, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahsa Heidari-Foroozan
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Banihashemian
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamed Ghorani
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Rashidi-Nezhad
- Maternal, Fetal and Neonatal Research Centre, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Kazemi
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiology, Amiralam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Morteza Sanei Taheri
- Department of Radiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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14
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Cacheiro P, Smedley D. Essential genes: a cross-species perspective. Mamm Genome 2023; 34:357-363. [PMID: 36897351 PMCID: PMC10382395 DOI: 10.1007/s00335-023-09984-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/17/2023] [Indexed: 03/11/2023]
Abstract
Protein coding genes exhibit different degrees of intolerance to loss-of-function variation. The most intolerant genes, whose function is essential for cell or/and organism survival, inform on fundamental biological processes related to cell proliferation and organism development and provide a window on the molecular mechanisms of human disease. Here we present a brief overview of the resources and knowledge gathered around gene essentiality, from cancer cell lines to model organisms to human development. We outline the implications of using different sources of evidence and definitions to determine which genes are essential and highlight how information on the essentiality status of a gene can inform novel disease gene discovery and therapeutic target identification.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK.
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15
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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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16
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Jones AC, Patki A, Claas SA, Tiwari HK, Chaudhary NS, Absher DM, Lange LA, Lange EM, Zhao W, Ratliff SM, Kardia SLR, Smith JA, Irvin MR, Arnett DK. Differentially Methylated DNA Regions and Left Ventricular Hypertrophy in African Americans: A HyperGEN Study. Genes (Basel) 2022; 13:genes13101700. [PMID: 36292585 PMCID: PMC9601679 DOI: 10.3390/genes13101700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Left ventricular (LV) hypertrophy (LVH) is an independent risk factor for cardiovascular disease, and African Americans experience a disparate high risk of LVH. Genetic studies have identified potential candidate genes and variants related to the condition. Epigenetic modifications may continue to help unravel disease mechanisms. We used methylation and echocardiography data from 636 African Americans selected from the Hypertension Genetic Epidemiology Network (HyperGEN) to identify differentially methylated regions (DMRs) associated with LVH. DNA extracted from whole blood was assayed on Illumina Methyl450 arrays. We fit linear mixed models to examine associations between co-methylated regions and LV traits, and we then conducted single CpG analyses within significant DMRs. We identified associations between DMRs and ejection fraction (XKR6), LV internal diastolic dimension (TRAK1), LV mass index (GSE1, RPS15 A, PSMD7), and relative wall thickness (DNHD1). In single CpG analysis, CpG sites annotated to TRAK1 and DNHD1 were significant. These CpGs were not associated with LV traits in replication cohorts but the direction of effect for DNHD1 was consistent across cohorts. Of note, DNHD1, GSE1, and PSMD7 may contribute to cardiac structural function. Future studies should evaluate relationships between regional DNA methylation patterns and the development of LVH.
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Affiliation(s)
- Alana C. Jones
- Department of Epidemiology, School of Public Health, University of Alabama-Birmingham, Birmingham, AL 35233, USA
| | - Amit Patki
- Department of Biostatistics, School of Public Health, University of Alabama-Birmingham, Birmingham, AL 35233, USA
| | - Steven A. Claas
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
| | - Hemant K. Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama-Birmingham, Birmingham, AL 35233, USA
| | - Ninad S. Chaudhary
- Department of Epidemiology, School of Public Health, University of Alabama-Birmingham, Birmingham, AL 35233, USA
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Devin M. Absher
- Hudson Alpha Institute of Biotechnology, Huntsville, AL 35806, USA
| | - Leslie A. Lange
- Department of Epidemiology, School of Public Health, University of Colorado, Aurora, CO 80045, USA
- Department of Biomedical Informatics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Ethan M. Lange
- Department of Biomedical Informatics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
- Department of Biostatistics and Informatics, School of Public Health, University of Colorado, Aurora, CO 80045, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marguerite R. Irvin
- Department of Epidemiology, School of Public Health, University of Alabama-Birmingham, Birmingham, AL 35233, USA
- Correspondence:
| | - Donna K. Arnett
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
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17
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Pauta M, Martinez-Portilla RJ, Borrell A. Diagnostic yield of exome sequencing in fetuses with multisystem malformations: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 59:715-722. [PMID: 35041238 DOI: 10.1002/uog.24862] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/27/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To determine the diagnostic yield of exome sequencing (ES) above that of chromosomal microarray analysis (CMA) or karyotyping in fetuses with multisystem structural anomalies (at least two major anomalies in different anatomical systems). METHOD This was a systematic review conducted in accordance with PRISMA guidelines. Searching PubMed, Web of Knowledge and Cochrane database, we identified studies describing ES, whole-genome and/or next-generation sequencing in fetuses with multisystem malformations. Included were observational studies involving five or more eligible fetuses. A fetus was eligible for inclusion if it had at least two major anomalies of different anatomical systems and a negative CMA or karyotyping result. Only positive variants classified as likely pathogenic or pathogenic determined to be causative of the fetal phenotype were considered. A negative CMA or karyotype result was treated as the reference standard. The diagnostic yield of the primary outcome was calculated by single-proportion analysis using random-effects modeling. A subgroup analysis was performed to compare the diagnostic yield of the solo approach (fetus alone sequenced) with that of the trio approach (fetus and both parents sequenced). RESULTS Seventeen articles with data on ES diagnostic yield, including 694 individuals with multisystem malformations, were identified. Overall, a pathogenic or likely pathogenic variant potentially causative of the fetal phenotype was found in 213 fetuses, giving a 33% (95% CI, 27-40%) incremental yield of ES. A stratified analysis showed similar diagnostic yields of ES using the solo approach (30%; 95% CI, 11-52%) and the trio approach (35%; 95% CI, 26-44%). CONCLUSIONS ES applied in fetuses with multisystem structural anomalies was able to identify a potentially causative gene when CMA or karyotyping had failed to do so in an additional one-third of cases. No differences were observed between the solo and trio approaches for ES. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- M Pauta
- BCNatal, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - R J Martinez-Portilla
- Clinical Research Division, Evidence-Based Medicine Department, National Institute of Perinatology, Mexico City, Mexico
| | - A Borrell
- BCNatal, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
- Barcelona Centre for Maternal-Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Universitat de Barcelona, Barcelona, Catalonia, Spain
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18
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Liu P, Vossaert L. Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing. Prenat Diagn 2022; 42:686-696. [PMID: 35416301 PMCID: PMC10014115 DOI: 10.1002/pd.6146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/10/2022]
Abstract
DNA sequencing technologies for clinical genetic testing have been rapidly evolving in recent years, and steadily become more important within the field of prenatal diagnostics. This review aims to give an overview of recent developments and to describe how they have the potential to fill the gaps of the currently clinically implemented methods for prenatal diagnosis of various genetic disorders. It has been shown for postnatal testing that whole genome sequencing provides a set of added benefits compared to exome sequencing, and it is to be expected that this will be the case for prenatal testing as well. RNA-sequencing, already used postnatally, can provide valuable complementary data to DNA-based testing, and aid in variant interpretation. While not ready for clinical implementation, emerging technologies such as long-read and Hi-C sequencing analyses might add to the toolbox for interpreting the expanding genetic data sets generated by genome-wide sequencing. Lastly, we also discuss some more practical implications of introducing these emerging technologies, which generate larger and larger genomic data sets, in the prenatal field.
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Affiliation(s)
- Pengfei Liu
- Baylor College of Medicine and Baylor Genetics, Houston, Texas, USA
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19
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Chen G, Xiong S, Zou G, Wu F, Qu X, Alawbathani S, Sun L. A 6.3 Mb maternally derived microduplication of 20p13p12.2 in a fetus with Brachydactyly type D and related literature review. Mol Cytogenet 2022; 15:6. [PMID: 35227291 PMCID: PMC8887085 DOI: 10.1186/s13039-022-00584-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/26/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
With the introduction of genetic tests such as chromosomal microarray analysis (CMA) and exome sequencing (ES) into fetal medical practices, genotype–phenotype correlations in intrauterine-onset disorders have substantially improved. The BMP2 gene, located on the long arm of chromosome 20 plays a role in bone and cartilage development and is associated with Brachydactyly type A2, an autosomal dominant disease characterized by malformations of the middle phalanx of the index finger and abnormalities of the second toe. However, the BMP2 gene has so far never been reported as a candidate gene for Brachydactyly type D (BDD) affecting only the thumbs.
Methods and
results
Here, we report one family possessing a maternally inherited 6.3 Mb microduplication of 20p13p12.2 including the BMP2 gene with discordant phenotypes between the mother and the fetus. The mother was affected with BDD alongside mild facial dysmorphism and learning difficulties, while the female fetus showed BDD, severe symmetric intrauterine growth restriction combined with oligohydramnios. The CMA and Trio ES tests were implemented. Trio ES ruled out other possible monogenic causes for the family. After reviewing cases and literature with duplications within this genomic region, we found that they are extremely rare and most of the cited cases were too small for comparison. The disturbance of the BMP2 gene could explain BDD, but the other clinical presentations in the mother and fetus are not yet fully understood.
Conclusion
This study provides important evidence for the current understanding of genotype–phenotype association of this 6.3 Mb size duplication in the 20p13p12.2 region. This duplication is a unique CNV occurring so far only in this family. Further cases and research are needed to understand the discordance in the phenotypes between the mother and fetus and establish the relationship between BMP2 gene and BDD.
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20
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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: 8] [Impact Index Per Article: 4.0] [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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21
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Mellis R, Oprych K, Scotchman E, Hill M, Chitty LS. Diagnostic yield of exome sequencing for prenatal diagnosis of fetal structural anomalies: A systematic review and meta-analysis. Prenat Diagn 2022; 42:662-685. [PMID: 35170059 PMCID: PMC9325531 DOI: 10.1002/pd.6115] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/10/2022]
Abstract
Objectives We conducted a systematic review and meta‐analysis to determine the diagnostic yield of exome sequencing (ES) for prenatal diagnosis of fetal structural anomalies, where karyotype/chromosomal microarray (CMA) is normal. Methods Following electronic searches of four databases, we included studies with ≥10 structurally abnormal fetuses undergoing ES or whole genome sequencing. The incremental diagnostic yield of ES over CMA/karyotype was calculated and pooled in a meta‐analysis. Sub‐group analyses investigated effects of case selection and fetal phenotype on diagnostic yield. Results We identified 72 reports from 66 studies, representing 4350 fetuses. The pooled incremental yield of ES was 31% (95% confidence interval (CI) 26%–36%, p < 0.0001). Diagnostic yield was significantly higher for cases pre‐selected for likelihood of monogenic aetiology compared to unselected cases (42% vs. 15%, p < 0.0001). Diagnostic yield differed significantly between phenotypic sub‐groups, ranging from 53% (95% CI 42%–63%, p < 0.0001) for isolated skeletal abnormalities, to 2% (95% CI 0%–5%, p = 0.04) for isolated increased nuchal translucency. Conclusion Prenatal ES provides a diagnosis in an additional 31% of structurally abnormal fetuses when CMA/karyotype is non‐diagnostic. The expected diagnostic yield depends on the body system(s) affected and can be optimised by pre‐selection of cases following multi‐disciplinary review to determine that a monogenic cause is likely.
What's already known about this topic?
Prenatal exome sequencing (ES) increases genetic diagnoses in fetuses with structural abnormalities and a normal karyotype and chromosomal microarray. Published diagnostic yields from ES are varied and may be influenced by study size, case selection and fetal phenotype.
What does this study add?
This study provides a comprehensive systematic review of the literature to date and investigates the diagnostic yield of ES for a range of isolated system anomalies, to support clinical decision‐making on how to offer prenatal ES.
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Affiliation(s)
- Rhiannon Mellis
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | | | - Elizabeth Scotchman
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Melissa Hill
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Lyn S Chitty
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
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22
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Buonaiuto S, Biase ID, Aleotti V, Ravaei A, Marino AD, Damaggio G, Chierici M, Pulijala M, D'Ambrosio P, Esposito G, Ayub Q, Furlanello C, Greco P, Capalbo A, Rubini M, Biase SD, Colonna V. Prioritization of putatively detrimental variants in euploid miscarriages. Sci Rep 2022; 12:1997. [PMID: 35132093 PMCID: PMC8821623 DOI: 10.1038/s41598-022-05737-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/11/2022] [Indexed: 12/21/2022] Open
Abstract
Miscarriage is the spontaneous termination of a pregnancy before 24 weeks of gestation. We studied the genome of euploid miscarried embryos from mothers in the range of healthy adult individuals to understand genetic susceptibility to miscarriage not caused by chromosomal aneuploidies. We developed GP , a pipeline that we used to prioritize 439 unique variants in 399 genes, including genes known to be associated with miscarriages. Among the prioritized genes we found STAG2 coding for the cohesin complex subunit, for which inactivation in mouse is lethal, and TLE4 a target of Notch and Wnt, physically interacting with a region on chromosome 9 associated to miscarriages.
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Affiliation(s)
| | | | - Valentina Aleotti
- Department of Neurosciences and Rehabilitation, University of Ferrara, Ferrara, 44121, Italy
| | - Amin Ravaei
- Department of Neurosciences and Rehabilitation, University of Ferrara, Ferrara, 44121, Italy
| | | | | | | | - Madhuri Pulijala
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500, Bandar Sunway, Malaysia
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Malaysia
| | | | | | - Qasim Ayub
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500, Bandar Sunway, Malaysia
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Malaysia
| | | | - Pantaleo Greco
- Department of Medical Sciences, University of Ferrara, Ferrara, 44121, Italy
| | | | - Michele Rubini
- Department of Neurosciences and Rehabilitation, University of Ferrara, Ferrara, 44121, Italy
| | | | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy.
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23
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Lead (Pb) and neurodevelopment: A review on exposure and biomarkers of effect (BDNF, HDL) and susceptibility. Int J Hyg Environ Health 2021; 238:113855. [PMID: 34655857 DOI: 10.1016/j.ijheh.2021.113855] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022]
Abstract
Lead (Pb) is a ubiquitous environmental pollutant and a potent toxic compound. Humans are exposed to Pb through inhalation, ingestion, and skin contact via food, water, tobacco smoke, air, dust, and soil. Pb accumulates in bones, brain, liver and kidney. Fetal exposure occurs via transplacental transmission. The most critical health effects are developmental neurotoxicity in infants and cardiovascular effects and nephrotoxicity in adults. Pb exposure has been steadily decreasing over the past decades, but there are few recent exposure data from the general European population; moreover, no safe Pb limit has been set. Sensitive biomarkers of exposure, effect and susceptibility, that reliably and timely indicate Pb-associated toxicity are required to assess human exposure-health relationships in a situation of low to moderate exposure. Therefore, a systematic literature review based on PubMed entries published before July 2019 that addressed Pb exposure and biomarkers of effect and susceptibility, neurodevelopmental toxicity, epigenetic modifications, and transcriptomics was conducted. Finally included were 58 original papers on Pb exposure and 17 studies on biomarkers. The biomarkers that are linked to Pb exposure and neurodevelopment were grouped into effect biomarkers (serum brain-derived neurotrophic factor (BDNF) and serum/saliva cortisol), susceptibility markers (epigenetic markers and gene sequence variants) and other biomarkers (serum high-density lipoprotein (HDL), maternal iron (Fe) and calcium (Ca) status). Serum BDNF and plasma HDL are potential candidates to be further validated as effect markers for routine use in HBM studies of Pb, complemented by markers of Fe and Ca status to also address nutritional interactions related to neurodevelopmental disorders. For several markers, a causal relationship with Pb-induced neurodevelopmental toxicity is likely. Results on BDNF are discussed in relation to Adverse Outcome Pathway (AOP) 13 ("Chronic binding of antagonist to N-methyl-D-aspartate receptors (NMDARs) during brain development induces impairment of learning and memory abilities") of the AOP-Wiki. Further studies are needed to validate sensitive, reliable, and timely effect biomarkers, especially for low to moderate Pb exposure scenarios.
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24
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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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25
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Kalantari S, Carlston C, Alsaleh N, Abdel-Salam GMH, Alkuraya F, Kato M, Matsumoto N, Miyatake S, Yamamoto T, Fares-Taie L, Rozet JM, Chassaing N, Vincent-Delorme C, Kang-Bellin A, McWalter K, Bupp C, Palen E, Wagner MD, Niceta M, Cesario C, Milone R, Kaplan J, Wadman E, Dobyns WB, Filges I. Expanding the KIF4A-associated phenotype. Am J Med Genet A 2021; 185:3728-3739. [PMID: 34346154 PMCID: PMC9291479 DOI: 10.1002/ajmg.a.62443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 01/30/2023]
Abstract
Kinesin super family (KIF) genes encode motor kinesins, a family of evolutionary conserved proteins, involved in intracellular trafficking of various cargoes. These proteins are critical for various physiological processes including neuron function and survival, ciliary function and ciliogenesis, and cell‐cycle progression. Recent evidence suggests that alterations in motor kinesin genes can lead to a variety of human diseases, including monogenic disorders. Neuropathies, impaired higher brain functions, structural brain abnormalities and multiple congenital anomalies (i.e., renal, urogenital, and limb anomalies) can result from pathogenic variants in many KIF genes. We expand the phenotype associated with KIF4A variants from developmental delay and intellectual disability with or without epilepsy to a congenital anomaly phenotype with hydrocephalus and various brain anomalies at the more severe end of phenotypic manifestations. Additional anomalies of the kidneys and urinary tract, congenital lymphedema, eye, and dental anomalies seem to be variably associated and overlap with clinical signs observed in other kinesinopathies. Caution still applies to missense variants, but hopefully, future work will further establish genotype–phenotype correlations in a larger number of patients and functional studies may give further insights into the complex function of KIF4A.
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Affiliation(s)
- Silvia Kalantari
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Colleen Carlston
- Division of Medical Genetics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Norah Alsaleh
- Division of Medical Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ghada M H Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Fowzan Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Shinagawa-ku, Japan
| | - Naomichi Matsumoto
- 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
| | - Tatsuya Yamamoto
- Department of Pediatrics, Hirosaki University School of Medicine, Hirosaki, Japan
| | - Lucas Fares-Taie
- INSERM UMR1163, Imagine - Institute of Genetic Diseases, Paris Descartes University, Paris, France
| | - Jean-Michel Rozet
- INSERM UMR1163, Imagine - Institute of Genetic Diseases, Paris Descartes University, Paris, France
| | - Nicolas Chassaing
- Department of Medical Genetics, CHU Toulouse, Purpan Hospital, Toulouse, France
| | | | | | | | - Caleb Bupp
- Spectrum Health, Grand Rapids, Michigan, USA
| | - Emily Palen
- Autism & Developmental Medicine Institute, Danville, Pennsylvania, USA
| | - Monisa D Wagner
- Autism & Developmental Medicine Institute, Danville, Pennsylvania, USA
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Claudia Cesario
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Roberta Milone
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Calambrone, Pisa, Italy
| | - Julie Kaplan
- Division of Genetics, Department of Pediatrics, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, Delaware, USA
| | - Erin Wadman
- Division of Genetics, Department of Pediatrics, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, Delaware, USA
| | - William B Dobyns
- Division of Genetics, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
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26
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Han G, Jin T, Zhang L, Guo C, Gui H, Na R, Wang X, Bai H. Application of Combined Ultrasound and Maternal Serum Biochemical Indexes in the Detection of Fetal Structural Abnormalities and Chromosomal Abnormalities. JOURNAL OF MEDICAL IMAGING AND HEALTH INFORMATICS 2021. [DOI: 10.1166/jmihi.2021.3551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
By exploring different prenatal diagnosis indications of fetal chromosomal abnormalities, it can provide a theoretical basis and reference value for clinical consultation of pregnant women with similar high-risk factors. In this paper, 1800 pregnant women undergoing amniotic fluid aspiration
chromosomal examination in the prenatal diagnosis center were selected as the object of this study. Amniocentesis, fetal cell culture, and karyotype analysis were performed on pregnant women who were 14-20 weeks pregnant and had signed an informed consent. After amniocentesis fetal chromosome
analysis, the type of fetal chromosomal abnormality was determined, and the detection rate of chromosomal abnormality was statistically described. Chi-square test was used for comparison between groups, P < 0.05. This study shows that the use of ultrasound screening combined with
maternal serum indicators is effective in screening fetal structural abnormalities and chromosomal abnormalities in early pregnancy, and significantly improves the detection rate of chromosomal abnormalities. The detection of fetal structural malformations is also very high, but it should
be combined with ultrasound screening of mid-to-late pregnancy. The tricuspid regurgitation and umbilical vein a-wave reversal in the soft ultrasound index can be used as predictors of fetal congenital heart disease in early pregnancy.
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Affiliation(s)
- Guowei Han
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Tianliang Jin
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Li Zhang
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Chen Guo
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Hua Gui
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Risu Na
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Xuesong Wang
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Haihua Bai
- Inner Mongolia Engineering and Technical Research Center for Personalized Medicine, Tongliao City, Inner Mongolia, 028000, China
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27
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Importance of determining variations in the number of copies in newborns with autosomal aneuploidies. ACTA ACUST UNITED AC 2021; 41:282-292. [PMID: 34214269 PMCID: PMC8387016 DOI: 10.7705/biomedica.5354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Indexed: 11/21/2022]
Abstract
Introducción. Las aneuploidías son trastornos genéticos frecuentes en la práctica clínica; sin embargo, se conoce poco sobre las otras variantes genéticas que modifican el fenotipo final. Objetivo. Determinar las variantes en el número de copias y las regiones con pérdida de heterocigosidad autosómica mayor de 0,5 % o de regiones mayores de 10 Mb en neonatos con aneuploidías autosómicas. Materiales y métodos. Se hizo el análisis cromosómico por micromatrices a los neonatos con aneuploidías autosómicas (n=7), trisomía 21 (n=5) y trisomía 18 (n=2) evaluados en los hospitales Antonio Lorena y Regional de Cusco, Perú, en el 2018. Resultados. En dos neonatos se encontraron variantes en el número de copias, patogénicas o probablemente patogénicas, en regiones diferentes al cromosoma 21 o al 18. Además, se observaron dos variantes del número de copias con más de 500 kpb de patogenia desconocida. Conclusiones. Si bien el número de pacientes era muy reducido, es importante resaltar que se encontraron otras variantes en el número de copias que se han descrito asociadas con trastornos del neurodesarrollo, varias anomalías congénitas, hipoacusia y talla baja o alta, entre otras, lo que probablemente influye negativamente en el fenotipo de este grupo de pacientes.
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28
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Cannata G, Caporilli C, Grassi F, Perrone S, Esposito S. Management of Congenital Diaphragmatic Hernia (CDH): Role of Molecular Genetics. Int J Mol Sci 2021; 22:ijms22126353. [PMID: 34198563 PMCID: PMC8231903 DOI: 10.3390/ijms22126353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 12/11/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a relatively common major life-threatening birth defect that results in significant mortality and morbidity depending primarily on lung hypoplasia, persistent pulmonary hypertension, and cardiac dysfunction. Despite its clinical relevance, CDH multifactorial etiology is still not completely understood. We reviewed current knowledge on normal diaphragm development and summarized genetic mutations and related pathways as well as cellular mechanisms involved in CDH. Our literature analysis showed that the discovery of harmful de novo variants in the fetus could constitute an important tool for the medical team during pregnancy, counselling, and childbirth. A better insight into the mechanisms regulating diaphragm development and genetic causes leading to CDH appeared essential to the development of new therapeutic strategies and evidence-based genetic counselling to parents. Integrated sequencing, development, and bioinformatics strategies could direct future functional studies on CDH; could be applied to cohorts and consortia for CDH and other birth defects; and could pave the way for potential therapies by providing molecular targets for drug discovery.
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Affiliation(s)
- Giulia Cannata
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
| | - Chiara Caporilli
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
| | - Federica Grassi
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
| | - Serafina Perrone
- Neonatology Unit, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy;
| | - Susanna Esposito
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
- Correspondence: ; Tel.: +39-0521-7047
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29
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Li N, Zhou P, Tang H, He L, Fang X, Zhao J, Wang X, Qi Y, Sun C, Lin Y, Qin F, Yang M, Zhang Z, Liao C, Zheng S, Peng X, Xue T, Zhu Q, Li H, Li Y, Liu L, Huang J, Liu L, Peng C, Kaindl AM, Gecz J, Han D, Liu D, Xu K, Hu H. In-depth analysis reveals complex molecular aetiology in a cohort of idiopathic cerebral palsy. Brain 2021; 145:119-141. [PMID: 34077496 PMCID: PMC8967106 DOI: 10.1093/brain/awab209] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/27/2021] [Accepted: 05/17/2021] [Indexed: 12/02/2022] Open
Abstract
Cerebral palsy is the most prevalent physical disability in children; however, its inherent molecular mechanisms remain unclear. In the present study, we performed in-depth clinical and molecular analysis on 120 idiopathic cerebral palsy families, and identified underlying detrimental genetic variants in 45% of these patients. In addition to germline variants, we found disease-related postzygotic mutations in ∼6.7% of cerebral palsy patients. We found that patients with more severe motor impairments or a comorbidity of intellectual disability had a significantly higher chance of harbouring disease-related variants. By a compilation of 114 known cerebral-palsy-related genes, we identified characteristic features in terms of inheritance and function, from which we proposed a dichotomous classification system according to the expression patterns of these genes and associated cognitive impairments. In two patients with both cerebral palsy and intellectual disability, we revealed that the defective TYW1, a tRNA hypermodification enzyme, caused primary microcephaly and problems in motion and cognition by hindering neuronal proliferation and migration. Furthermore, we developed an algorithm and demonstrated in mouse brains that this malfunctioning hypermodification specifically perturbed the translation of a subset of proteins involved in cell cycling. This finding provided a novel and interesting mechanism for congenital microcephaly. In another cerebral palsy patient with normal intelligence, we identified a mitochondrial enzyme GPAM, the hypomorphic form of which led to hypomyelination of the corticospinal tract in both human and mouse models. In addition, we confirmed that the aberrant Gpam in mice perturbed the lipid metabolism in astrocytes, resulting in suppressed astrocytic proliferation and a shortage of lipid contents supplied for oligodendrocytic myelination. Taken together, our findings elucidate novel aspects of the aetiology of cerebral palsy and provide insights for future therapeutic strategies.
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Affiliation(s)
- Na Li
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Pei Zhou
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Hongmei Tang
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510120, Guangzhou, China
| | - Lu He
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510120, Guangzhou, China
| | - Xiang Fang
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Jinxiang Zhao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Nantong University, 226001, Nantong, China
| | - Xin Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Nantong University, 226001, Nantong, China
| | - Yifei Qi
- Division of Uterine Vascular Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Yunting Lin
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Fengying Qin
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Miaomiao Yang
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Zhan Zhang
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Caihua Liao
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Shuxin Zheng
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Xiaofang Peng
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Ting Xue
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Qianying Zhu
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Hong Li
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Yan Li
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Liru Liu
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510120, Guangzhou, China
| | - Jingyu Huang
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510120, Guangzhou, China
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Changgeng Peng
- The First Rehabilitation Hospital of Shanghai, Tongji University School of Medicine, 200029, Shanghai, China
| | - Angela M Kaindl
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin, 13353, Berlin, Germany.,Department of Pediatric Neurology, Charité-Universitätsmedizin, 13353, Berlin, Germany.,Center for Chronically Sick Children, Charité-Universitätsmedizin, 13353, Berlin, Germany
| | - Jozef Gecz
- Adelaide Medical School, University of Adelaide, SA5005, Adelaide, Australia
| | - Dingding Han
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Dong Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Nantong University, 226001, Nantong, China
| | - Kaishou Xu
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510120, Guangzhou, China
| | - Hao Hu
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China.,Third Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
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30
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Sun L, Yang X, Xu Y, Sun S, Wu Q. Prenatal diagnosis of familial recessive PIGN mutation associated with multiple anomalies: A case report. Taiwan J Obstet Gynecol 2021; 60:530-533. [PMID: 33966742 DOI: 10.1016/j.tjog.2021.03.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2020] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE We present a novel homozygous splice site mutation in the PIGN gene identified by whole exome sequencing and explored the genotype-phenotype correlation. CASE REPORT A healthy 32-year-old woman underwent an ultrasound at 13 + 5 weeks of gestation. The ultrasound revealed multiple anomalies again including cystic hygroma, omphalocele and a ventricular septal defect. The pregnancy was subsequently terminated, and whole exome sequencing revealed a novel homozygous splice site mutation in the PIGN gene c.963 G > A (p.Gln321Gln). The same variant was also detected by pedigree-based Sanger sequencing in both parents as heterozygous, while they had normal karyotypes. CONCLUSION Our case report enhances the phenotype-genotype correlation associated with homozygous loss of function mutations in the PIGN gene.
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Affiliation(s)
- Li Sun
- Center of Prenatal Diagnosis, Women and Children's Hospital Affiliated to Xiamen University, PR China
| | - Xiaomei Yang
- Center of Prenatal Diagnosis, Women and Children's Hospital Affiliated to Xiamen University, PR China
| | - Yasong Xu
- Center of Prenatal Diagnosis, Women and Children's Hospital Affiliated to Xiamen University, PR China
| | - Shiyu Sun
- Center of Prenatal Diagnosis, Women and Children's Hospital Affiliated to Xiamen University, PR China
| | - Qichang Wu
- Center of Prenatal Diagnosis, Women and Children's Hospital Affiliated to Xiamen University, PR China.
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31
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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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32
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Zhou J, Yang Z, Sun J, Liu L, Zhou X, Liu F, Xing Y, Cui S, Xiong S, Liu X, Yang Y, Wei X, Zou G, Wang Z, Wei X, Wang Y, Zhang Y, Yan S, Wu F, Zeng F, Wang J, Duan T, Peng Z, Sun L. Whole Genome Sequencing in the Evaluation of Fetal Structural Anomalies: A Parallel Test with Chromosomal Microarray Plus Whole Exome Sequencing. Genes (Basel) 2021; 12:genes12030376. [PMID: 33800913 PMCID: PMC7999180 DOI: 10.3390/genes12030376] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/23/2022] Open
Abstract
Whole genome sequencing (WGS) is a powerful tool for postnatal genetic diagnosis, but relevant clinical studies in the field of prenatal diagnosis are limited. The present study aimed to prospectively evaluate the utility of WGS compared with chromosomal microarray (CMA) and whole exome sequencing (WES) in the prenatal diagnosis of fetal structural anomalies. We performed trio WGS (≈40-fold) in parallel with CMA in 111 fetuses with structural or growth anomalies, and sequentially performed WES when CMA was negative (CMA plus WES). In comparison, WGS not only detected all pathogenic genetic variants in 22 diagnosed cases identified by CMA plus WES, yielding a diagnostic rate of 19.8% (22/110), but also provided additional and clinically significant information, including a case of balanced translocations and a case of intrauterine infection, which might not be detectable by CMA or WES. WGS also required less DNA (100 ng) as input and could provide a rapid turnaround time (TAT, 18 ± 6 days) compared with that (31 ± 8 days) of the CMA plus WES. Our results showed that WGS provided more comprehensive and precise genetic information with a rapid TAT and less DNA required than CMA plus WES, which enables it as an alternative prenatal diagnosis test for fetal structural anomalies.
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Affiliation(s)
- Jia Zhou
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
| | - Ziying Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Jun Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Lipei Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Xinyao Zhou
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
| | - Fengxia Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Ya Xing
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
| | - Shuge Cui
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Shiyi Xiong
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
| | - Xiaoyu Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Yingjun Yang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
| | - Xiuxiu Wei
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Gang Zou
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
| | - Zhonghua Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Xing Wei
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
| | - Yaoshen Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Yun Zhang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
| | - Saiying Yan
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Fengyu Wu
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
| | - Fanwei Zeng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Department of Biology, Faculty of Science, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, China;
| | - Tao Duan
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; (Z.Y.); (J.S.); (L.L.); (F.L.); (S.C.); (X.L.); (X.W.); (Z.W.); (Y.W.); (S.Y.); (F.Z.)
- Correspondence: (Z.P.); (L.S.)
| | - Luming Sun
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China; (J.Z.); (X.Z.); (Y.X.); (S.X.); (Y.Y.); (G.Z.); (X.W.); (Y.Z.); (F.W.); (T.D.)
- Correspondence: (Z.P.); (L.S.)
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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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Wu S, Li H, Wang L, Mak N, Wu X, Ge R, Sun F, Cheng CY. Motor Proteins and Spermatogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1288:131-159. [PMID: 34453735 DOI: 10.1007/978-3-030-77779-1_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Unlike the intermediate filament- and septin-based cytoskeletons which are apolar structures, the microtubule (MT) and actin cytoskeletons are polarized structures in mammalian cells and tissues including the testis, most notable in Sertoli cells. In the testis, these cytoskeletons that stretch across the epithelium of seminiferous tubules and lay perpendicular to the basement membrane of tunica propria serve as tracks for corresponding motor proteins to support cellular cargo transport. These cargoes include residual bodies, phagosomes, endocytic vesicles and most notably developing spermatocytes and haploid spermatids which lack the ultrastructures of motile cells (e.g., lamellipodia, filopodia). As such, these developing germ cells require the corresponding motor proteins to facilitate their transport across the seminiferous epithelium during the epithelial cycle of spermatogenesis. Due to the polarized natures of these cytoskeletons with distinctive plus (+) and minus (-) end, directional cargo transport can take place based on the use of corresponding actin- or MT-based motor proteins. These include the MT-based minus (-) end directed motor proteins: dyneins, and the plus (+) end directed motor proteins: kinesins, as well as the actin-based motor proteins: myosins, many of which are plus (+) end directed but a few are also minus (-) end directed motor proteins. Recent studies have shown that these motor proteins are essential to support spermatogenesis. In this review, we briefly summarize and evaluate these recent findings so that this information will serve as a helpful guide for future studies and for planning functional experiments to better understand their role mechanistically in supporting spermatogenesis.
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Affiliation(s)
- Siwen Wu
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Zhejiang, China.,The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, NY, USA
| | - Huitao Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Zhejiang, China.,The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, NY, USA
| | - Lingling Wang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Zhejiang, China.,The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, NY, USA.,Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu, China
| | - Nathan Mak
- The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, NY, USA
| | - Xiaolong Wu
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu, China
| | - Renshan Ge
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Zhejiang, China
| | - Fei Sun
- Sir Run Run Shaw Hospital (SRRSH), Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - C Yan Cheng
- Sir Run Run Shaw Hospital (SRRSH), Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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35
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Chitty LS, Ghidini A, Deprest J, Van Mieghem T, Levy B, Hui L, Bianchi DW. Right or wrong? Looking through the retrospectoscope to analyse predictions made a decade ago in prenatal diagnosis and fetal surgery. Prenat Diagn 2020; 40:1627-1635. [PMID: 33231306 DOI: 10.1002/pd.5870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Lyn 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
| | - Alessandro Ghidini
- Department of Obstetrics and Gynecology, Georgetown University Hospital, Washington, DC.,Antenatal Testing Center, Inova Alexandria Hospital, Alexandria, VA
| | - Jan Deprest
- Department of Obstetrics and Gynaecology, University of Leuven, Leuven, Belgium and the Institute for Women's Health, UCL, London
| | - Tim Van Mieghem
- Fetal Medicine Unit and Ontario Fetal Centre, Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Brynn Levy
- Division of Personalized Genomic Medicine, Columbia University Medical Center & the New York Presbyterian Hospital, New York, New York, USA
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Victoria, Australia.,Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Murdoch Children's Research Institute, Parkville, Victoria, Australia.,The Northern Hospital, Epping, Victoria, Australia
| | - Diana W Bianchi
- Division of Prenatal Genomics and Fetal Therapy, Medical Genomics and Metabolic Genetics Branch, National Human Genome Institute, National Human Genome Institute, National Institutes of Health, Bethesda, Maryland, USA
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Lefebvre M, Bruel AL, Tisserant E, Bourgon N, Duffourd Y, Collardeau-Frachon S, Attie-Bitach T, Kuentz P, Assoum M, Schaefer E, El Chehadeh S, Antal MC, Kremer V, Girard-Lemaitre F, Mandel JL, Lehalle D, Nambot S, Jean-Marçais N, Houcinat N, Moutton S, Marle N, Lambert L, Jonveaux P, Foliguet B, Mazutti JP, Gaillard D, Alanio E, Poirisier C, Lebre AS, Aubert-Lenoir M, Arbez-Gindre F, Odent S, Quélin C, Loget P, Fradin M, Willems M, Bigi N, Perez MJ, Blesson S, Francannet C, Beaufrere AM, Patrier-Sallebert S, Guerrot AM, Goldenberg A, Brehin AC, Lespinasse J, Touraine R, Capri Y, Saint-Frison MH, Laurent N, Philippe C, Tran Mau-Them F, Thevenon J, Faivre L, Thauvin-Robinet C, Vitobello A. Genotype-first in a cohort of 95 fetuses with multiple congenital abnormalities: when exome sequencing reveals unexpected fetal phenotype-genotype correlations. J Med Genet 2020; 58:400-413. [PMID: 32732226 DOI: 10.1136/jmedgenet-2020-106867] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/04/2020] [Accepted: 05/21/2020] [Indexed: 11/03/2022]
Abstract
PURPOSE Molecular diagnosis based on singleton exome sequencing (sES) is particularly challenging in fetuses with multiple congenital abnormalities (MCA). Indeed, some studies reveal a diagnostic yield of about 20%, far lower than in live birth individuals showing developmental abnormalities (30%), suggesting that standard analyses, based on the correlation between clinical hallmarks described in postnatal syndromic presentations and genotype, may underestimate the impact of the genetic variants identified in fetal analyses. METHODS We performed sES in 95 fetuses with MCA. Blind to phenotype, we applied a genotype-first approach consisting of combined analyses based on variants annotation and bioinformatics predictions followed by reverse phenotyping. Initially applied to OMIM-morbid genes, analyses were then extended to all genes. We complemented our approach by using reverse phenotyping, variant segregation analysis, bibliographic search and data sharing in order to establish the clinical significance of the prioritised variants. RESULTS sES rapidly identified causal variant in 24/95 fetuses (25%), variants of unknown significance in OMIM genes in 8/95 fetuses (8%) and six novel candidate genes in 6/95 fetuses (6%). CONCLUSIONS This method, based on a genotype-first approach followed by reverse phenotyping, shed light on unexpected fetal phenotype-genotype correlations, emphasising the relevance of prenatal studies to reveal extreme clinical presentations associated with well-known Mendelian disorders.
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Affiliation(s)
- Mathilde Lefebvre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Laboratoire d'Anatomo-Pathologie, Plateforme de Biologie Hospitalo-Universitaire, CHU de Dijon Bourgogne, Dijon, France
| | - Ange-Line Bruel
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Emilie Tisserant
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Nicolas Bourgon
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Yannis Duffourd
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | | | - Tania Attie-Bitach
- Laboratoire d'Embryologie et de Génétique des Malformations Congénitales, Hopital Necker, APHP, Paris Cedex 15, France
| | - Paul Kuentz
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Mirna Assoum
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France
| | - Elise Schaefer
- Service de Génétique Médicale, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Salima El Chehadeh
- Service de Génétique Médicale, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Maria Cristina Antal
- Service de Fœtopathologie, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Valérie Kremer
- Laboratoire de Cytogénétique constitutionnelle et prénatale, CHU de Strasbourg, Strasbourg, France
| | - Françoise Girard-Lemaitre
- Département Médecine translationnelle et neurogénétique, Institut de génétique et de biologie moléculaire et cellulaire, Strasbourg, France
| | - Jean-Louis Mandel
- Département Médecine translationnelle et neurogénétique, Institut de génétique et de biologie moléculaire et cellulaire, Strasbourg, France
| | - Daphne Lehalle
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Nolwenn Jean-Marçais
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Nada Houcinat
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sébastien Moutton
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire de Génétique chromosomique et moléculaire, CHU de Dijon Bourgogne, Dijon, France
| | - Laetita Lambert
- UF de Génétique médicale, Maternité régionale, CHU de Nancy, Nancy, France
| | | | - Bernard Foliguet
- Laboratoire de Biologie de la Reproduction et du Développement Maternité de Nancy, CHU de Nancy, Nancy, France
| | - Jean-Pierre Mazutti
- Laboratoire de Biologie de la Reproduction et du Développement Maternité de Nancy, CHU de Nancy, Nancy, France
| | | | | | | | - Anne-Sophie Lebre
- Service de Génétique et Biologie de la Reproduction, CHU de Reims, Reims, France
| | | | | | - Sylvie Odent
- Service de Génétique Clinique, Hôpital Sud, CLAD Ouest, CNRS UMR6290 Génétique et Pathologies du Développement, Université de Rennes, Rennes, France
| | - Chloé Quélin
- Service de Génétique Clinique, Hôpital Sud, CLAD Ouest, CNRS UMR6290 Génétique et Pathologies du Développement, Université de Rennes, Rennes, France.,Service de Fœtopathologie, CHU de Rennes, Rennes, France
| | - Philippe Loget
- Service de Fœtopathologie, CHU de Rennes, Rennes, France
| | - Melanie Fradin
- Service de Génétique Clinique, Hôpital Sud, CLAD Ouest, CNRS UMR6290 Génétique et Pathologies du Développement, Université de Rennes, Rennes, France
| | - Marjolaine Willems
- Equipe Maladies Génétiques de l'Enfant et de l'Adulte, CHU de Montpellier, Montpellier, France
| | - Nicole Bigi
- Service de Fœtopathologie, CHU de Montpellier, Montpellier, France
| | - Marie-José Perez
- Service de Fœtopathologie, CHU de Montpellier, Montpellier, France
| | | | - Christine Francannet
- Service de Génétique médicale, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | | | | | | | | | | | | | - Renaud Touraine
- Service de Genetique Clinique, C.H.U. De Saint Etienne-Hopital Nord, Saint Etienne Cedex 2, France
| | - Yline Capri
- Service de génétique clinique, Hôpital Robert Debré - APHP, Paris, France
| | | | - Nicole Laurent
- Laboratoire d'Anatomo-Pathologie, Plateforme de Biologie Hospitalo-Universitaire, CHU de Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Frederic Tran Mau-Them
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Julien Thevenon
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Département de Génétique et Procréation, CHU Grenoble Alpes, Université Grenoble Alpes, Grenoble, France
| | - Laurence Faivre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de L'Est, Hôpital D'Enfants, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France .,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD « Génétique des Anomalies du Développement », FHU-TRANSLAD, Dijon, France .,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
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37
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Corsten-Janssen N, Bouman K, Diphoorn JCD, Scheper AJ, Kinds R, El Mecky J, Breet H, Verheij JBGM, Suijkerbuijk R, Duin LK, Manten GTR, van Langen IM, Sijmons RH, Sikkema-Raddatz B, Westers H, van Diemen CC. A prospective study on rapid exome sequencing as a diagnostic test for multiple congenital anomalies on fetal ultrasound. Prenat Diagn 2020; 40:1300-1309. [PMID: 32627857 PMCID: PMC7540374 DOI: 10.1002/pd.5781] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 06/11/2020] [Accepted: 06/27/2020] [Indexed: 12/22/2022]
Abstract
Objective Conventional genetic tests (quantitative fluorescent‐PCR [QF‐PCR] and single nucleotide polymorphism‐array) only diagnose ~40% of fetuses showing ultrasound abnormalities. Rapid exome sequencing (rES) may improve this diagnostic yield, but includes challenges such as uncertainties in fetal phenotyping, variant interpretation, incidental unsolicited findings, and rapid turnaround times. In this study, we implemented rES in prenatal care to increase diagnostic yield. Methods We prospectively studied 55 fetuses. Inclusion criteria were: (a) two or more independent major fetal anomalies, (b) hydrops fetalis or bilateral renal cysts alone, or (c) one major fetal anomaly and a first‐degree relative with the same anomaly. In addition to conventional genetic tests, we performed trio rES analysis using a custom virtual gene panel of ~3850 Online Mendelian Inheritance in Man (OMIM) genes. Results We established a genetic rES‐based diagnosis in 8 out of 23 fetuses (35%) without QF‐PCR or array abnormalities. Diagnoses included MIRAGE (SAMD9), Zellweger (PEX1), Walker‐Warburg (POMGNT1), Noonan (PTNP11), Kabuki (KMT2D), and CHARGE (CHD7) syndrome and two cases of Osteogenesis Imperfecta type 2 (COL1A1). In six cases, rES diagnosis aided perinatal management. The median turnaround time was 14 (range 8‐20) days. Conclusion Implementing rES as a routine test in the prenatal setting is challenging but technically feasible, with a promising diagnostic yield and significant clinical relevance.
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Affiliation(s)
- Nicole Corsten-Janssen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Katelijne Bouman
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Janouk C D Diphoorn
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arjen J Scheper
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rianne Kinds
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Julia El Mecky
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Clinical Ethics and Law, University of Southampton, Southampton, UK
| | - Hanna Breet
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Joke B G M Verheij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ron Suijkerbuijk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Leonie K Duin
- Department of Obstetrics, Gynecology and Prenatal Diagnosis, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Irene M van Langen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Helga Westers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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38
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Kalantari S, Filges I. 'Kinesinopathies': emerging role of the kinesin family member genes in birth defects. J Med Genet 2020; 57:797-807. [PMID: 32430361 PMCID: PMC7691813 DOI: 10.1136/jmedgenet-2019-106769] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/23/2020] [Accepted: 03/28/2020] [Indexed: 12/19/2022]
Abstract
Motor kinesins are a family of evolutionary conserved proteins involved in intracellular trafficking of various cargoes, first described in the context of axonal transport. They were discovered to have a key importance in cell-cycle dynamics and progression, including chromosomal condensation and alignment, spindle formation and cytokinesis, as well as ciliogenesis and cilia function. Recent evidence suggests that impairment of kinesins is associated with a variety of human diseases consistent with their functions and evolutionary conservation. Through the advent of gene identification using genome-wide sequencing approaches, their role in monogenic disorders now emerges, particularly for birth defects, in isolated as well as multiple congenital anomalies. We can observe recurrent phenotypical themes such as microcephaly, certain brain anomalies, and anomalies of the kidney and urinary tract, as well as syndromic phenotypes reminiscent of ciliopathies. Together with the molecular and functional data, we suggest understanding these ‘kinesinopathies’ as a recognisable entity with potential value for research approaches and clinical care.
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Affiliation(s)
- Silvia Kalantari
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland .,Department of Clinical Research, University Hospital Basel and University of Basel, Basel, Switzerland
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39
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Peron A, Iascone M, Salvatici E, Cavirani B, Marchetti D, Corno S, Vignoli A. PIGW-related glycosylphosphatidylinositol deficiency: Description of a new patient and review of the literature. Am J Med Genet A 2020; 182:1477-1482. [PMID: 32198969 DOI: 10.1002/ajmg.a.61555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/20/2020] [Accepted: 03/02/2020] [Indexed: 12/13/2022]
Abstract
Inherited glycosylphosphatidylinositol (GPI) deficiencies are a group of clinically and genetically heterogeneous conditions belonging to the congenital disorders of glycosylation. PIGW is involved in GPI biosynthesis and modification, and biallelic pathogenic variants in this gene cause autosomal recessive GPI biosynthesis defect 11. Only five patients and two fetuses have been reported in the literature thus far. Here we describe a new patient with a novel homozygous missense variant in PIGW, who presented with hypotonia, severe intellectual disability, early-onset epileptic seizures, brain abnormalities, nystagmus, hand stereotypies, recurrent respiratory infections, distinctive facial features, and hyperphosphatasia. Our report expands the phenotype of GPI biosynthesis defect 11 to include stereotypies and recurrent respiratory infections. A detailed and long-term analysis of the electroclinical characteristics and review of the literature suggest that early-onset epileptic seizures are a key manifestation of GPI biosynthesis defect 11. West syndrome and focal-onset epileptic seizures are the most common seizure types, and the fronto-temporal regions may be the most frequently involved areas in these patients.
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Affiliation(s)
- Angela Peron
- Child Neuropsychiatry Unit-Epilepsy Center (Medical Genetics Clinic), ASST Santi Paolo e Carlo, San Paolo Hospital, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,Department of Pediatrics, Division of Medical Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Elisabetta Salvatici
- Department of Pediatrics, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy
| | - Benedetta Cavirani
- Child Neuropsychiatry Unit-Epilepsy Center, ASST Santi Paolo e Carlo, San Paolo Hospital, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Daniela Marchetti
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Silvia Corno
- Child Neuropsychiatry Unit-Epilepsy Center, ASST Santi Paolo e Carlo, San Paolo Hospital, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Aglaia Vignoli
- Child Neuropsychiatry Unit-Epilepsy Center, ASST Santi Paolo e Carlo, San Paolo Hospital, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
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40
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Meier N, Bruder E, Miny P, Tercanli S, Filges I. Expanding the spectrum of SMAD3-related phenotypes to agnathia-otocephaly. Mol Genet Genomic Med 2020; 8:e1178. [PMID: 32100971 PMCID: PMC7196462 DOI: 10.1002/mgg3.1178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/12/2020] [Accepted: 01/30/2020] [Indexed: 12/20/2022] Open
Abstract
Background Agnathia‐otocephaly is a rare and lethal anomaly affecting craniofacial structures derived from the first pharyngeal arch. It is characterized by agnathia, microstomia, aglossia, and abnormally positioned auricles with or without associated anomalies. Variants affecting function of OTX2 and PRRX1, which together regulate the neural crest cells and the patterning of the first pharyngeal arch as well as skeletal and limb development, were identified to be causal for the anomaly in a few patients. Methods Family‐based exome sequencing (ES) on a fetus with severe agnathia‐otocephaly, cheilognathopalatoschisis, laryngeal hypoplasia, fused lung lobes and other organ abnormalities and mRNA expression analysis were performed. Results Exome sequencing detected a de novo SMAD3 missense variant in exon 6 (c.860G>A) associated with decreased mRNA expression. Variants in SMAD3 cause Loeys–Dietz syndrome 3 presenting with craniofacial anomalies such as mandibular hypoplasia, micro‐ or retro‐gnathia, bifid uvula and cleft palate as well as skeletal anomalies and arterial tortuosity. The SMAD3 protein acts as a transcriptional regulator in the transforming growth factor β (TGFB) and bone morphogenetic (BMP) signaling pathways, which play a key role in the development of craniofacial structures originating from the pharyngeal arches. Conclusion Agnathia‐otocephaly with or without associated anomalies may represent the severe end of a phenotypic spectrum related to variants in genes in the interacting SMAD/TGFB/BMP/SHH/FGF developmental pathways.
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Affiliation(s)
- Nicole Meier
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Elisabeth Bruder
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Peter Miny
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.,Department of Clinical Research, University Hospital Basel, Basel, Switzerland
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Chitty LS, Hui L, Ghidini A, Levy B, Deprest J, Van Mieghem T, Bianchi DW. In case you missed it: The Prenatal Diagnosis editors bring you the most significant advances of 2019. Prenat Diagn 2020; 40:287-293. [PMID: 31875323 DOI: 10.1002/pd.5632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/21/2022]
Affiliation(s)
- L S Chitty
- London North Genomic Laboratory, Great Ormond Street NHS Foundation Trust, and Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - L Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - A Ghidini
- Antenatal Testing Centre, Inova Alexandria Hospital, Alexandria, VA
| | - B Levy
- Departments of Pathology and Cell Biology, Columbia University, New York, NY
| | - J Deprest
- Departments of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - T Van Mieghem
- Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - D W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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42
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Aggarwal S, Vineeth VS, Das Bhowmik A, Tandon A, Kulkarni A, Narayanan DL, Bhattacherjee A, Dalal A. Exome sequencing for perinatal phenotypes: The significance of deep phenotyping. Prenat Diagn 2019; 40:260-273. [PMID: 31742715 DOI: 10.1002/pd.5616] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To ascertain the performance of exome sequencing (ES) technology for determining the etiological basis of abnormal perinatal phenotypes and to study the impact of comprehensive phenotyping on variant prioritization. METHODS A carefully selected cohort of 32/204 fetuses with abnormal perinatal phenotypes following postmortem/postnatal deep phenotyping underwent ES to identify a causative variant for the fetal phenotype. A retrospective comparative analysis of the prenatal versus postmortem/postnatal phenotype-based variant prioritization was performed with aid of Phenolyzer software. A review of selected literature reports was done to examine the completeness of phenotypic information for cases in those reports and how it impacted the performance of fetal ES. RESULTS In 18/32 (56%) fetuses, a pathogenic/likely pathogenic variant was identified. This included novel genotype-phenotype associations, expanded prenatal phenotypes of known Mendelian disorders and dual Mendelian diagnoses. The retrospective analysis revealed that the putative diagnostic variant could not be identified on basis of prenatal findings alone in 15/22 (68%) cases, indicating the importance of comprehensive postmortem/postnatal phenotype information. Literature review was supportive of these findings but could not be conclusive due to marked heterogeneity of involved studies. CONCLUSION Comprehensive phenotyping is essential for improving diagnostic performance and facilitating identification of novel genotype-phenotype associations in perinatal cohorts undergoing ES.
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Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Aneek Das Bhowmik
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwani Tandon
- Department of Pathology, All India Institute of Medical Sciences, Bhopal, India
| | | | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Amrita Bhattacherjee
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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43
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Sabbagh R, Van den Veyver IB. The current and future impact of genome-wide sequencing on fetal precision medicine. Hum Genet 2019; 139:1121-1130. [PMID: 31754893 DOI: 10.1007/s00439-019-02088-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/30/2019] [Indexed: 12/11/2022]
Abstract
Next-generation sequencing and other genomic technologies are transforming prenatal and reproductive screening and testing for fetal genetic disorders at an unprecedented pace. Original approaches of screening and testing for fetal genetic and genomic disorders were focused on a few more prevalent conditions that were easily diagnosable with pre-genomic era diagnostic tools. First, chromosomal microarray analysis and then next-generation sequencing brought technology capable of more detailed genomic evaluation to prenatal genetic screening and diagnosis. This has facilitated parallel introduction of a variety of new tests on maternal blood samples, including expanded carrier screening and cell-free DNA-based non-invasive screening for fetal aneuploidy, selected copy number variants, and single-gene disorders. Genomic tests on fetal DNA samples, obtained primarily through amniocentesis or chorionic villus sampling, include chromosomal microarray analysis and gene panel and exome sequencing. All these form the diagnostic pillar of the emerging field of fetal precision medicine, but their implementation is associated with ethical, counseling and healthcare resource utilization challenges. We discuss where in the reproductive and prenatal care continuum these exciting new technologies are integrated, along with associated challenges. We propose areas of priority for research to gain the data in support of their responsible implementation into clinical reproductive and prenatal care.
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Affiliation(s)
- Riwa Sabbagh
- Department of Obstetrics and Gynecology, Baylor College of Medicine, 1250 Moursund Street, Room 1025.14, Houston, TX, 77030, USA.,Pavilion for Women, Texas Children's Hospital, Houston, TX, USA
| | - Ignatia B Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, 1250 Moursund Street, Room 1025.14, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Pavilion for Women, Texas Children's Hospital, Houston, TX, USA. .,Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
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44
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CUGC for Stromme syndrome and CENPF-related disorders. Eur J Hum Genet 2019; 28:132-136. [PMID: 31488893 DOI: 10.1038/s41431-019-0498-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/16/2019] [Accepted: 08/02/2019] [Indexed: 11/09/2022] Open
Abstract
NAME OF THE DISEASE (SYNONYMS) Stromme syndrome.Jejunal atresia with microcephaly and ocular anomalies.Apple peel syndrome with microcephaly and ocular anomalies.Ciliopathy phenotype.Primary microcephaly and intellectual disability.OMIM# of the disease 243605.Name of the analysed genes or DNA/chromosome segments CENPF.OMIM# of the gene(s) 600236.Review of the analytical and clinical validity as well as of the clinical utility of DNA-based testing for mutations in CENPF genes in diagnostic, prenatal settings, and for risk assessment in relatives.
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45
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Filges I, Tercanli S, Hall JG. Fetal arthrogryposis: Challenges and perspectives for prenatal detection and management. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:327-336. [PMID: 31318155 DOI: 10.1002/ajmg.c.31723] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/23/2019] [Accepted: 06/27/2019] [Indexed: 12/28/2022]
Abstract
Antenatal identification of fetuses with multiple congenital contractures or arthrogryposis multiplex congenita (AMC) may be challenging. The first clinical sign is often reduced fetal movement and/or contractures, as seen on prenatal ultrasounds. This can be apparent at any point, from early to late pregnancy, may range from mild to severe involvement, with or without associated other structural anomalies. Possible etiologies and their prognosis need to be interpreted with respect to developmental timing. The etiology of AMC is highly heterogeneous and making the specific diagnosis will guide prognosis, counseling and prenatal and perinatal management. Current ultrasound practice identifies only approximately 25% of individuals with arthrogryposis prenatally before 24 weeks of pregnancy in a general obstetrics care population. There are currently no studies and guidelines that address the question of when and how to assess for fetal contractures and movements during pregnancy. The failure to identify fetuses with arthrogryposis before 24 weeks of pregnancy means that physicians and families are denied reproductive options and interventions that may improve outcome. We review current practice and recommend adjusting the current prenatal imaging and genetic diagnostic strategies to achieve early prenatal detection and etiologic diagnosis. We suggest exploring options for in utero therapy to increase fetal movement for ongoing pregnancies.
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Affiliation(s)
- Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Sevgi Tercanli
- Center for Prenatal Ultrasound, Basel and University of Basel, Basel, Switzerland
| | - Judith G Hall
- Department of Medical Genetics and Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
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