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Lederbogen RC, Hoffjan S, Thiels C, Mau-Holzmann UA, Singer S, Yusenko MV, Nguyen HHP, Gerding WM. Optical Genome Mapping Reveals Disruption of the RASGRF2 Gene in a Patient with Developmental Delay Carrying a De Novo Balanced Reciprocal Translocation. Genes (Basel) 2024; 15:809. [PMID: 38927744 PMCID: PMC11203114 DOI: 10.3390/genes15060809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/10/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
While balanced reciprocal translocations are relatively common, they often remain clinically silent unless they lead to the disruption of functional genes. In this study, we present the case of a boy exhibiting developmental delay and mild intellectual disability. Initial karyotyping revealed a translocation t(5;6)(q13;q23) between chromosomes 5 and 6 with limited resolution. Optical genome mapping (OGM) enabled a more precise depiction of the breakpoint regions involved in the reciprocal translocation. While the breakpoint region on chromosome 6 did not encompass any known gene, OGM revealed the disruption of the RASGRF2 (Ras protein-specific guanine nucleotide releasing factor 2) gene on chromosome 5, implicating RASGRF2 as a potential candidate gene contributing to the observed developmental delay in the patient. Variations in RASGRF2 have so far not been reported in developmental delay, but research on the RASGRF2 gene underscores its significance in various aspects of neurodevelopment, including synaptic plasticity, signaling pathways, and behavioral responses. This study highlights the utility of OGM in identifying breakpoint regions, providing possible insights into the understanding of neurodevelopmental disorders. It also helps affected individuals in gaining more knowledge about potential causes of their conditions.
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Affiliation(s)
- Rosa Catalina Lederbogen
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (R.C.L.); (S.H.); (M.V.Y.); (H.H.P.N.)
| | - Sabine Hoffjan
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (R.C.L.); (S.H.); (M.V.Y.); (H.H.P.N.)
| | - Charlotte Thiels
- Department of Neuropediatrics, University Children’s Hospital, Ruhr-University Bochum, 44791 Bochum, Germany;
| | - Ulrike Angelika Mau-Holzmann
- Institute of Medical Genetics and Applied Genomics, University Tübingen, 72074 Tübingen, Germany; (U.A.M.-H.); (S.S.)
| | - Sylke Singer
- Institute of Medical Genetics and Applied Genomics, University Tübingen, 72074 Tübingen, Germany; (U.A.M.-H.); (S.S.)
| | - Maria Viktorovna Yusenko
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (R.C.L.); (S.H.); (M.V.Y.); (H.H.P.N.)
| | - Hoa Huu Phuc Nguyen
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (R.C.L.); (S.H.); (M.V.Y.); (H.H.P.N.)
| | - Wanda Maria Gerding
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (R.C.L.); (S.H.); (M.V.Y.); (H.H.P.N.)
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Campbell TL, Xie LY, Johnson RH, Hultman CM, van den Oord EJCG, Aberg KA. Investigating neonatal health risk variables through cell-type specific methylome-wide association studies. Clin Epigenetics 2024; 16:69. [PMID: 38778395 PMCID: PMC11112760 DOI: 10.1186/s13148-024-01681-3] [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: 11/06/2023] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Adverse neonatal outcomes are a prevailing risk factor for both short- and long-term mortality and morbidity in infants. Given the importance of these outcomes, refining their assessment is paramount for improving prevention and care. Here we aim to enhance the assessment of these often correlated and multifaceted neonatal outcomes. To achieve this, we employ factor analysis to identify common and unique effects and further confirm these effects using criterion-related validity testing. This validation leverages methylome-wide profiles from neonatal blood. Specifically, we investigate nine neonatal health risk variables, including gestational age, Apgar score, three indicators of body size, jaundice, birth diagnosis, maternal preeclampsia, and maternal age. The methylomic profiles used for this research capture data from nearly all 28 million methylation sites in human blood, derived from the blood spot collected from 333 neonates, within 72 h post-birth. Our factor analysis revealed two common factors, size factor, that captured the shared effects of weight, head size, height, and gestational age and disease factor capturing the orthogonal shared effects of gestational age, combined with jaundice and birth diagnosis. To minimize false positives in the validation studies, validation was limited to variables with significant cumulative association as estimated through an in-sample replication procedure. This screening resulted in that the two common factors and the unique effects for gestational age, jaundice and Apgar were further investigated with full-scale cell-type specific methylome-wide association analyses. Highly significant, cell-type specific, associations were detected for both common effect factors and for Apgar. Gene Ontology analyses revealed multiple significant biologically relevant terms for the five fully investigated neonatal health risk variables. Given the established links between adverse neonatal outcomes and both immediate and long-term health, the distinct factor effects (representing the common and unique effects of the risk variables) and their biological profiles confirmed in our work, suggest their potential role as clinical biomarkers for assessing health risks and enhancing personalized care.
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Affiliation(s)
- Thomas L Campbell
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA
| | - Lin Y Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA
| | - Ralen H Johnson
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, P. O. Box 980533, Richmond, VA, 23298-0581, USA.
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Chow JC, Hormozdiari F. Prediction of Neurodevelopmental Disorders Based on De Novo Coding Variation. J Autism Dev Disord 2023; 53:963-976. [PMID: 35596027 PMCID: PMC9986216 DOI: 10.1007/s10803-022-05586-z] [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] [Accepted: 04/21/2022] [Indexed: 11/27/2022]
Abstract
The early detection of neurodevelopmental disorders (NDDs) can significantly improve patient outcomes. The differential burden of non-synonymous de novo mutation among NDD cases and controls indicates that de novo coding variation can be used to identify a subset of samples that will likely display an NDD phenotype. Thus, we have developed an approach for the accurate prediction of NDDs with very low false positive rate (FPR) using de novo coding variation for a small subset of cases. We use a shallow neural network that integrates de novo likely gene-disruptive and missense variants, measures of gene constraint, and conservation information to predict a small subset of NDD cases at very low FPR and prioritizes NDD risk genes for future clinical study.
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Affiliation(s)
- Julie C Chow
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
| | - Fereydoun Hormozdiari
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
- MIND Institute, University of California, Davis, 95817, USA.
- Biochemistry and Molecular Medicine, University of California, Davis, 95616, USA.
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Poszewiecka B, Pienkowski VM, Nowosad K, Robin JD, Gogolewski K, Gambin A. TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure. Nucleic Acids Res 2022; 50:W744-W752. [PMID: 35524567 PMCID: PMC9252839 DOI: 10.1093/nar/gkac318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 01/01/2023] Open
Abstract
In recent years great progress has been made in identification of structural variants (SV) in the human genome. However, the interpretation of SVs, especially located in non-coding DNA, remains challenging. One of the reasons stems in the lack of tools exclusively designed for clinical SVs evaluation acknowledging the 3D chromatin architecture. Therefore, we present TADeus2 a web server dedicated for a quick investigation of chromatin conformation changes, providing a visual framework for the interpretation of SVs affecting topologically associating domains (TADs). This tool provides a convenient visual inspection of SVs, both in a continuous genome view as well as from a rearrangement’s breakpoint perspective. Additionally, TADeus2 allows the user to assess the influence of analyzed SVs within flaking coding/non-coding regions based on the Hi-C matrix. Importantly, the SVs pathogenicity is quantified and ranked using TADA, ClassifyCNV tools and sampling-based P-value. TADeus2 is publicly available at https://tadeus2.mimuw.edu.pl.
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Affiliation(s)
- Barbara Poszewiecka
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Victor Murcia Pienkowski
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, MMG, Marseille, France.,Department of Medical Genetics, Medical University of Warsaw, Adolfa Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Karol Nowosad
- Department of Cell Biology, Erasmus Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, Netherlands.,Department of Biomedical Sciences, Laboratory of Molecular Genetics, Medical University of Lublin, Doktora Witolda Chodźki 1, 20-400 Lublin, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, MMG, Marseille, France
| | - Krzysztof Gogolewski
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Anna Gambin
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
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Wolańska E, Pollak A, Rydzanicz M, Pesz K, Kłaniewska M, Rozensztrauch A, Skiba P, Stawiński P, Płoski R, Śmigiel R. The Role of the Reanalysis of Genetic Test Results in the Diagnosis of Dysmorphic Syndrome Caused by Inherited xq24 Deletion including the UBE2A and CXorf56 Genes. Genes (Basel) 2021; 12:genes12030350. [PMID: 33673493 PMCID: PMC7997426 DOI: 10.3390/genes12030350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/21/2021] [Accepted: 02/26/2021] [Indexed: 12/31/2022] Open
Abstract
Psychomotor delay, hypotonia, and intellectual disability, as well as heart defects, urogenital malformations, and characteristic cranio-facial dysmorphism are the main symptoms of dysmorphic syndrome associated with intergenic deletion in the Xq24 chromosome region including the UBE2A and CXorf56 genes. To date, there is limited information in the literature about the symptoms and clinical course of the Xq24 deletion. Here, we present a case of Xq24 deletion including the UBE2A and CXorf56 genes in a nine-year-old boy, in whom the array comparative genomic hybridization (array-CGH) and whole exome sequencing (WES) tests were performed in 2015 with normal results. The WES results were reanalyzed in 2019. Intergenic, hemizygous deletion in the Xq24 chromosome region including the UBE2A and CXorf56 genes was revealed and subsequently confirmed in the array-CGH study as the deletion of 35kb in the Xq24 region. Additionally, the carriership of deletion in the mother of the child was confirmed.
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Affiliation(s)
- Ewelina Wolańska
- Department of Pediatrics, Division of Propaedeutic of Pediatrics and Rare Disorders, Wroclaw Medical University, 51-618 Wroclaw, Poland; (M.K.); (R.Ś.)
- Correspondence:
| | - Agnieszka Pollak
- Department of Medical Genetics, Warsaw Medical University, 02-106 Warsaw, Poland; (A.P.); (M.R.); (P.S.); (R.P.)
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Warsaw Medical University, 02-106 Warsaw, Poland; (A.P.); (M.R.); (P.S.); (R.P.)
| | - Karolina Pesz
- Department of Genetics, Wroclaw Medical University, 50-368 Wroclaw, Poland; (K.P.); (P.S.)
| | - Magdalena Kłaniewska
- Department of Pediatrics, Division of Propaedeutic of Pediatrics and Rare Disorders, Wroclaw Medical University, 51-618 Wroclaw, Poland; (M.K.); (R.Ś.)
| | - Anna Rozensztrauch
- Department of Pediatrics, Division of Neonatology, Wroclaw Medical University, 51-618 Wroclaw, Poland;
| | - Paweł Skiba
- Department of Genetics, Wroclaw Medical University, 50-368 Wroclaw, Poland; (K.P.); (P.S.)
| | - Piotr Stawiński
- Department of Medical Genetics, Warsaw Medical University, 02-106 Warsaw, Poland; (A.P.); (M.R.); (P.S.); (R.P.)
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, 02-106 Warsaw, Poland; (A.P.); (M.R.); (P.S.); (R.P.)
| | - Robert Śmigiel
- Department of Pediatrics, Division of Propaedeutic of Pediatrics and Rare Disorders, Wroclaw Medical University, 51-618 Wroclaw, Poland; (M.K.); (R.Ś.)
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