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Büki G, Bekő A, Bödör C, Urbán P, Németh K, Hadzsiev K, Fekete G, Kehrer-Sawatzki H, Bene J. Identification of an NF1 Microdeletion with Optical Genome Mapping. Int J Mol Sci 2023; 24:13580. [PMID: 37686382 PMCID: PMC10487413 DOI: 10.3390/ijms241713580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is a clinically heterogeneous neurocutaneous disorder inherited in autosomal dominant manner. Approximately 5-10% of the cases are caused by NF1 microdeletions involving the NF1 gene and its flanking regions. Microdeletions, which lead to more severe clinical manifestations, can be subclassified into four different types (type 1, 2, 3 and atypical) according to their size, the genomic location of the breakpoints and the number of genes included within the deletion. Besides the prominent hallmarks of NF1, patients with NF1 microdeletions frequently exhibit specific additional clinical manifestations like dysmorphic facial features, macrocephaly, overgrowth, global developmental delay, cognitive disability and an increased risk of malignancies. It is important to identify the genes co-deleted with NF1, because they are likely to have an effect on the clinical manifestation. Multiplex ligation-dependent probe amplification (MLPA) and microarray analysis are the primary techniques for the investigation of NF1 microdeletions. However, based on previous research, optical genome mapping (OGM) could also serve as an alternative method to identify copy number variations (CNVs). Here, we present a case with NF1 microdeletion identified by means of OGM and demonstrate that this novel technology is a suitable tool for the identification and classification of the NF1 microdeletions.
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Affiliation(s)
- Gergely Büki
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, 7624 Pécs, Hungary; (G.B.); (K.H.)
| | - Anna Bekő
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary; (A.B.); (C.B.)
| | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary; (A.B.); (C.B.)
| | - Péter Urbán
- Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary;
| | - Krisztina Németh
- Pediatric Center, Tűzoltó Street Department, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary; (K.N.); (G.F.)
| | - Kinga Hadzsiev
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, 7624 Pécs, Hungary; (G.B.); (K.H.)
| | - György Fekete
- Pediatric Center, Tűzoltó Street Department, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary; (K.N.); (G.F.)
| | | | - Judit Bene
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, 7624 Pécs, Hungary; (G.B.); (K.H.)
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Bedics G, Egyed B, Kotmayer L, Benard-Slagter A, de Groot K, Bekő A, Hegyi LL, Bátai B, Krizsán S, Kriván G, Erdélyi DJ, Müller J, Haltrich I, Kajtár B, Pajor L, Vojcek Á, Ottóffy G, Ujfalusi A, Szegedi I, Tiszlavicz LG, Bartyik K, Csanádi K, Péter G, Simon R, Hauser P, Kelemen Á, Sebestyén E, Jakab Z, Matolcsy A, Kiss C, Kovács G, Savola S, Bödör C, Alpár D. PersonALL: a genetic scoring guide for personalized risk assessment in pediatric B-cell precursor acute lymphoblastic leukemia. Br J Cancer 2023; 129:455-465. [PMID: 37340093 PMCID: PMC10403542 DOI: 10.1038/s41416-023-02309-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/08/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Recurrent genetic lesions provide basis for risk assessment in pediatric acute lymphoblastic leukemia (ALL). However, current prognostic classifiers rely on a limited number of predefined sets of alterations. METHODS Disease-relevant copy number aberrations (CNAs) were screened genome-wide in 260 children with B-cell precursor ALL. Results were integrated with cytogenetic data to improve risk assessment. RESULTS CNAs were detected in 93.8% (n = 244) of the patients. First, cytogenetic profiles were combined with IKZF1 status (IKZF1normal, IKZF1del and IKZF1plus) and three prognostic subgroups were distinguished with significantly different 5-year event-free survival (EFS) rates, IKAROS-low (n = 215): 86.3%, IKAROS-medium (n = 27): 57.4% and IKAROS-high (n = 18): 37.5%. Second, contribution of genetic aberrations to the clinical outcome was assessed and an aberration-specific score was assigned to each prognostically relevant alteration. By aggregating the scores of aberrations emerging in individual patients, personalized cumulative values were calculated and used for defining four prognostic subgroups with distinct clinical outcomes. Two favorable subgroups included 60% of patients (n = 157) with a 5-year EFS of 96.3% (excellent risk, n = 105) and 87.2% (good risk, n = 52), respectively; while 40% of patients (n = 103) showed high (n = 74) or ultra-poor (n = 29) risk profile (5-year EFS: 67.4% and 39.0%, respectively). CONCLUSIONS PersonALL, our conceptually novel prognostic classifier considers all combinations of co-segregating genetic alterations, providing a highly personalized patient stratification.
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Affiliation(s)
- Gábor Bedics
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bálint Egyed
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Lili Kotmayer
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | | | | | - Anna Bekő
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Lajos László Hegyi
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bence Bátai
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Szilvia Krizsán
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gergely Kriván
- Central Hospital of Southern Pest - National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | - Dániel J Erdélyi
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Judit Müller
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Irén Haltrich
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Béla Kajtár
- Department of Pathology, University of Pécs Medical School, Pécs, Hungary
| | - László Pajor
- Department of Pathology, University of Pécs Medical School, Pécs, Hungary
| | - Ágnes Vojcek
- Department of Pediatrics, University of Pécs Medical School, Pécs, Hungary
| | - Gábor Ottóffy
- Department of Pediatrics, University of Pécs Medical School, Pécs, Hungary
| | - Anikó Ujfalusi
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - István Szegedi
- Division of Pediatric Hematology-Oncology, Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Lilla Györgyi Tiszlavicz
- Department of Paediatrics and Paediatric Health Care Center, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Katalin Bartyik
- Department of Paediatrics and Paediatric Health Care Center, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Krisztina Csanádi
- Hemato-Oncology Unit, Heim Pál Children's Hospital, Budapest, Hungary
| | - György Péter
- Hemato-Oncology Unit, Heim Pál Children's Hospital, Budapest, Hungary
| | - Réka Simon
- Hemato-Oncology and Stem Cell Transplantation Unit, Velkey László Children's Health Center, Miskolc, Hungary
| | - Péter Hauser
- Hemato-Oncology and Stem Cell Transplantation Unit, Velkey László Children's Health Center, Miskolc, Hungary
| | - Ágnes Kelemen
- Hemato-Oncology and Stem Cell Transplantation Unit, Velkey László Children's Health Center, Miskolc, Hungary
| | - Endre Sebestyén
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna Jakab
- Hungarian Childhood Cancer Registry, Hungarian Pediatric Oncology Network, Budapest, Hungary
| | - András Matolcsy
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- Department of Laboratory Medicine, Karolinska Institute, Solna, Sweden
| | - Csongor Kiss
- Division of Pediatric Hematology-Oncology, Institute of Pediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Kovács
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | | | - Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Donát Alpár
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.
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Bedics G, Csóka M, Reiniger L, Varga E, Liptai Z, Papp G, Bekő A, Cervi C, Bödör C, Scheich B. Novel actionable ROS1::GIT2 fusion in non-Langerhans cell histiocytosis with central nervous system involvement. Acta Neuropathol 2023; 145:153-156. [PMID: 36416966 PMCID: PMC9807475 DOI: 10.1007/s00401-022-02520-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/05/2022] [Accepted: 11/12/2022] [Indexed: 11/24/2022]
Affiliation(s)
- Gábor Bedics
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Monika Csóka
- 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9., Budapest, 1094, Hungary
| | - Lilla Reiniger
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Edit Varga
- 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9., Budapest, 1094, Hungary
| | - Zoltán Liptai
- 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9., Budapest, 1094, Hungary
| | - Gergő Papp
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Anna Bekő
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Catherine Cervi
- 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9., Budapest, 1094, Hungary
| | - Csaba Bödör
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Bálint Scheich
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary.
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