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For:	Yoshida M, Kato M. [Genetic basis of subsequent malignant neoplasms]. Rinsho Ketsueki 2020;61:1174-1178. [PMID: 33162513 DOI: 10.11406/rinketsu.61.1174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]

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Cited by Other Article(s)

Lühmann JL, Stelter M, Wolter M, Kater J, Lentes J, Bergmann AK, Schieck M, Göhring G, Möricke A, Cario G, Žaliová M, Schrappe M, Schlegelberger B, Stanulla M, Steinemann D. The Clinical Utility of Optical Genome Mapping for the Assessment of Genomic Aberrations in Acute Lymphoblastic Leukemia. Cancers (Basel) 2021;13:cancers13174388. [PMID: 34503197 PMCID: PMC8431583 DOI: 10.3390/cancers13174388] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 01/01/2023] Open

Abstract

Simple Summary

The stratification of childhood ALL is currently based on various diagnostic assays. This study investigates the feasibility of Optical Genome Mapping (OGM) to determine the genetic risk profile of ALL using fresh and frozen blood cells in an all-in-one approach. Acute lymphoblastic leukemia samples with data available from SNP-array/array-CGH, RNA-Seq, MLPA, karyotyping and FISH were compared to results obtained by OGM. We show that OGM has the potential to simplify the diagnostic workflow and to identify new structural variants helpful for classifying patients into treatment groups.

Abstract

Acute lymphoblastic leukemia (ALL) is the most prevalent type of cancer occurring in children. ALL is characterized by structural and numeric genomic aberrations that strongly correlate with prognosis and clinical outcome. Usually, a combination of cyto- and molecular genetic methods (karyotyping, array-CGH, FISH, RT-PCR, RNA-Seq) is needed to identify all aberrations relevant for risk stratification. We investigated the feasibility of optical genome mapping (OGM), a DNA-based method, to detect these aberrations in an all-in-one approach. As proof of principle, twelve pediatric ALL samples were analyzed by OGM, and results were validated by comparing OGM data to results obtained from routine diagnostics. All genomic aberrations including translocations (e.g., dic(9;12)), aneuploidies (e.g., high hyperdiploidy) and copy number variations (e.g., IKZF1, PAX5) known from other techniques were also detected by OGM. Moreover, OGM was superior to well-established techniques for resolution of the more complex structure of a translocation t(12;21) and had a higher sensitivity for detection of copy number alterations. Importantly, a new and unknown gene fusion of JAK2 and NPAT due to a translocation t(9;11) was detected. We demonstrate the feasibility of OGM to detect well-established as well as new putative prognostic markers in an all-in-one approach in ALL. We hope that these limited results will be confirmed with testing of more samples in the future.

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Affiliation(s)

Jonathan Lukas Lühmann Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany; (J.L.L.); (M.S.); (M.W.); (J.K.); (J.L.); (A.K.B.); (M.S.); (G.G.); (B.S.)
Marie Stelter Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany; (J.L.L.); (M.S.); (M.W.); (J.K.); (J.L.); (A.K.B.); (M.S.); (G.G.); (B.S.)
Marie Wolter Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany; (J.L.L.); (M.S.); (M.W.); (J.K.); (J.L.); (A.K.B.); (M.S.); (G.G.); (B.S.)
Josephine Kater Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany; (J.L.L.); (M.S.); (M.W.); (J.K.); (J.L.); (A.K.B.); (M.S.); (G.G.); (B.S.)
Jana Lentes Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany; (J.L.L.); (M.S.); (M.W.); (J.K.); (J.L.); (A.K.B.); (M.S.); (G.G.); (B.S.)
Anke Katharina Bergmann Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany; (J.L.L.); (M.S.); (M.W.); (J.K.); (J.L.); (A.K.B.); (M.S.); (G.G.); (B.S.)
Maximilian Schieck Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany; (J.L.L.); (M.S.); (M.W.); (J.K.); (J.L.); (A.K.B.); (M.S.); (G.G.); (B.S.)
Gudrun Göhring Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany; (J.L.L.); (M.S.); (M.W.); (J.K.); (J.L.); (A.K.B.); (M.S.); (G.G.); (B.S.)
Anja Möricke Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.M.); (G.C.); (M.S.)
Gunnar Cario Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.M.); (G.C.); (M.S.)
Markéta Žaliová Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, CZ-15006 Prague, Czech Republic;
Martin Schrappe Department of Pediatrics I, ALL-BFM Study Group, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; (A.M.); (G.C.); (M.S.)
Brigitte Schlegelberger Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany; (J.L.L.); (M.S.); (M.W.); (J.K.); (J.L.); (A.K.B.); (M.S.); (G.G.); (B.S.)
Martin Stanulla Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany;
Doris Steinemann Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany; (J.L.L.); (M.S.); (M.W.); (J.K.); (J.L.); (A.K.B.); (M.S.); (G.G.); (B.S.) Correspondence:

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