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.

Department of Human Genetics Hannover Medical School 30625 Hannover Germany

Department of Paediatric Haematology and Oncology 2nd Faculty of Medicine Charles University and University Hospital Motol CZ 15006 Prague Czech Republic

Department of Pediatrics 1 ALL BFM Study Group Christian Albrechts University Kiel and University Medical Center Schleswig Holstein 24105 Kiel Germany

Pediatric Hematology and Oncology Hannover Medical School 30625 Hannover Germany

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Larsen: E.C., Devidas M., Chen S., Salzer W.L., Raetz E.A., Loh M.L., Mattano L.A., Jr., Cole C., Eicher A., Haugan M., et al. Dexamethasone and High-Dose Methotrexate Improve Outcome for Children and Young Adults With High-Risk B-Acute Lymphoblastic Leukemia: A Report From Children’s Oncology Group Study aall0232. Clin. Oncol. 2016;34:2380–2388. doi: 10.1200/JCO.2015.62.4544. PubMed DOI PMC

Möricke A., Zimmermann M., Valsecchi M.G., Stanulla M., Biondi A., Mann G., Locatelli F., Cazzaniga G., Niggli F., Aricò M., et al. Dexamethasone vs prednisone in induction treatment of pediatric ALL: Results of the randomized trial AIEOP-BFM all 2000. Blood. 2016;127:2101–2112. doi: 10.1182/blood-2015-09-670729. PubMed DOI

Schmiegelow K., Levinsen M.F., Attarbaschi A., Baruchel A., Devidas M., Escherich G., Gibson B., Heydrich C., Horibe K., Ishida Y., et al. Second Malignant Neoplasms After Treatment of Childhood Acute Lymphoblastic Leukemia. J. Clin. Oncol. 2013;31:2469–2476. doi: 10.1200/JCO.2012.47.0500. PubMed DOI PMC

Schrappe M., Valsecchi M.G., Bartram C.R., Schrauder A., Panzer-Grümayer R., Möricke A., Parasole R., Zimmermann M., Dworzak M., Buldini B., et al. Late MRD response determines relapse risk overall and in subsets of childhood T-cell ALL: Results of the AIEOP-BFM-ALL 2000 study. Blood. 2011;118:2077–2084. doi: 10.1182/blood-2011-03-338707. PubMed DOI

Aricò M., Schrappe M., Hunger S.P., Carroll W.L., Conter V., Galimberti S., Manabe A., Saha V., Baruchel A., Vettenranta K., et al. Clinical Outcome of Children With Newly Diagnosed Philadelphia Chromosome–Positive Acute Lymphoblastic Leukemia Treated Between 1995 and 2005. J. Clin. Oncol. 2010;28:4755–4761. doi: 10.1200/JCO.2010.30.1325. PubMed DOI PMC

Fischer U., Forster M., Rinaldi A., Risch T., Sungalee S., Warnatz H.-J., Bornhauser B., Gombert M., Kratsch C., Stütz A.M., et al. Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options. Nat. Genet. 2015;47:1020–1029. doi: 10.1038/ng.3362. PubMed DOI PMC

Holmfeldt L., Wei L., Diaz-Flores E., Walsh M., Zhang J., Ding L., Payne-Turner D., Churchman M., Andersson A., Chen S.-C., et al. The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat. Genet. 2013;45:242–252. doi: 10.1038/ng.2532. PubMed DOI PMC

Mullighan C.G., Goorha S., Radtke I., Miller C.B., Coustan-Smith E., Dalton J.D., Girtman K., Mathew S., Ma J., Pounds S.B., et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature. 2007;446:758–764. doi: 10.1038/nature05690. PubMed DOI

Forestier E., Heyman M., Andersen M.K., Autio K., Blennow E., Borgström G., Golovleva I., Heim S., Heinonen K., Hovland R., et al. Outcome of ETV6/RUNX1-positive childhood acute lymphoblastic leukaemia in the NOPHO-ALL-1992 protocol: Frequent late relapses but good overall survival. Br. J. Haematol. 2008;140:665–672. doi: 10.1111/j.1365-2141.2008.06980.x. PubMed DOI

Bhojwani D., Pei D., Sandlund J.T., Jeha S., Ribeiro R.C., Rubnitz J.E., Raimondi S.C., Shurtleff S., Onciu M., Cheng C., et al. ETV6-RUNX1-positive childhood acute lymphoblastic leukemia: Improved outcome with contemporary therapy. Leukemia. 2012;26:265–270. doi: 10.1038/leu.2011.227. PubMed DOI PMC

Schrappe M., Bleckmann K., Zimmermann M., Biondi A., Möricke A., Locatelli F., Cario G., Rizzari C., Attarbaschi A., Valsecchi M.G., et al. Reduced-Intensity Delayed Intensification in Standard-Risk Pediatric Acute Lymphoblastic Leukemia Defined by Undetectable Minimal Residual Disease: Results of an International Randomized Trial (AIEOP-BFM ALL 2000) J. Clin. Oncol. 2018;36:244–253. doi: 10.1200/JCO.2017.74.4946. PubMed DOI

Roberts K.G., Pei D., Campana D., Payne-Turner D., Li Y., Cheng C., Sandlund J.T., Jeha S., Easton J., Becksfort J., et al. Outcomes of Children With BCR-ABL1–Like Acute Lymphoblastic Leukemia Treated With Risk-Directed Therapy Based on the Levels of Minimal Residual Disease. J. Clin. Oncol. 2014;32:3012–3020. doi: 10.1200/JCO.2014.55.4105. PubMed DOI PMC

Cario G., Leoni V., Conter V., Attarbaschi A., Zaliova M., Sramkova L., Cazzaniga G., Fazio G., Sutton R., Elitzur S., et al. Relapses and treatment-related events contributed equally to poor prognosis in children with ABL-class fusion positive B-cell acute lymphoblastic leukemia treated according to AIEOP-BFM protocols. Haematologica. 2020;105:1887–1894. doi: 10.3324/haematol.2019.231720. PubMed DOI PMC

Brown P.A., Kairalla J.A., Hilden J.M., Dreyer Z.E., Carroll A.J., Heerema N.A., Wang C., Devidas M., Gore L., Salzer W.L., et al. Flt3 inhibitor lestaurtinib plus chemotherapy for newly diagnosed kmt2a-rearranged infant acute lymphoblastic leukemia: Children’s oncology group trial AALL0631. Leukemia. 2021;35:1279–1290. doi: 10.1038/s41375-021-01177-6. PubMed DOI PMC

Li J.-F., Dai Y.-T., Lilljebjörn H., Shen S.-H., Cui B.-W., Bai L., Liu Y.-F., Qian M.-X., Kubota Y., Kiyoi H., et al. Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1223 cases. Proc. Natl. Acad. Sci. USA. 2018;115:E11711–E11720. doi: 10.1073/pnas.1814397115. PubMed DOI PMC

Den Boer M.L., Cario G., Moorman A.V., Boer J.M., de Groot-Kruseman H.A., Fiocco M., Escherich G., Imamura T., Yeoh A., Sutton R., et al. Outcomes of paediatric patients with B-cell acute lymphocytic leukaemia with ABL-class fusion in the pre-tyrosine-kinase inhibitor era: A multicentre, retrospective, cohort study. Lancet Haematol. 2021;8:e55–e66. doi: 10.1016/S2352-3026(20)30353-7. PubMed DOI PMC

Hamadeh L., Enshaei A., Schwab C., Alonso C.N., Attarbaschi A., Barbany G., den Boer M.L., Boer J.M., Braun M., Dalla Pozza L., et al. Validation of the United Kingdom copy-number alteration classifier in 3239 children with B-cell precursor ALL. Blood Adv. 2019;3:148–157. doi: 10.1182/bloodadvances.2018025718. PubMed DOI PMC

Stanulla M., Dagdan E., Zaliova M., Möricke A., Palmi C., Cazzaniga G., Eckert C., Te Kronnie G., Bourquin J.P., Bornhauser B., et al. IKZF1(plus) Defines a New Minimal Residual Disease–Dependent Very-Poor Prognostic Profile in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia. J. Clin. Oncol. 2018;36:1240–1249. doi: 10.1200/JCO.2017.74.3617. PubMed DOI

Chan S., Lam E., Saghbini M., Bocklandt S., Hastie A., Cao H., Holmlin E., Borodkin M. Structural Variation Detection and Analysis Using Bionano Optical Mapping. Methods Mol. Biol. 2018;1833:193–203. doi: 10.1007/978-1-4939-8666-8_16. PubMed DOI

Chan E.K.F., Cameron D.L., Petersen D.C., Lyons R.J., Baldi B.F., Papenfuss A.T., Thomas D.M., Hayes V.M. Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer. Genome Res. 2018;28:726–738. doi: 10.1101/gr.227975.117. PubMed DOI PMC

Eisfeldt J., Pettersson M., Vezzi F., Wincent J., Käller M., Gruselius J., Nilsson D., Syk Lundberg E., Carvalho C.M.B., Lindstrand A. Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements. PLoS Genet. 2019;15:e1007858. doi: 10.1371/journal.pgen.1007858. PubMed DOI PMC

Neveling K., Mantere T., Vermeulen S., Oorsprong M., van Beek R., Kater-Baats E., Pauper M., van der Zande G., Smeets D., Weghuis D.O., et al. Next generation cytogenetics: Comprehensive assessment of 52 hematological malignancy genomes by genome imaging. Am. J. Hum. Genet. 2021;108:1423–1435. doi: 10.1016/j.ajhg.2021.06.001. PubMed DOI PMC

Schieck M., Lentes J., Thomay K., Hofmann W., Behrens Y.L., Hagedorn M., Ebersold J., Davenport C.F., Fazio G., Möricke A., et al. Implementation of RNA sequencing and array CGH in the diagnostic workflow of the AIEOP-BFM ALL 2017 trial on acute lymphoblastic leukemia. Ann. Hematol. 2020;99:809–818. doi: 10.1007/s00277-020-03953-3. PubMed DOI PMC

Lestringant V., Duployez N., Penther D., Luquet I., Derrieux C., Lutun A., Preudhomme C., West M., Ouled-Haddou H., Devoldere C., et al. Optical genome mapping, a promising alternative to gold standard cytogenetic approaches in a series of acute lymphoblastic leukemias. Genes Chromosom. Cancer. 2021 doi: 10.1002/gcc.22971. PubMed DOI

Roberts K.G., Li Y., Payne-Turner D., Harvey R.C., Yang Y.-L., Pei D., McCastlain K., Ding L., Lu C., Song G., et al. Targetable Kinase-Activating Lesions in Ph-like Acute Lymphoblastic Leukemia. N. Engl. J. Med. 2014;371:1005–1015. doi: 10.1056/NEJMoa1403088. PubMed DOI PMC

Chen X., Wang F., Zhang Y., Ma X., Liu M., Cao P., Zhou L., Wang L., Zhang X., Wang T., et al. Identification of RNPC3 as a novel JAK2 fusion partner gene in B-acute lymphoblastic leukemia refractory to combination therapy including ruxolitinib. Mol. Genet. Genom. Med. 2020;8:e1110. doi: 10.1002/mgg3.1110. PubMed DOI PMC

Ding Y.-Y., Stern J.W., Jubelirer T.F., Wertheim G.B., Lin F., Chang F., Gu Z., Mullighan C.G., Li Y., Harvey R.C., et al. Clinical efficacy of ruxolitinib and chemotherapy in a child with Philadelphia chromosome-like acute lymphoblastic leukemia with GOLGA5-JAK2 fusion and induction failure. Haematologica. 2018;103:e427–e431. doi: 10.3324/haematol.2018.192088. PubMed DOI PMC

Wouters Y., Nevejan L., Louwagie A., Devos H., Dewaele B., Selleslag D., Michaux L. Efficacy of ruxolitinib in B-lymphoblastic leukaemia with the PCM1–JAK2 fusion gene. Br. J. Haematol. 2021;192:e112–e115. doi: 10.1111/bjh.17340. PubMed DOI

Maude S.L., Tasian S.K., Vincent T., Hall J.W., Sheen C., Roberts K.G., Seif A.E., Barrett D.M., Chen I.M., Collins J.R., et al. Targeting jak1/2 and mtor in murine xenograft models of ph-like acute lymphoblastic leukemia. Blood. 2012;120:3510–3518. doi: 10.1182/blood-2012-03-415448. PubMed DOI PMC

Carroll M., Ohno-Jones S., Tamura S., Buchdunger E., Zimmermann J., Lydon N.B., Gilliland D.G., Druker B.J. Cgp 57148, a tyrosine kinase inhibitor, inhibits the growth of cells expressing bcr-abl, tel-abl, and tel-pdgfr fusion proteins. Blood. 1997;90:4947–4952. doi: 10.1182/blood.V90.12.4947. PubMed DOI

Zaliova M., Moorman A.V., Cazzaniga G., Stanulla M., Harvey R.C., Roberts K.G., Heatley S.L., Loh M.L., Konopleva M., Chen I.-M., et al. Characterization of leukemias with ETV6-ABL1 fusion. Haematologica. 2016;101:1082–1093. doi: 10.3324/haematol.2016.144345. PubMed DOI PMC

Yoshida M., Kato M. Genetic basis of subsequent malignant neoplasms. Rinsho Ketsueki. 2020;61:1174–1178. PubMed

Dreisig K., Brünner E.D., Marquart H.V., Helt L.R., Nersting J., Frandsen T.L., Jonsson O.G., Taskinen M., Vaitkeviciene G., Lund B., et al. TPMT polymorphisms and minimal residual disease after 6-mercaptopurine post-remission consolidation therapy of childhood acute lymphoblastic leukaemia. Pediatr. Hematol. Oncol. 2020;138:227–238. doi: 10.1080/08880018.2020.1842570. PubMed DOI

Stanulla M., Schaeffeler E., Flohr T., Cario G., Schrauder A., Zimmermann M., Welte K., Ludwig W.D., Bartram C.R., Zanger U.M., et al. Thiopurine methyltransferase (tpmt) genotype and early treatment response to mercaptopurine in childhood acute lymphoblastic leukemia. JAMA. 2005;293:1485–1489. doi: 10.1001/jama.293.12.1485. PubMed DOI

Clark R., Byatt S.-A., Bennett C.F., Brama M., Martineau M., Moorman A.V., Roberts K., Secker-Walker L.M., Richards S., Eden O.B., et al. Monosomy 20 as a pointer to dicentric (9;20) in acute lymphoblastic leukemia. Leukemia. 2000;14:241–246. doi: 10.1038/sj.leu.2401654. PubMed DOI

Zachariadis V., Gauffin F., Kuchinskaya E., Heyman M., Schoumans J., Blennow E., Gustafsson B., Barbany G., Golovleva I., Ehrencrona H., et al. The frequency and prognostic impact of dic(9;20)(p13.2;q11.2) in childhood B-cell precursor acute lymphoblastic leukemia: Results from the NOPHO ALL-2000 trial. Leukemia. 2011;25:622–628. doi: 10.1038/leu.2010.318. PubMed DOI

Pichler H., Möricke A., Mann G., Teigler-Schlegel A., Niggli F., Nebral K., König M., Inthal A., Krehan D., Dworzak M.N., et al. Prognostic relevance of dic(9;20)(p11;q13) in childhood B-cell precursor acute lymphoblastic leukaemia treated with Berlin-Frankfurt-Münster (BFM) protocols containing an intensive induction and post-induction consolidation therapy. Br. J. Haematol. 2010;149:93–100. doi: 10.1111/j.1365-2141.2009.08059.x. PubMed DOI

An Q., Wright S.L., Moorman A.V., Parker H., Griffiths M., Ross F.M., Davies T., Harrison C.J., Strefford J.C. Heterogeneous breakpoints in patients with acute lymphoblastic leukemia and the dic(9;20)(p11 13;q11) show recurrent involvement of genes at 20q11.21. Haematologica. 2009;94:1164–1169. doi: 10.3324/haematol.2008.002808. PubMed DOI PMC

Letouzey M., Penther D., Roche-Lestienne C., Nelken B., Devoldère C., Vannier J.-P., Schneider P. Detection of dicentric chromosome (9;20) in paediatric B-cell acute lymphoblastic leukaemia: Prognostic significance. Ann. Hematol. 2015;94:187–193. doi: 10.1007/s00277-014-2204-z. PubMed DOI

Strehl S., König M., Dworzak M.N., Kalwak K., Haas O.A. PAX5/ETV6 fusion defines cytogenetic entity dic(9;12)(p13;p13) Leukemia. 2003;17:1121–1123. doi: 10.1038/sj.leu.2402923. PubMed DOI

Jawhar M., Naumann N., Knut M., Score J., Ghazzawi M., Schneider B., Kreuzer K.-A., Hallek M., Drexler H.G., Chacko J., et al. Cytogenetically cryptic ZMYM2-FLT3 and DIAPH1-PDGFRB gene fusions in myeloid neoplasms with eosinophilia. Leukemia. 2017;31:2271–2273. doi: 10.1038/leu.2017.240. PubMed DOI PMC

Roberts K.G., Gu Z., Payne-Turner D., McCastlain K., Harvey R.C., Chen I.-M., Pei D., Iacobucci I., Valentine M., Pounds S.B., et al. High Frequency and Poor Outcome of Philadelphia Chromosome–Like Acute Lymphoblastic Leukemia in Adults. J. Clin. Oncol. 2017;35:394–401. doi: 10.1200/JCO.2016.69.0073. PubMed DOI PMC

Skucha A., Ebner J., Grebien F. Roles of SETD2 in Leukemia—Transcription, DNA-Damage, and Beyond. Int. J. Mol. Sci. 2019;20:1029. doi: 10.3390/ijms20051029. PubMed DOI PMC

Mar B.G., Bullinger L.B., McLean K.M., Grauman P.V., Harris M.H., Stevenson K., Neuberg D.S., Sinha A.U., Sallan S.E., Silverman L.B., et al. Mutations in epigenetic regulators including SETD2 are gained during relapse in paediatric acute lymphoblastic leukaemia. Nat. Commun. 2014;5:3469. doi: 10.1038/ncomms4469. PubMed DOI PMC

Chimeric JAK2 Kinases Trigger Non-uniform Changes of Cellular Metabolism in BCR-ABL1-like Childhood ALL