Measurable residual disease (MRD) monitoring in childhood acute myeloid leukemia (AML) is used to assess response to treatment and for early detection of imminent relapse. In childhood AML, MRD is typically evaluated using flow cytometry, or by quantitative detection of leukemia-specific aberrations at the mRNA level. Both methods, however, have significant limitations. Recently, we demonstrated the feasibility of MRD monitoring in selected subgroups of AML at the genomic DNA (gDNA) level. To evaluate the potential of gDNA-based MRD monitoring across all AML subtypes, we conducted a comprehensive analysis involving 133 consecutively diagnosed children. Integrating next-generation sequencing into the diagnostic process, we identified (presumed) primary genetic aberrations suitable as MRD targets in 97% of patients. We developed patient-specific quantification assays and monitored MRD in 122 children. The gDNA-based MRD monitoring via quantification of primary aberrations with a sensitivity of at least 10-4 was possible in 86% of patients; via quantification with sensitivity of 5 × 10-4, of secondary aberrations, or at the mRNA level in an additional 8%. Importantly, gDNA-based MRD exhibited independent prognostic value at early time-points in patients stratified to intermediate-/high-risk treatment arms. Our study demonstrates the broad applicability, feasibility, and clinical significance of gDNA-based MRD monitoring in childhood AML.

CLIP Prague Czech Republic

Department of Paediatric Haematology and Oncology 2nd Faculty of Medicine Charles University Prague Czech Republic

Department of Pediatrics Faculty of Medicine and Dentistry Palacky University and University Hospital Olomouc Olomouc Czech Republic

Institute of Pharmaceutical Biology Diagnostic Center of Acute Leukemia Goethe University Frankfurt am Main Germany

Pediatric Oncology Department University Hospital and Faculty of Medicine Masaryk University Brno Czech Republic

University Hospital Motol Prague Czech Republic

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Inaba H, Mullighan CG. Pediatric acute lymphoblastic leukemia. Haematologica. 2020;105:2524–39. doi: 10.3324/haematol.2020.247031. PubMed DOI PMC

Rasche M, Zimmermann M, Borschel L, Bourquin JP, Dworzak M, Klingebiel T, et al. Successes and challenges in the treatment of pediatric acute myeloid leukemia: a retrospective analysis of the AML-BFM trials from 1987 to 2012. Leukemia. 2018;32:2167–77. doi: 10.1038/s41375-018-0071-7. PubMed DOI PMC

Zwaan CM, Kolb EA, Reinhardt D, Abrahamsson J, Adachi S, Aplenc R, et al. Collaborative efforts driving progress in pediatric acute myeloid leukemia. J Clin Oncol. 2015;33:2949–62. doi: 10.1200/JCO.2015.62.8289. PubMed DOI PMC

van der Velden VH, Cazzaniga G, Schrauder A, Hancock J, Bader P, Panzer-Grumayer ER, et al. Analysis of minimal residual disease by Ig/TCR gene rearrangements: guidelines for interpretation of real-time quantitative PCR data. Leukemia. 2007;21:604–11. doi: 10.1038/sj.leu.2404586. PubMed DOI

Boeckx N, Willemse MJ, Szczepanski T, van der Velden VH, Langerak AW, Vandekerckhove P, et al. Fusion gene transcripts and Ig/TCR gene rearrangements are complementary but infrequent targets for PCR-based detection of minimal residual disease in acute myeloid leukemia. Leukemia. 2002;16:368–75. doi: 10.1038/sj.leu.2402387. PubMed DOI

Conneely SE, Rau RE. The genomics of acute myeloid leukemia in children. Cancer Metastasis Rev. 2020;39:189–209. doi: 10.1007/s10555-020-09846-1. PubMed DOI PMC

Blachly JS, Walter RB, Hourigan CS. The present and future of measurable residual disease testing in acute myeloid leukemia. Haematologica. 2022;107:2810–22. doi: 10.3324/haematol.2022.282034. PubMed DOI PMC

Buldini B, Maurer-Granofszky M, Varotto E, Dworzak MN. Flow-cytometric monitoring of minimal residual disease in pediatric patients with acute myeloid leukemia: recent advances and future strategies. Front Pediatr. 2019;7:412. doi: 10.3389/fped.2019.00412. PubMed DOI PMC

Hourigan CS, Gale RP, Gormley NJ, Ossenkoppele GJ, Walter RB. Measurable residual disease testing in acute myeloid leukaemia. Leukemia. 2017;31:1482–90. doi: 10.1038/leu.2017.113. PubMed DOI

Segerink WH, de Haas V, Kaspers GJL. Measurable residual disease in pediatric acute myeloid leukemia: a systematic review. Expert Rev Anticancer Ther. 2021;21:451–9. doi: 10.1080/14737140.2021.1860763. PubMed DOI

Lukes J, Jr., Winkowska L, Zwyrtkova M, Starkova J, Sramkova L, Stary J, et al. Identification of fusion gene breakpoints is feasible and facilitates accurate sensitive minimal residual disease monitoring on genomic level in patients with PML-RARA, CBFB-MYH11, and RUNX1-RUNX1T1. HemaSphere. 2020;4:e489. doi: 10.1097/HS9.0000000000000489. PubMed DOI PMC

Maurer-Granofszky M, Kohrer S, Fischer S, Schumich A, Nebral K, Larghero P, et al. Genomic breakpoint specific monitoring of measurable residual disease in pediatric non-standard risk acute myeloid leukemia. Haematologica. 2023 doi: 10.3324/haematol.2022.282424. PubMed DOI PMC

Zaliova M, Stuchly J, Winkowska L, Musilova A, Fiser K, Slamova M, et al. Genomic landscape of pediatric B-other acute lymphoblastic leukemia in a consecutive European cohort. Haematologica. 2019;104:1396–406. doi: 10.3324/haematol.2018.204974. PubMed DOI PMC

McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol. 2011;7:e1001138. doi: 10.1371/journal.pcbi.1001138. PubMed DOI PMC

Roberts KG, Li Y, Payne-Turner D, Harvey RC, Yang YL, Pei D, et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med. 2014;371:1005–15. doi: 10.1056/NEJMoa1403088. PubMed DOI PMC

Meyer C, Lopes BA, Caye-Eude A, Cave H, Arfeuille C, Cuccuini W, et al. Human MLL/KMT2A gene exhibits a second breakpoint cluster region for recurrent MLL-USP2 fusions. Leukemia. 2019;33:2306–40. doi: 10.1038/s41375-019-0451-7. PubMed DOI PMC

Meyer C, Schneider B, Reichel M, Angermueller S, Strehl S, Schnittger S, et al. Diagnostic tool for the identification of MLL rearrangements including unknown partner genes. Proc Natl Acad Sci USA. 2005;102:449–54. doi: 10.1073/pnas.0406994102. PubMed DOI PMC

Noort S, Oosterwijk JV, Ma J, Garfinkle EAR, Nance S, Walsh M, et al. Analysis of rare driving events in pediatric acute myeloid leukemia. Haematologica. 2023;108:48–60. doi: 10.3324/haematol.2021.280250. PubMed DOI PMC

Liu T, Rao J, Hu W, Cui B, Cai J, Liu Y, et al. Distinct genomic landscape of Chinese pediatric acute myeloid leukemia impacts clinical risk classification. Nat Commun. 2022;13:1640. doi: 10.1038/s41467-022-29336-y. PubMed DOI PMC

Liu Y, Easton J, Shao Y, Maciaszek J, Wang Z, Wilkinson MR, et al. The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia. Nat Genet. 2017;49:1211–8. doi: 10.1038/ng.3909. PubMed DOI PMC

Panagopoulos I, Aman P, Fioretos T, Hoglund M, Johansson B, Mandahl N, et al. Fusion of the FUS gene with ERG in acute myeloid leukemia with t(16;21)(p11;q22) Genes Chromosomes Cancer. 1994;11:256–62. doi: 10.1002/gcc.2870110408. PubMed DOI

Torkildsen S, Gorunova L, Beiske K, Tjonnfjord GE, Heim S, Panagopoulos I. Novel ZEB2-BCL11B fusion gene identified by RNA-sequencing in acute myeloid leukemia with t(2;14)(q22;q32) PLoS ONE. 2015;10:e0132736. doi: 10.1371/journal.pone.0132736. PubMed DOI PMC

Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, et al. Genomic classification and prognosis in acute myeloid leukemia. N Engl J Med. 2016;374:2209–21. doi: 10.1056/NEJMoa1516192. PubMed DOI PMC

Thol F, Gabdoulline R, Liebich A, Klement P, Schiller J, Kandziora C, et al. Measurable residual disease monitoring by NGS before allogeneic hematopoietic cell transplantation in AML. Blood. 2018;132:1703–13. doi: 10.1182/blood-2018-02-829911. PubMed DOI PMC

Yin JA, O’Brien MA, Hills RK, Daly SB, Wheatley K, Burnett AK. Minimal residual disease monitoring by quantitative RT-PCR in core binding factor AML allows risk stratification and predicts relapse: results of the United Kingdom MRC AML-15 trial. Blood. 2012;120:2826–35. doi: 10.1182/blood-2012-06-435669. PubMed DOI

Matsuo H, Iijima-Yamashita Y, Yamada M, Deguchi T, Kiyokawa N, Shimada A, et al. Monitoring of fusion gene transcripts to predict relapse in pediatric acute myeloid leukemia. Pediatr Int. 2018;60:41–6. doi: 10.1111/ped.13440. PubMed DOI

Ommen HB, Hokland P, Haferlach T, Abildgaard L, Alpermann T, Haferlach C, et al. Relapse kinetics in acute myeloid leukaemias with MLL translocations or partial tandem duplications within the MLL gene. Br J Haematol. 2014;165:618–28. doi: 10.1111/bjh.12792. PubMed DOI

Juul-Dam KL, Ommen HB, Nyvold CG, Walter C, Valerhaugen H, Kairisto V, et al. Measurable residual disease assessment by qPCR in peripheral blood is an informative tool for disease surveillance in childhood acute myeloid leukaemia. Br J Haematol. 2020;190:198–208. doi: 10.1111/bjh.16560. PubMed DOI

Dillon LW, Hayati S, Roloff GW, Tunc I, Pirooznia M, Mitrofanova A, et al. Targeted RNA-sequencing for the quantification of measurable residual disease in acute myeloid leukemia. Haematologica. 2019;104:297–304. doi: 10.3324/haematol.2018.203133. PubMed DOI PMC

Sievers EL, Lange BJ, Alonzo TA, Gerbing RB, Bernstein ID, Smith FO, et al. Immunophenotypic evidence of leukemia after induction therapy predicts relapse: results from a prospective Children’s Cancer Group study of 252 patients with acute myeloid leukemia. Blood. 2003;101:3398–406. doi: 10.1182/blood-2002-10-3064. PubMed DOI

van der Velden VH, van der Sluijs-Geling A, Gibson BE, te Marvelde JG, Hoogeveen PG, Hop WC, et al. Clinical significance of flowcytometric minimal residual disease detection in pediatric acute myeloid leukemia patients treated according to the DCOG ANLL97/MRC AML12 protocol. Leukemia. 2010;24:1599–606. doi: 10.1038/leu.2010.153. PubMed DOI

Rubnitz JE, Inaba H, Dahl G, Ribeiro RC, Bowman WP, Taub J, et al. Minimal residual disease-directed therapy for childhood acute myeloid leukaemia: results of the AML02 multicentre trial. Lancet Oncol. 2010;11:543–52. doi: 10.1016/S1470-2045(10)70090-5. PubMed DOI PMC

Loken MR, Alonzo TA, Pardo L, Gerbing RB, Raimondi SC, Hirsch BA, et al. Residual disease detected by multidimensional flow cytometry signifies high relapse risk in patients with de novo acute myeloid leukemia: a report from Children’s Oncology Group. Blood. 2012;120:1581–8. doi: 10.1182/blood-2012-02-408336. PubMed DOI PMC

Tierens A, Bjorklund E, Siitonen S, Marquart HV, Wulff-Juergensen G, Pelliniemi TT, et al. Residual disease detected by flow cytometry is an independent predictor of survival in childhood acute myeloid leukaemia; results of the NOPHO-AML 2004 study. Br J Haematol. 2016;174:600–9. doi: 10.1111/bjh.14093. PubMed DOI

Buldini B, Rizzati F, Masetti R, Fagioli F, Menna G, Micalizzi C, et al. Prognostic significance of flow-cytometry evaluation of minimal residual disease in children with acute myeloid leukaemia treated according to the AIEOP-AML 2002/01 study protocol. Br J Haematol. 2017;177:116–26. doi: 10.1111/bjh.14523. PubMed DOI

Distinct pattern of genomic breakpoints in CML and BCR::ABL1-positive ALL: analysis of 971 patients