BACKGROUND: ABL-class fusions including NUP214-ABL1 and EBF1-PDGFRB occur in high risk acute lymphoblastic leukaemia (ALL) with gene expression patterns similar to BCR-ABL-positive ALL. Our aim was to evaluate new DNA-based measurable residual disease (MRD) tests detecting these fusions and IKZF1-deletions in comparison with conventional immunoglobulin/T-cell receptor (Ig/TCR) markers. METHODS: Precise genomic breakpoints were defined from targeted or whole genome next generation sequencing for ABL-fusions and BCR-ABL1. Quantitative PCR assays were designed and used to re-measure MRD in remission bone marrow samples previously tested using Ig/TCR markers. All MRD testing complied with EuroMRD guidelines. RESULTS: ABL-class patients had 46% 5year event-free survival and 79% 5year overall survival. All had sensitive fusion tests giving high concordance between Ig/TCR and ABL-class fusion results (21 patients, n = 257 samples, r2 = 0.9786, P < 0.0001) and Ig/TCR and IKZF1-deletion results (9 patients, n = 143 samples, r2 = 0.9661, P < 0.0001). In contrast, in BCR-ABL1 patients, Ig/TCR and BCR-ABL1 tests were discordant in 32% (40 patients, n = 346 samples, r2 = 0.4703, P < 0.0001) and IKZF1-deletion results were closer to Ig/TCR (25 patients, n = 176, r2 = 0.8631, P < 0.0001). CONCLUSIONS: MRD monitoring based on patient-specific assays detecting gene fusions or recurrent assays for IKZF1-deletions is feasible and provides good alternatives to Ig/TCR tests to monitor MRD in ABL-class ALL.

Blood and Bone Marrow Transplant Program Queensland Children's Hospital Brisbane QLD Australia

Cancer Centre for Children The Children's Hospital at Westmead Sydney NSW Australia

Children's Cancer Centre The Royal Children's Hospital Melbourne VIC Australia

Children's Haematology Oncology Centre Christchurch Hospital Christchurch New Zealand

CLIP Childhood Leukaemia Investigation Prague Prague Czech Republic

Computational Biology Children's Cancer Institute Lowy Cancer Research Centre UNSW Sydney NSW Australia

Department of Clinical Haematology and Oncology Women's and Children's Hospital Adelaide SA Australia

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

Kids Cancer Centre Sydney Children's Hospital Randwick NSW Australia

Molecular Diagnostics Children's Cancer Institute Lowy Cancer Research Centre UNSW Sydney NSW Australia

Paediatric Oncology Queensland Children's Hospital Brisbane QLD Australia

Precision Medicine Theme South Australian Health and Medical Research Institute Adelaide SA Australia

School of Medicine University of Adelaide Adelaide SA Australia

School of Women's and Children's Health University of New South Wales Sydney NSW Australia

University Hospital Motol Prague Czech Republic

Zobrazit více v PubMed

Cario G, Leoni V, Conter V, Attarbaschi A, Zaliova M, Sramkova L, 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;105:1887–94. doi: 10.3324/haematol.2019.231720. PubMed DOI PMC

den Boer ML, Cario G, Moorman AV, Boer JM, de Groot-Kruseman HA, Fiocco M, 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

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

Tanasi I, Ba I, Sirvent N, Braun T, Cuccuini W, Ballerini P, et al. Efficacy of tyrosine kinase inhibitors in Ph-like acute lymphoblastic leukemia harboring ABL-class rearrangements. Blood. 2019;134:1351–5. doi: 10.1182/blood.2019001244. PubMed DOI

Moorman AV, Schwab C, Winterman E, Hancock J, Castleton A, Cummins M, et al. Adjuvant tyrosine kinase inhibitor therapy improves outcome for children and adolescents with acute lymphoblastic leukaemia who have an ABL-class fusion. Br J Haematol. 2020;191:844–51. doi: 10.1111/bjh.17093. PubMed DOI

Schultz KR, Carroll A, Heerema NA, Bowman WP, Aledo A, Slayton WB, et al. Long-term follow-up of imatinib in pediatric Philadelphia chromosome-positive acute lymphoblastic leukemia: Children’s Oncology Group Study AALL0031. Leukemia. 2014;28:1467–71. doi: 10.1038/leu.2014.30. PubMed DOI PMC

Hovorkova L, Zaliova M, Venn NC, Bleckmann K, Trkova M, Potuckova E, et al. Monitoring of childhood ALL using BCR-ABL1 genomic breakpoints identifies a subgroup with CML-like biology. Blood. 2017;129:2771–81. doi: 10.1182/blood-2016-11-749978. PubMed DOI

Burmeister T, Marschalek R, Schneider B, Meyer C, Gokbuget N, Schwartz S, et al. Monitoring minimal residual disease by quantification of genomic chromosomal breakpoint sequences in acute leukemias with MLL aberrations. Leukemia. 2006;20:451–7. doi: 10.1038/sj.leu.2404082. PubMed DOI

Van der Velden VH, Corral L, Valsecchi MG, Jansen MW, De Lorenzo P, Cazzaniga G, et al. Prognostic significance of minimal residual disease in infants with acute lymphoblastic leukemia treated within the Interfant-99 protocol. Leukemia. 2009;23:1073–9. doi: 10.1038/leu.2009.17. PubMed DOI

Mullighan CG, Su X, Zhang J, Radtke I, Phillips LAA, Miller CB, et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med. 2009;360:470–80. doi: 10.1056/NEJMoa0808253. PubMed DOI PMC

van der Veer A, Waanders E, Pieters R, Willemse ME, Van Reijmersdal SV, Russell LJ, et al. Independent prognostic value of BCR-ABL1-like signature and IKZF1 deletion, but not high CRLF2 expression, in children with B-cell precursor ALL. Blood. 2013;122:2622–9. doi: 10.1182/blood-2012-10-462358. PubMed DOI PMC

Kuiper RP, Waanders E, van der Velden VHJ, van Reijmersdal SV, Venkatachalam R, Scheijen B, et al. IKZF1 deletions predict relapse in uniformly treated pediatric precursor B-ALL. Leukemia. 2010;24:1258–64. doi: 10.1038/leu.2010.87. PubMed DOI

Dorge P, Meissner B, Zimmermann M, Moricke A, Schrauder A, Bouquin JP, et al. IKZF1 deletion is an independent predictor of outcome in pediatric acute lymphoblastic leukemia treated according to the ALL-BFM 2000 protocol. Haematologica. 2013;98:428–32. doi: 10.3324/haematol.2011.056135. PubMed DOI PMC

Palmi C, Valsecchi MG, Longinotti G, Silvestri D, Carrino V, Conter V, et al. What is the relevance of Ikaros gene deletions as a prognostic marker in pediatric Philadelphia-negative B-cell precursor acute lymphoblastic leukemia? Haematologica. 2013;98:1226–31. doi: 10.3324/haematol.2012.075432. PubMed DOI PMC

Sutton R, Venn NC, Law T, Boer JM, Trahair TN, Ng A, et al. A risk score including microdeletions improves relapse prediction for standard and medium risk precursor B-cell acute lymphoblastic leukaemia in children. Br J Haematol. 2018;180:550–62. doi: 10.1111/bjh.15056. PubMed DOI

Hamadeh L, Enshaei A, Schwab C, Alonso CN, Attarbaschi A, Barbany G, et al. Validation of the United Kingdom copy-number alteration classifier in 3239 children with B-cell precursor ALL. Blood Adv. 2019;3:148–57. doi: 10.1182/bloodadvances.2018025718. PubMed DOI PMC

Stanulla M, Cave H, Moorman AV. IKZF1 deletions in pediatric acute lymphoblastic leukemia: still a poor prognostic marker? Blood. 2020;135:252–60. doi: 10.1182/blood.2019000813. PubMed DOI PMC

Boer JM, van der Veer A, Rizopoulos D, Fiocco M, Sonneveld E, de Groot-Kruseman HA, et al. Prognostic value of rare IKZF1 deletion in childhood B-cell precursor acute lymphoblastic leukemia: an international collaborative study. Leukemia. 2016;30:32–8. doi: 10.1038/leu.2015.199. PubMed DOI

Venn NC, van der Velden VH, de Bie M, Waanders E, Giles JE, Law T, et al. Highly sensitive MRD tests for ALL based on the IKZF1 Delta3-6 microdeletion. Leukemia. 2012;26:1414–6. doi: 10.1038/leu.2011.348. PubMed DOI PMC

Caye A, Beldjord K, Mass-Malo K, Drunat S, Soulier J, Gandemer V, et al. Breakpoint-specific multiplex polymerase chain reaction allows the detection of IKZF1 intragenic deletions and minimal residual disease monitoring in B-cell precursor acute lymphoblastic leukemia. Haematologica. 2013;98:597–601. doi: 10.3324/haematol.2012.073965. PubMed DOI PMC

Heatley SL, Sadras T, Kok CH, Nievergall E, Quek K, Dang P, et al. High prevalence of relapse in children with Philadelphia-like acute lymphoblastic leukemia despite risk-adapted treatment. Haematologica. 2017;102:e490–e3. doi: 10.3324/haematol.2016.162925. PubMed DOI PMC

Wong M, Mayoh C, Lau LMS, Khuong-Quang DA, Pinese M, Kumar A, et al. Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer. Nat Med. 2020;26:1742–53. doi: 10.1038/s41591-020-1072-4. PubMed DOI

Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv. 2013; https://arxiv.org/abs/1303.3997.

Cameron DL, Baber J, Shale C, Papenfuss AT, Valle-Inclan JE, Besselink N, et al. GRIDSS, PURPLE, LINX: unscrambling the tumor genome via integrated analysis of structural variation and copy number. Preprint at bioRxiv. 2019; https://www.biorxiv.org/content/10.1101/781013v1. DOI

Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012;6:80–92. doi: 10.4161/fly.19695. PubMed DOI PMC

Cameron DL, Schroder J, Penington JS, Do H, Molania R, Dobrovic A, et al. GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Res. 2017;27:2050–60.. doi: 10.1101/gr.222109.117. PubMed DOI PMC

Shale C, Baber C, Cameron DL, Wong M, Cowley MJ, Papenfuss AT, et al. Unscrambling cancer genomes via integrated analysis of structural variation and copy number. Preprint for BioRxiv. 2020; https://www.biorxiv.org/content/10.1101/2020.12.03.410860v1. PubMed DOI PMC

Sutton R, Shaw PJ, Venn NC, Law T, Dissanayake A, Kilo T, et al. Persistent MRD before and after allogeneic BMT predicts relapse in children with acute lymphoblastic leukaemia. Br J Haematol. 2015;168:395–404. doi: 10.1111/bjh.13142. PubMed DOI

Irving JA, Enshaei A, Parker CA, Sutton R, Kuiper RP, Erhorn A, et al. Integration of genetic and clinical risk factors improves prognostication in relapsed childhood B-cell precursor acute lymphoblastic leukemia. Blood. 2016;128:911–22. doi: 10.1182/blood-2016-03-704973. PubMed DOI PMC

Subhash VV, Huang L, Kamili A, Wong M, Chen D, Venn NC, et al. Whole genome sequencing facilitates patient-specific quantitative PCR-based minimal residual disease monitoring in acute lymphoblastic leukaemia, neuroblastoma and Ewing sarcoma. British J Cancer. 2022;126;482–91. PubMed PMC

Flohr T, Schrauder A, Cazzaniga G, Panzer-Grümayer R, van der Velden V, Fischer S, et al. Minimal residual disease-directed risk stratification using real-time quantitative PCR analysis of immunoglobulin and T-cell receptor gene rearrangements in the international multicenter trial AIEOP-BFM ALL 2000 for childhood acute lymphoblastic leukemia. Leukemia. 2008;22:771–82. doi: 10.1038/leu.2008.5. PubMed DOI

Choi S, Henderson M, Kwan EN, Sutton R, Giles J, Venn NC, et al. Relapse in children with acute lymphoblastic leukaemia involving selection of a pre-existing drug resistant subclone. Blood. 2007;110:632–9. doi: 10.1182/blood-2007-01-067785. PubMed DOI

van der Velden V, Cazzaniga G, Schrauder A, Hancock JF, Bader P, Panzer E, 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

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

Analysis of measurable residual disease by IG/TR gene rearrangements: quality assurance and updated EuroMRD guidelines