Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients

Research output: Contribution to journalJournal articleResearchpeer-review

  • A Wesołowska-Andersen
  • L Borst
  • M D Dalgaard
  • R Yadav
  • K K Rasmussen
  • P S Wehner
  • Morten Rasmussen
  • T F Ørntoft
  • I Nordentoft
  • R Koehler
  • C R Bartram
  • M Schrappe
  • T Sicheritz-Ponten
  • L Gautier
  • H Marquart
  • H O Madsen
  • S Brunak
  • M Stanulla
  • R Gupta
  • Schmiegelow, K.

Childhood acute lymphoblastic leukemia survival approaches 90%. New strategies are needed to identify the 10-15% who evade cure. We applied targeted, sequencing-based genotyping of 25 000 to 34 000 preselected potentially clinically relevant single-nucleotide polymorphisms (SNPs) to identify host genome profiles associated with relapse risk in 352 patients from the Nordic ALL92/2000 protocols and 426 patients from the German Berlin-Frankfurt-Munster (BFM) ALL2000 protocol. Patients were enrolled between 1992 and 2008 (median follow-up: 7.6 years). Eleven cross-validated SNPs were significantly associated with risk of relapse across protocols. SNP and biologic pathway level analyses associated relapse risk with leukemia aggressiveness, glucocorticosteroid pharmacology/response and drug transport/metabolism pathways. Classification and regression tree analysis identified three distinct risk groups defined by end of induction residual leukemia, white blood cell count and variants in myeloperoxidase (MPO), estrogen receptor 1 (ESR1), lamin B1 (LMNB1) and matrix metalloproteinase-7 (MMP7) genes, ATP-binding cassette transporters and glucocorticosteroid transcription regulation pathways. Relapse rates ranged from 4% (95% confidence interval (CI): 1.6-6.3%) for the best group (72% of patients) to 76% (95% CI: 41-90%) for the worst group (5% of patients, P<0.001). Validation of these findings and similar approaches to identify SNPs associated with toxicities may allow future individualized relapse and toxicity risk-based treatments adaptation.

Original languageEnglish
Issue number2
Pages (from-to)297-303
Number of pages7
Publication statusPublished - 2015

    Research areas

  • Adolescent, Child, Child, Preschool, Denmark, Female, Genome, Human, Genomics, Genotype, Germany, Humans, Infant, Male, Neoplasm Recurrence, Local, Neoplasm, Residual, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Risk Factors, Treatment Outcome

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