Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk

Nat Commun. 2019 Nov 25;10(1):5348. doi: 10.1038/s41467-019-13069-6.

Abstract

There is increasing evidence for a strong inherited genetic basis of susceptibility to acute lymphoblastic leukaemia (ALL) in children. To identify new risk variants for B-cell ALL (B-ALL) we conducted a meta-analysis with four GWAS (genome-wide association studies), totalling 5321 cases and 16,666 controls of European descent. We herein describe novel risk loci for B-ALL at 9q21.31 (rs76925697, P = 2.11 × 10-8), for high-hyperdiploid ALL at 5q31.1 (rs886285, P = 1.56 × 10-8) and 6p21.31 (rs210143 in BAK1, P = 2.21 × 10-8), and ETV6-RUNX1 ALL at 17q21.32 (rs10853104 in IGF2BP1, P = 1.82 × 10-8). Particularly notable are the pleiotropic effects of the BAK1 variant on multiple haematological malignancies and specific effects of IGF2BP1 on ETV6-RUNX1 ALL evidenced by both germline and somatic genomic analyses. Integration of GWAS signals with transcriptomic/epigenomic profiling and 3D chromatin interaction data for these leukaemia risk loci suggests deregulation of B-cell development and the cell cycle as central mechanisms governing genetic susceptibility to ALL.

Publication types

  • Meta-Analysis
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Child
  • Core Binding Factor Alpha 2 Subunit / genetics*
  • Epigenomics
  • Genetic Predisposition to Disease / genetics*
  • Genome-Wide Association Study
  • Humans
  • Oncogene Proteins, Fusion / genetics*
  • Polymorphism, Single Nucleotide*
  • Precursor B-Cell Lymphoblastic Leukemia-Lymphoma / genetics*
  • Precursor B-Cell Lymphoblastic Leukemia-Lymphoma / pathology
  • RNA-Binding Proteins / genetics*
  • Risk Factors
  • Transcriptome
  • bcl-2 Homologous Antagonist-Killer Protein / genetics*

Substances

  • BAK1 protein, human
  • Core Binding Factor Alpha 2 Subunit
  • IGF2BP1 protein, human
  • Oncogene Proteins, Fusion
  • RNA-Binding Proteins
  • TEL-AML1 fusion protein
  • bcl-2 Homologous Antagonist-Killer Protein