• Childhood acute lymphoblastic leukemia (cALL)

  • Caron et al. 2020
  • the most common pediatric cancer
  • characterized by bone marrow lymphoid precursors
  • that acquire genetic alterations,
  • resulting in disrupted maturation and uncontrollable proliferation
  • up to 85–90% of patients are cured
  • others do not respond to treatment or relapse and die
  • Aim: characterise the heterogeneity of gene expression at the cell level, within and between patients
  • cells: Bone Marrow Mononuclear cells (BMMCs)

• Adult bone marrow

  • ‘HCA’: adult BMMCs (ABMMCs) obtained from the Human Cell Atlas (HCA)

Four types of sample are considered:

• B-ALL patients:
  • four ‘t(12;21)’ or ‘ETV6-RUNX1’
  • two ‘High hyper diploid’ or ‘HHD’
• T-ALL patients
  • two ‘PRE-T’
• three healthy pediatric controls
• eight healthy adult controls, publicly available

As the study aims at identifying cell populations, large numbers of cells were sequenced with the droplet-based 10x Chromium assay.

We will follow several steps:

• sequencing quality check
• alignment of reads to the human genome (GRCh38) with 10x software cellranger
• quality control (cell calls, cells and genes filtering)
• UMI count normalisation
• feature selection and dimensionality reduction
• data set integration (PBMMC and ETV6-RUNX1)
• clustering
• identification of cluster marker genes
• differential expression and abundance between conditions
• (trajectory analysis)