• 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)

Five types of sample are considered:

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

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)