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

Four type of samples are considered:

• eight patients:
  • six B-ALL
    • four ‘t(12;21)’ or ‘ETV6-RUNX1’
    • two ‘High hyper diploid’ or ‘HHD’
  • two T-ALL (‘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
• data set integration (PBMMC and ETV6-RUNX1)
• feature selection and dimensionality reduction
• clustering
• marker gene identification
• differential expression and abundance between conditions
• trajectory analysis