• 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)

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

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 with 10x software cellranger
• Quality control (filter poor quality cells and remove uninformative genes)
• UMI count normalisation
• Feature selection and dimensionality reduction
• Data set integration
• Clustering
• Identification of cluster marker genes
• Differential expression and abundance between conditions