Investigating changes in cell type proportions, gene expression and gene regulation impacted by the 16p11.2 copy number variants

Copy number variants (CNVs) represent significant risk factors for Autism Spectrum Disorders (ASD). One of the most frequent CNVs involved in ASD is a deletion or duplication of the 16p11.2 CNV locus, spanning 29 protein-coding genes. Despite the progress in linking 16p11.2 genetic changes with the phenotypic (macrocephaly and microcephaly) abnormalities in the patients and model organisms, the specific molecular pathways impacted by this CNV remain unknown. We generated 10x multiome data from brain organoids carrying 16p11.2 deletions and duplications at various time points. The goal of this rotation project is to analyze these data to discover pathways and gene regulatory networks dysregulated by the 16p11.2 CNV. The student is required to have familiarity with single cell RNA data analyses.