GenomePaint

GenomePaint visualizes whole-genome, whole-exome, transcriptome, and epigenomic cancer sequencing data to enable exploration of relationships between coding and non-coding DNA variants, RNA expression, and 3D genome features within individual tumor samples and cohorts.

Key Features:

• Integrated Multi-Omics Visualization: Combines whole-genome, whole-exome, transcriptome, and epigenomic datasets to display coding and non-coding variants alongside expression and epigenomic signals.
• Functional Impact Analysis: Examines regulatory non-coding variants and coding variants in a spatial genomic context by integrating 3D genome data from cancer cell lines.

Scientific Applications:

• Patient outcome correlation: Correlates mutation and expression patterns with patient outcomes for translational research.
• Aberrant splicing discovery: Enabled identification of aberrant splicing events disrupting the RING domain of CREBBP.
• Oncogene activation insights: Revealed cis activation of the MYC oncogene via duplication of the NOTCH1-MYC enhancer in B-lineage acute lymphoblastic leukemia.
• Tumor heterogeneity exploration: Investigated inter- and intra-tumor heterogeneity at EGFR in adult glioblastomas.

Methodology:

Integration and visualization of multi-layered genomic data from whole-genome, whole-exome, transcriptome, and epigenomic sources, including coding and non-coding variants and 3D genome contacts from cancer cell lines.