Understanding the functional implications of genomic variants is critical in cancer research, as these variants can influence gene expression, protein structure, and key biological pathways, driving cancer progression. This pipeline offers a structured methodology for variant annotation and analysis, enabling researchers to uncover potential biomarkers and identify therapeutic targets.
Key Highlights:
Utilizes Ensembl's Variant Effect Predictor (VEP) through the biomaRt package to provide detailed annotations for genomic variants.
Assesses how variants might alter protein function by leveraging SIFT and PolyPhen scores.
Detects the biological pathways most affected by the annotated variants using Reactome pathway analysis.
Produces clear and informative visualizations of variant consequences and pathway enrichments.
Each step of the process is thoroughly explained, enhancing both understanding and reproducibility.