PersonaDrive

PersonaDrive prioritizes patient-specific cancer driver genes by integrating genomic alterations with pathway and protein network data to distinguish drivers from passengers.

Key Features:

• Personalized Bipartite Graph Construction: Constructs a personalized bipartite graph for each patient that integrates genomic data with biological pathways and protein connectivity information.
• Pairwise Pathway Coverage Scoring: Computes "pairwise pathway coverage" scores by summing weighted contributions from all patients, where weights are derived from pairwise patient similarity scores to normalize personalized gene rankings.
• Comparison with State-of-the-Art Methods: Was compared against three patient-specific cancer gene prioritization methods using a novel evaluation framework and demonstrated superior performance on TCGA and cell-line datasets.
• Pathway Enrichment Analysis: Identifies KEGG and Reactome pathways significantly enriched among prioritized genes and reports overlap with reference sets from cell-line studies.

Scientific Applications:

• Personalized Medicine: Provides patient-specific prioritized lists of driver mutations to support individualized therapeutic decision-making based on each tumor's genetic profile.
• Research and Development: Facilitates investigation of cancer heterogeneity and the discovery of candidate therapeutic targets by linking mutated genes to pathways and protein networks.

Methodology:

Constructs personalized bipartite patient graphs, computes pairwise pathway coverage scores using weighted sums with pairwise patient similarity weights, and performs pathway enrichment analysis against KEGG and Reactome; performance was evaluated against three patient-specific methods on TCGA and cell-line datasets.