InferAMP

InferAMP infers genomic amplicon boundaries and co-amplified gene content from gene-level copy-number calls in clinical tumor NGS panel reports to contextualize somatic amplifications.

Key Features:

• Amplicon boundary inference: Infers boundaries of genome-wide amplicons from gene-level amplification calls reported by somatic NGS gene panel analyses.
• Co-amplification analysis: Identifies genes that are co-amplified and estimates the likely physical size of amplified genomic regions.
• Identification of unassessed genes: Predicts cancer-relevant genes that may be co-amplified but were not evaluated in the original assay.
• Optimization for Foundation One reports: Maintains compatibility with Foundation One reports from Foundation Medicine as an example clinical panel output.
• Implementation: Implemented in Python for computational inference of amplicon boundaries and co-amplified gene content.

Scientific Applications:

• Clinical interpretation of somatic amplifications: Provides genomic context to gene-level amplification calls from clinical tumor profiling reports to aid assessment of potential drivers of tumor growth.
• Therapeutic target nomination: Elucidates the size and composition of amplified regions to support identification of candidate therapeutic targets and selection of targeted therapies.
• Extension of panel results for research: Enables researchers to infer additional co-amplified cancer genes beyond those assayed on NGS gene panels.

Methodology:

Python-based analysis of gene-level copy-number/amplification calls from somatic NGS panel reports (e.g., Foundation One) to infer amplicon boundaries, identify co-amplified genes, estimate amplicon size, and predict unassessed co-amplified cancer-relevant genes.