AeQTL

AeQTL performs region-based aggregation testing to detect expression quantitative trait loci (eQTLs) associated with rare germline and somatic coding and noncoding variants.

Key Features:

• Region-Based Aggregation: Aggregates genetic variants within user-specified genomic regions to increase detection power for rare variant eQTLs.
• Compatibility with Standard Genomic Files: Accepts standard genomic file formats for input data.
• Germline and Somatic Mutation Analysis: Analyzes both germline and somatic mutations, including rare germline truncations and somatic events.
• Coding and Noncoding Variant Analysis: Supports analysis of both coding and noncoding variants for association with gene expression.
• Mutation-Type Differentiation: Differentiates impacts of missense versus truncation mutations on gene expression.
• Implementation: Implemented in Python.

Scientific Applications:

• Rare Variant eQTL Discovery: Identifies associations between aggregated rare germline truncations and gene expression, exemplified by BRCA1 and SLC25A39 in breast tumors.
• Pan-Cancer Somatic Analysis: Evaluates somatic mutation effects across cancers and distinguishes missense versus truncation impacts on expression to study driver and tumor suppressor genes.
• Multi-Omic Classification: Identifies somatic truncation eQTLs that can serve as a multi-omic classifier to distinguish oncogenes from tumor-suppressor genes.

Methodology:

Aggregates genetic variants within user-specified regions and performs aggregation-based eQTL tests on rare germline and somatic coding and noncoding variants, differentiates missense versus truncation mutation effects, and is implemented in Python while accepting standard genomic file formats.