seismic

seismic integrates single-cell RNA sequencing (scRNA-seq) data with Genome-Wide Association Studies (GWAS) to identify associations between complex traits and cell types using a novel specificity score.

Key Features:

• Novel specificity score: Characterizes cell types using a new specificity score for rapid and accurate association detection.
• Scalable comparison framework: Enables systematic comparison across over 1,000 cell type characterizations at different granularities and 28 traits.
• Driver gene accessibility: Provides access to specific genes driving cell type-trait associations for further biological analysis.
• GWAS endpoint sensitivity: Supports analysis of different GWAS endpoints, such as clinical diagnoses and biomarker endpoints.

Scientific Applications:

• Complex trait-cell type association: Identifies disease-relevant cell groups underlying complex traits and diseases.
• Neurodegenerative disease research: Pinpoints cell-specific and brain region-specific manifestations in Parkinson's and Alzheimer's diseases.
• Alzheimer's disease case study: Reveals microglial associations from clinical diagnosis GWAS and neuronal associations from tau biomarker GWAS endpoints.

Methodology:

seismic employs a novel specificity score to characterize cell types from scRNA-seq data for integration with GWAS data; specific genes driving associations can be accessed and analyzed within the framework.