TreeMap

TreeMap performs fine-mapping of expression quantitative trait loci (eQTL) to identify causal regulatory variants that influence gene transcription.

Key Features:

• Hierarchical LD utilization: Leverages the hierarchical structure of linkage disequilibrium (LD) to systematically search for single and multiple causal variants within a locus.
• Multisite effects and linkage modeling: Accounts for multisite effects and genetic linkage to distinguish causal variants from linked noncausal variants.
• Genome-wide and long-range eQTL analysis: Enables genome-wide scans including detection of long-range (distal) eQTLs across extended flanking regions.
• Extensive simulations: Performs extensive simulations to evaluate detection of co-regulating variants and method performance.
• Parallel processing support: Supports parallel computation to accelerate large-scale analyses.

Scientific Applications:

• GTEx tissue eQTL mapping: Applied to Genotype-Tissue Expression (GTEx) data from brain hippocampus and transverse colon to map eQTLs.
• Long-range regulatory variant discovery: Identified numerous distal eQTLs within gene bodies and up to 4 megabases (Mbps) of flanking regions, including concordant distal eQTLs across brain and colon samples suggesting long-range regulation.

Methodology:

Uses hierarchical LD structure for systematic searches of single and multiple causal variants, models multisite effects and genetic linkage, performs extensive simulations, and employs parallel computation for genome-wide and long-range eQTL analyses.