AdaLiftOver

AdaLiftOver maps orthologous non-coding regulatory regions between human and model organism genomes to identify conserved regulatory elements and support interpretation of GWAS loci.

Key Features:

• Enhanced Mapping Precision: Builds upon the UCSC liftOver framework and extends query regions to improve mapping accuracy and reduce multi-mapping, low precision, and low mapping rates for non-coding regions.
• Conservation-Based Prioritization: Prioritizes candidate target regions by evaluating conservation of epigenomic features and sequence grammar.
• Versatility Across Genomic Datasets: Handles genomic intervals derived from diverse epigenome datasets, multiple model organisms, and GWAS SNPs.
• Facilitation of Epigenomic Research: Identifies orthologous loci for GWAS SNPs to aid derivation and comparison of human and model organism epigenome datasets.

Scientific Applications:

• Model Organism Research: Facilitates translation of regulatory findings from model organisms to human biology.
• GWAS Interpretation: Links GWAS SNPs to orthologous regulatory elements across species to aid interpretation of genetic associations.
• Epigenomic Studies: Enables exploration of conserved epigenomic landscapes and gene regulation mechanisms across species.

Methodology:

AdaLiftOver builds on UCSC liftOver by extending query regions and integrating conservation metrics of epigenomic features and sequence grammar to prioritize mapped candidate regions.