SNP HiTLink

SNP HiTLink facilitates integration of microarray-based SNP data with linkage analysis programs to enable high-throughput genetic linkage studies for disease gene mapping.

Key Features:

• Direct Import and Compatibility: Directly imports SNP chip data from Affymetrix Mapping 100 k/500 k array sets and Genome-Wide Human SNP arrays 5.0/6.0 and interfaces with MLINK, Superlink, Merlin, and Allegro for linkage analysis.
• High-Throughput Processing: Processes large-scale SNP datasets to reduce analysis time relative to traditional microsatellite-based analyses.
• Marker Selection Functions: Implements marker-selection functions to mitigate typing errors, handle markers in linkage equilibrium, and select informative markers for analysis.
• Performance and Efficiency: Optimized for runtime efficiency, with whole-genome analyses typically completing within a few hours on general personal computers.
• LOD Score Performance: Produces LOD scores comparable to or superior to those obtained from microsatellite markers.

Scientific Applications:

• Disease Locus Identification: Identification of loci associated with disease genes through linkage analysis using microarray-based SNP markers.
• Genome-Wide Linkage Scans: Enabling genome-wide linkage studies using high-density SNP arrays such as Affymetrix Mapping 100 k/500 k and Genome-Wide Human SNP arrays 5.0/6.0.
• Comparative Linkage Analysis: Comparing SNP-based linkage results to microsatellite marker-based analyses via LOD score assessment.

Methodology:

Direct importation of SNP data into linkage analysis programs, application of marker-selection functions to filter and select informative SNPs, and support for parametric and model-free linkage analyses.