GeneRecon

GeneRecon performs fine-scale association mapping using a coalescent-based model to localize disease locus positions from case-control genetic data.

Key Features:

• Coalescent-based modeling: Uses a coalescent model to relate genealogical relationships to observed genetic variation for association mapping.
• Metropolis-Hastings sampling: Explores the state space of genealogies via Metropolis-Hastings sampling to estimate posterior quantities.
• Posterior inference of disease loci: Determines the posterior distribution of disease locus positions.
• Supported genotype types: Accommodates phased and unphased SNP and microsatellite genotypes from case-control datasets.
• Extensible configuration via Guile Scheme: Allows customization of input formats, search strategies, and sampled statistics through Guile Scheme scripting.
• Implementation languages: Source code implemented in C++ and Scheme.

Scientific Applications:

• Fine-scale association mapping: Localizing disease-associated loci by integrating genealogical inference with genetic marker data.
• Case-control association studies: Analyzing phased and unphased SNP and microsatellite genotypes from case-control cohorts to infer locus positions.
• Genetic mapping of disease loci: Investigating the genetic architecture and precise localization of disease-associated regions.

Methodology:

Uses a coalescent model with Metropolis-Hastings sampling within the state space of genealogies to determine the posterior distribution of disease locus positions from phased and unphased SNP and microsatellite case-control genotypes.