inveRsion

inveRsion detects and classifies genetic inversions from genome-wide SNP genotype (SNP array) data to support association and population-genetic analyses.

Key Features:

• Identification of Polymorphic Inversions: Detects genomic regions likely to contain inversions by performing a sliding-window scan across SNP genotype data.
• Classification of Individuals: Classifies individuals as carrying normal or inverted alleles within identified regions based on genotype patterns.
• Utilization of Linkage Disequilibrium (LD): Leverages linkage between groups of SNPs to partition individuals into subpopulations corresponding to inversion status.
• Direct Genotype Analysis: Operates directly on genotype data rather than relying solely on haplotype tagging or LD differences.
• Genotype- and Haplotype-Based Implementation in R: Provides implementations for both genotype- and haplotype-based methods within an R package.

Scientific Applications:

• Genome-Wide Association Studies (GWAS): Enables association of inversion alleles with phenotypic traits or disease susceptibility in GWAS.
• Population Genetics: Characterizes known inversions in population genotype datasets such as HapMap Phase III, including regions 17q21 and 8p23.
• Detection of Novel Inversions: Performs genome-wide scans to provide population-based evidence for known autosomal inversions and to identify candidate novel inversion regions supported by independent experimental predictions.

Methodology:

Applies a generalized method developed for haplotype data that uses a sliding-window scan across SNPs, leverages linkage between SNP groups to partition individuals into normal and inverted subpopulations, and has been validated on simulated genotypes generated by coalescent models of inversion events; implementations exist for genotype- and haplotype-based analyses in R.