HomozygosityMapper

HomozygosityMapper identifies runs of homozygosity shared among affected individuals to map recessive loci in consanguineous pedigrees across human, rodent, and other mammalian genomes.

Key Features:

• Input data formats: Supports SNP genotype files, major genotyping platforms, and Next Generation Sequencing (NGS) *.vcf files.
• Homozygous region detection: Detects genome-wide homozygous stretches shared among affected individuals.
• Genotype inspection and region refinement: Provides genotype-level inspection across samples and manual refinement of detected homozygous regions.
• GeneDistiller integration: Integrates with the candidate gene search engine GeneDistiller to identify promising candidate genes.
• Species support: Includes analysis capabilities for human, common experimental rodents, and important farm animals.
• Export formats for enrichment and linkage: Generates *.bed files for targeted enrichment and produces files tailored for conventional linkage analyses limited to candidate regions.
• Loss of heterozygosity and single-family analyses: Supports loss of heterozygosity studies and single-family homozygosity mapping.
• Performance: Detects homozygous stretches in minutes, reducing computational time compared to traditional multipoint linkage analyses.

Scientific Applications:

• Recessive trait mapping: Mapping recessive disease loci in consanguineous families by identifying shared long homozygous regions.
• Candidate gene prioritization: Facilitating identification of candidate genes within homozygous intervals via integration with GeneDistiller.
• Targeted sequencing strategies: Enabling targeted enrichment and deep sequencing of candidate disease regions using exported *.bed files.
• Loss of heterozygosity investigations: Supporting studies of loss of heterozygosity in single-family and tumor-related contexts.

Methodology:

Uses a database-driven storage of marker data and advanced algorithms to detect homozygous stretches rapidly, thereby bypassing the lengthy computation of traditional multipoint linkage analyses.