HaploBlock

HaploBlock identifies haplotype blocks and performs SNP haplotyping and linkage disequilibrium mapping on high-density phased or unphased genotype SNP marker data to support genetic association studies.

Key Features:

• Integrated Approach: Integrates haplotype block identification, SNP haplotyping, and linkage disequilibrium mapping within a single analytical framework.
• Statistical Model: Employs a statistical model that accounts for recombination hotspots, genetic bottlenecks, genetic drift, and mutations.
• Markov Chain Core: Utilizes a Markov Chain mechanism to improve prediction and analysis accuracy in genomic datasets.
• Versatility with Data Types: Processes both phased and unphased genotype SNP data.
• Performance on High-density Data: Validated on high-density SNP datasets with reported superior performance relative to traditional SNP-based methods.
• Hidden SNP Identification: Identifies hidden SNPs and converts them into phenotype information to inform resequencing efforts.
• Application Scope: Applicable to mapping low penetrance diseases and analyzing complex trait architectures.

Scientific Applications:

• Genetic Mapping: Enhances linkage disequilibrium–based genetic mapping by leveraging haplotype block structure.
• Resequencing Guidance: Guides resequencing projects by identifying hidden SNPs for targeted follow-up.
• Disease Association Studies: Supports studies of complex and low penetrance disease associations through haplotype-based analyses.

Methodology:

Applies a statistical model that incorporates recombination hotspots, bottlenecks, genetic drift, and mutations and implements a Markov Chain mechanism, including conversion of hidden SNPs into phenotype information for resequencing guidance.