LocHap

LocHap identifies local haplotype variants (LHVs) from paired-end deep DNA-sequencing data to detect somatic mosaicism and cellular heterogeneity.

Key Features:

• Ultra-Fast Processing: Optimized for high-speed analysis of large sequencing datasets to support large-scale genomic studies.
• Paired-End DNA-Sequencing Data Utilization: Leverages paired-end reads to link scaffolded single nucleotide variants (SNVs) supported by the same reads.
• Identification of Local Haplotype Variants (LHVs): Detects local haplotypes (LHs) from scaffolded SNVs and classifies loci with more than two genotypes as LHVs.
• Evidence of Somatic Mosaicism: Reports LHVs as indicators of somatic mosaicism arising from genetically heterogeneous cell populations.

Scientific Applications:

• Disease Diagnosis and Research: Enables detection of widespread LHVs across the genome, aiding studies of cancer and other diseases where tumor samples show higher LHV frequencies than normal samples.
• Age-Related Genetic Studies: Facilitates comparison of LHV frequencies across age groups, supporting analyses that show increased LHVs in older adults.

Methodology:

Applies novel statistical modeling techniques to paired-end DNA-sequencing data to identify scaffolded SNVs supported by the same reads, assemble local haplotypes, and classify loci with more than two genotypes as LHVs.