Protocol for haplotype-resolved genome comparison and allele-specific expression analysis across multiple tissues and...

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology
• Population Genetics

Background:

• Haplotype-resolved genome comparison and allele-specific expression (ASE) analysis are vital for linking genomic variation to phenotypic differences.
• Current methods face challenges in reproducibility across diverse tissues and individuals.

Purpose of the Study:

• To present a standardized protocol for haplotype-resolved genome comparison.
• To extend this protocol for robust allele-specific expression (ASE) profiling across multiple tissues and individuals.
• To facilitate reproducible analysis of genomic diversity's impact on phenotypes.

Main Methods:

• Development of a protocol for identifying and comparing haplotype-divergent sequences and alleles.
• Detailed procedures for variant detection from RNA sequencing (RNA-seq) data.
• Methodology for identifying genes exhibiting allele-specific expression (ASE).

Main Results:

• A comprehensive protocol enabling haplotype-resolved genome comparison is established.
• The protocol successfully extends to ASE profiling across multiple tissues and individuals.
• The described methods facilitate the detection of variants and identification of ASE genes.

Conclusions:

• The presented protocol enhances reproducibility in haplotype-resolved genome comparison and ASE analysis.
• This standardized approach supports deeper understanding of how genomic diversity influences phenotypic variation.
• The protocol serves as a valuable resource for researchers in genomics and molecular biology.