aScan

aScan detects and quantifies allele-specific expression (ASE) in diploid organisms using matched genomic and RNA-Seq data to identify differential expression between paternal and maternal alleles.

Key Features:

• Identification of ASE: Analyzes paired genomic and RNA-Seq (transcriptomic) datasets to detect differential expression between alleles within an individual.
• High accuracy and sensitivity: Validated on real and simulated data, demonstrating high accuracy and sensitivity for ASE detection across varying experimental conditions.
• Application to private variants: Annotates low-frequency "private" genetic variants by assessing their regulatory impact on allele-specific expression in individuals not represented in public databases.
• Versatility across NGS assays: Applicable to quantitative next-generation sequencing (NGS) assays that provide matched genotypic and expression data beyond RNA-Seq.

Scientific Applications:

• Genetic regulation studies: Enables investigation of how genetic variation influences gene regulation at the allele level.
• Personalized medicine: Identifies individual-specific regulatory variants to inform personalized medicine approaches, including tailored therapeutic strategies based on individual genetic profiles.
• Functional genomics: Facilitates studies of gene expression regulation and its contribution to phenotypic diversity within populations.

Methodology:

aScan integrates genomic data to identify alleles with matched RNA-Seq (transcriptomic) data to quantify allele-specific expression, and its algorithm is designed to handle genetic heterogeneity and varying experimental conditions.