CHIT

CHIT combines allele-specific and total read counts from next-generation sequencing to test for genotype–phenotype interactions and increase power in association studies of molecular quantitative traits such as gene expression.

Key Features:

• Allele-Specific Analysis: Leverages allele-specific read counts from next-generation sequencing to capture subtle variations in molecular traits that may be missed by conventional analyses.
• Phenotype-Genotype Interaction Testing: Tests for interactions between phenotypic factors and genotypes that influence the expression of quantitative traits.
• Modeling Approach: Models both total read counts and allele-specific reads within a target genomic region rather than relying solely on standard linear regression methods.
• Supplementary Analysis Capability: Functions as an adjunct to conventional linear interaction regression analyses to provide additional insight into genetic architecture.

Scientific Applications:

• Genotype–Environment and Phenotype Interactions: Applied to studies assessing how genetic variants interact with environmental or phenotypic factors to affect molecular quantitative traits.
• Childhood Asthma (Puerto Ricans): Used to assess gene expression interactions with single nucleotide polymorphisms (SNPs) and atopy status in childhood asthma among Puerto Ricans.

Methodology:

Statistical framework that models total and allele-specific read counts, maintains non-inflated type I error rates, and yields greater power compared with traditional interaction quantitative trait locus approaches.