Simplifying Systems Genetics with QTLretrievR: An R Package for Molecular QTL Identification

Area of Science:

• Genomics
• Bioinformatics
• Statistical Genetics

Background:

• Systems genetics integrates molecular profiling and genetic mapping to link complex disease phenotypes to genetic variants.
• Computational intensity and inaccessibility of current methods limit their application, especially with multiple tissues or numerous -omics phenotypes.

Purpose of the Study:

• To develop an R package, QTLretrievR, that simplifies and streamlines the identification and downstream analysis of molecular quantitative trait loci (QTLs).
• To improve computational efficiency and accessibility for systems genetics studies in genetically diverse populations.

Main Methods:

• QTLretrievR is an R package building upon existing tools like r/qtl2 and r/intermediate.
• Incorporates parallelization features for enhanced computational efficiency.
• Includes functions for QTL peak detection, mediation analysis, and result visualization.

Main Results:

• QTLretrievR successfully reproduces results from previous QTL studies.
• Significantly reduces the time required for QTL detection and downstream analyses.
• Provides visualization tools for downstream analysis results.

Conclusions:

• QTLretrievR enhances the accessibility and efficiency of systems genetics analyses.
• Facilitates the identification of genetic variants and regulatory effects underlying complex traits.
• The R package is available for broader research community use.