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gwid: an R package and Shiny application for Genome-Wide analysis of IBD data.

Soroush Mahmoudiandehkordi1,2, Mehdi Maadooliat1,2, Steven J Schrodi2,3

  • 1Department of Mathematical and Statistical Sciences, Marquette University, Milwaukee, WI 53233, United States.

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|September 9, 2024
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Summary
This summary is machine-generated.

The genome-wide identity by descent (gwid) R package analyzes identity-by-descent data for binary traits, identifying genetic associations with diseases like rheumatoid arthritis. It offers tools for differential analysis and visualization, improving genetic research accessibility.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Statistical Genetics

Background:

  • Identity-by-descent (IBD) analysis is crucial for understanding genetic contributions to diseases.
  • Existing tools may lack comprehensive features for analyzing IBD in relation to dichotomous traits.
  • Efficient and accessible software is needed to analyze genome-wide IBD data.

Purpose of the Study:

  • To introduce the genome-wide identity by descent (gwid) R package.
  • To provide tools for assessing differential IBD levels between binary trait states.
  • To facilitate the visualization and interpretation of IBD analysis results.

Main Methods:

  • Development of an R package named gwid.
  • Implementation of functions for differential IBD analysis.
  • Utilizing real genotype data (SNPs) for package evaluation.
  • Application to investigate rheumatoid arthritis susceptibility.

Main Results:

  • The gwid package provides effective tools for analyzing IBD data in dichotomous traits.
  • Differential IBD analysis between trait states yields informative results.
  • Visualization functions enhance the interpretability of IBD analysis outcomes.
  • Package performance was validated using real genotype data for rheumatoid arthritis.

Conclusions:

  • The gwid R package offers a valuable resource for genetic association studies involving IBD and binary traits.
  • It enhances the accessibility and interpretability of complex genetic data analysis.
  • The package supports research into disease susceptibility, such as rheumatoid arthritis.