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Updated: May 10, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Using PLINK for Genome-Wide Association Studies (GWAS) and data analysis.

Miguel E Rentería¹, Adrian Cortes, Sarah E Medland

¹Queensland Institute of Medical Research, Brisbane, QLD, Australia.

Methods in Molecular Biology (Clifton, N.J.)

|June 13, 2013

Summary

This chapter introduces PLINK software for genetic data analysis, covering quality control and association studies. It demonstrates data management, population substructure assessment, and association analyses for quantitative and case-control traits.

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Area of Science:

Genetics
Bioinformatics
Population Genetics

Background:

Genetic association studies are crucial for understanding trait heritability.
Accurate data management and quality control are essential for reliable genetic analysis.
Population substructure can confound association study results.

Purpose of the Study:

To introduce fundamental PLINK functions for genetic data analysis.
To provide practical examples of data management, quality control, and association testing.
To illustrate the application of PLINK in analyzing both quantitative and qualitative traits.

Main Methods:

Utilizing PLINK software for data input and manipulation.
Implementing quality control procedures to ensure data integrity.
Performing association analyses, including quantitative trait loci (QTL) and case-control studies.

Main Results:

Demonstrated successful data loading and preprocessing using PLINK.
Illustrated methods for assessing and correcting for population substructure.
Showcased association analysis for quantitative traits and case-control cohorts.

Conclusions:

PLINK is a versatile tool for comprehensive genetic data analysis.
The provided examples facilitate the practical application of PLINK in genetic research.
Effective use of PLINK aids in identifying genetic variants associated with various traits.