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OPATs: Omnibus P-value association tests.

Chia-Wei Chen1, Hsin-Chou Yang1

  • 1Institute of Statistical Science, Academia Sinica.

Briefings in Bioinformatics
|October 6, 2017
PubMed
Summary
This summary is machine-generated.

Combining P-values from genome-wide association studies helps identify disease-linked genes and pathways. The Omnibus P-value Association Tests (OPATs) software offers a user-friendly tool for these powerful set-based analyses.

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Area of Science:

  • Genetics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Combining statistical significances (P-values) from single-locus tests in genome-wide association studies (GWAS) is crucial for identifying disease-associated genomic segments, genes, and pathways.
  • Existing methods for P-value combination in GWAS can be complex and require specialized tools.

Purpose of the Study:

  • To review P-value combination methods for GWAS.
  • To introduce Omnibus P-value Association Tests (OPATs), an integrated analysis tool for P-value combinations.
  • To provide a user-friendly software solution for set-based association tests in genetic studies.

Main Methods:

  • OPATs software programmed in R with a graphical user interface.
  • Includes modules for data quality control, single-locus association tests, and three types of set-based association tests (window-, gene-, and biopathway-based).
  • Offers P-value combinations with and without threshold and rank truncation, evaluated using resampling procedures.

Main Results:

  • OPATs provides an easy-to-use and statistically powerful analysis tool for P-value combinations.
  • Set-based association tests implemented in OPATs demonstrated improved statistical power, reduced multiple-testing burden, and mitigated genetic heterogeneity.
  • The software facilitates interpretation of association signals by integrating genetic effects of multiple variants in biologically relevant regions.

Conclusions:

  • P-value combinations are effective for identifying marker sets associated with disease susceptibility and uncovering missing heritability in GWAS.
  • OPATs establishes a foundation for the genetic dissection of complex diseases and traits by providing a robust analysis tool.
  • The software enhances the efficiency and interpretability of genetic association studies.