Testing genetic pleiotropy with GWAS summary statistics for marginal and conditional analyses

Yangqing Deng, Wei Pan

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


There is growing interest in testing genetic pleiotropy, which is when a single genetic variant influences multiple traits. Several methods have been proposed; however, these methods have some limitations. First, all the proposed methods are based on the use of individual-level genotype and phenotype data; in contrast, for logistical, and other, reasons, summary statistics of univariate SNP-trait associations are typically only available based on meta- or mega-analyzed large genome-wide association study (GWAS) data. Second, existing tests are based on marginal pleiotropy, which cannot distinguish between direct and indirect associations of a single genetic variant with multiple traits due to correlations among the traits. Hence, it is useful to consider conditional analysis, in which a subset of traits is adjusted for another subset of traits. For example, in spite of substantial lowering of low-density lipoprotein cholesterol (LDL) with statin therapy, some patients still maintain high residual cardiovascular risk, and, for these patients, it might be helpful to reduce their triglyceride (TG) level. For this purpose, in order to identify new therapeutic targets, it would be useful to identify genetic variants with pleiotropic effects on LDL and TG after adjusting the latter for LDL; otherwise, a pleiotropic effect of a genetic variant detected by a marginal model could simply be due to its association with LDL only, given the well-known correlation between the two types of lipids. Here, we develop a new pleiotropy testing procedure based only on GWAS summary statistics that can be applied for both marginal analysis and conditional analysis. Although the main technical development is based on published union-intersection testing methods, care is needed in specifying conditional models to avoid invalid statistical estimation and inference. In addition to the previously used likelihood ratio test, we also propose using generalized estimating equations under the working independence model for robust inference. We provide numerical examples based on both simulated and real data, including two large lipid GWAS summary association datasets based on ~100,000 and ~189,000 samples, respectively, to demonstrate the difference between marginal and conditional analyses, as well as the effectiveness of our new approach.

Original languageEnglish (US)
Pages (from-to)1285-1299
Number of pages15
Issue number4
StatePublished - Dec 2017

Bibliographical note

Funding Information:
We thank the editors and reviewers for many detailed and helpful comments. This research was supported by National Institutes of Health grants R01GM113250, R01HL105397, R01HL116720, and R21AG057038, and by the Minnesota Supercomputing Institute at the University of Minnesota.

Publisher Copyright:
© 2017 by the Genetics Society of America.


  • GEE
  • Likelihood ratio test
  • Multiple-trait association testing
  • Structural equation models
  • Union-intersection test
  • Wald test

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