Leveraging existing GWAS summary data of genetically correlated and uncorrelated traits to improve power for a new GWAS

Haoran Xue, Chong Wu, Wei Pan

Research output: Contribution to journalArticlepeer-review

Abstract

In spite of the tremendous success of genome-wide association studies (GWAS) in identifying genetic variants associated with complex traits and common diseases, many more are yet to be discovered. Hence, it is always desirable to improve the statistical power of GWAS. Paralleling with the intensive efforts of integrating GWAS with functional annotations or other omic data, we propose leveraging other published GWAS summary data to boost statistical power for a new/focus GWAS; the traits of the published GWAS may or may not be genetically correlated with the target trait of the new GWAS. Building on weighted hypothesis testing with a solid theoretical foundation, we develop a novel and effective method to construct single-nucleotide polymorphism (SNP)-specific weights based on 22 published GWAS data sets with various traits, detecting sometimes dramatically increased numbers of significant SNPs and independent loci as compared to the standard/unweighted analysis. For example, by integrating a schizophrenia GWAS summary data set with 19 other GWAS summary data sets of nonschizophrenia traits, our new method identified 1,585 genome-wide significant SNPs mapping to 15 linkage disequilibrium-independent loci, largely exceeding 818 significant SNPs in 13 independent loci identified by the standard/unweighted analysis; furthermore, using a later and larger schizophrenia GWAS summary data set as the validation data, 1,423 (out of 1,585) significant SNPs identified by the weighted analysis, compared to 705 (out of 818) by the unweighted analysis, were confirmed, while all 15 and 13 independent loci were also confirmed. Similar conclusions were reached with lipids and Alzheimer's disease (AD) traits. We conclude that the proposed approach is simple and cost-effective to improve GWAS power.

Original languageEnglish (US)
Pages (from-to)717-732
Number of pages16
JournalGenetic epidemiology
Volume44
Issue number7
DOIs
StatePublished - Oct 1 2020

Bibliographical note

Funding Information:
The authors thank the reviewers for many helpful comments and suggestions. This study was supported by National Institutes of Health grants R01AG065636, R21AG057038, R01HL116720, R01GM113250, and R01GM126002, and by the Minnesota Supercomputing Institute at the University of Minnesota.

Keywords

  • SNP
  • pleiotropy
  • statistical power
  • weighted hypothesis testing

PubMed: MeSH publication types

  • Journal Article

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