Dataset Information

Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits.

ABSTRACT: To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method, Primo, for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistics from different cellular conditions or studies. Primo examines association patterns of SNPs to complex and omics traits. In gene regions harboring known susceptibility loci, Primo performs conditional association analysis to account for linkage disequilibrium. Primo allows for unknown study heterogeneity and sample correlations. We show two applications using Primo to examine the molecular mechanisms of known susceptibility loci and to detect and interpret pleiotropic effects.

SUBMITTER: Gleason KJ

PROVIDER: S-EPMC7488447 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Publications

Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits.

Gleason Kevin J KJ Yang Fan F Pierce Brandon L BL He Xin X Chen Lin S LS

Genome biology 20200911 1

To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method, Primo, for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistics from different cellular conditions or studies. Primo examines association patterns of SNPs to complex and omics traits. In gene regions harboring known susceptibility loci, Primo performs conditional association analysis to account for linkage disequilibriu ...[more]

PMID: 32912334

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Project description: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.

Project description:BACKGROUND:Genome-wide association studies (GWAS) have been successful in identifying disease-associated genetic variants. Recently, an increasing number of GWAS summary statistics have been made available to the research community, providing extensive repositories for studies of human complex diseases. In particular, cross-trait associations at the genetic level can be beneficial from large-scale GWAS summary statistics by using genetic variants that are associated with multiple traits. However, direct assessment of cross-trait associations using susceptibility loci has been challenging due to the complex genetic architectures in most diseases, calling for advantageous methods that could integrate functional interpretation and imply biological mechanisms. RESULTS:We developed an analytical framework for systematic integration of cross-trait associations. It incorporates two different approaches to detect enriched pathways and requires only summary statistics. We demonstrated the framework using 25 traits belonging to four phenotype groups. Our results revealed an average of 54 significantly associated pathways (ranged between 18 and 175) per trait. We further proved that pathway-based analysis provided increased power to estimate cross-trait associations compared to gene-level analysis. Based on Fisher's Exact Test (FET), we identified a total of 24 (53) pairs of trait-trait association at adjusted pFET?<?1?×?10-?3 (pFET?<?0.01) among the 25 traits. Our trait-trait association network revealed not only many relationships among the traits within the same group but also novel relationships among traits from different groups, which warrants further investigation in future. CONCLUSIONS:Our study revealed that risk variants for 25 different traits aggregated in particular biological pathways and that these pathways were frequently shared among traits. Our results confirmed known mechanisms and also suggested several novel insights into the etiology of multi-traits.

Dataset Information

Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits.

Publications

Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits.

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