A Pleiotropy-Informed Bayesian False Discovery Rate adapted to a Shared Control Design Finds New Disease Associations From GWAS Summary Statistics
Authors: Liley James , Wallace Chris 
Published: February 2015

Genome-wide association studies (GWAS) have been successful in identifying single nucleotide polymorphisms (SNPs) associated with many traits and diseases. However, at existing sample sizes, these variants explain only part of the estimated heritability [1]. Leverage of GWAS results from related phenotypes may improve detection without the need for larger datasets [2].

The Bayesian conditional false discovery rate (cFDR) [3] constitutes an upper bound on the expected false discovery rate (FDR) across a set of SNPs whose p values for two diseases are both less than two disease-specific thresholds. Calculation of the cFDR requires only summary statistics and has several advantages over traditional GWAS analysis. However, existing methods require distinct control samples between studies. Here, we extend the technique to allow for some or all controls to be shared, increasing applicability. Several different SNP sets can be defined with the same cFDR value, and we show that the expected FDR across the union of these sets may exceed expected FDR in any single set. We describe a procedure to establish an upper bound for the expected FDR among the union of such sets of SNPs.

We apply our technique to pairwise analysis of p values from ten autoimmune diseases with variable sharing of controls, enabling discovery of 59 SNP-disease associations which do not reach GWAS significance after genomic control in individual datasets. Most of the SNPs we highlight have previously been confirmed using replication studies or larger GWAS, a useful validation of our technique; we report eight SNP-disease associations across five diseases not previously declared.

Our technique extends and strengthens the previous algorithm, and establishes robust limits on the expected FDR. This approach can improve SNP detection in GWAS, and give insight into shared aetiology between phenotypically related conditions.

Author Summary

Many diseases have a significant hereditary component, only part of which has been explained by analysis of genome-wide association studies (GWAS). Shared aetiology, treatment protocols, and overlapping results from existing GWAS suggest similarities in genetic susceptibility between related diseases, which may be exploited to detect more disease-associated SNPs without the need for further data.

We extend an existing method for detecting SNPs associated with a given disease by conditioning on association with another disease. Our extension allows GWAS for the two conditions to share control samples, enabling larger overall control groups and application to the common case when GWAS for related diseases pool control samples. We demonstrate that our technique limits the expected overall false discovery rate at a threshold dependent on the two diseases.

We apply our technique to genotype data from ten immune mediated diseases. Overall pleiotropy between phenotypes is demonstrated graphically. We are able to declare several SNPs significant at a genome-wide level whilst controlling at a lower false-discovery rate than would be possible using a conventional approach, identifying eight previously unknown disease associations.

This technique can improve SNP detection in GWAS by re-analysing existing data, and gives insight into the shared genetic bases of autoimmune diseases.