PT  - JOURNAL ARTICLE
AU  - Dominic Holland
AU  - Chun-Chieh Fan
AU  - Oleksandr Frei
AU  - Alexey A. Shadrin
AU  - Olav B. Smeland
AU  - V. S. Sundar
AU  - Ole A. Andreassen
AU  - Anders M. Dale
TI  - Estimating inflation in GWAS summary statistics due to variance distortion from cryptic relatedness
AID  - 10.1101/164939
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 164939
4099  - http://biorxiv.org/content/early/2017/07/21/164939.short
4100  - http://biorxiv.org/content/early/2017/07/21/164939.full
AB  - Cryptic relatedness is inherently a feature of large genome-wide association studies (GWAS), and can give rise to considerable inflation in summary statistics for single nucleotide polymorphism (SNP) associations with phenotypes. It has proven difficult to disentangle these inflationary effects from true polygenic effects. Here we present results of a model that enables estimation of polygenicity, mean strength of association, and residual inflation in GWAS summary statistics. We show that there is substantial residual inflation in recent large GWAS of height and schizophrenia; correcting for this reduces the number of independent genome-wide significant loci from the reported values of 697 for height and 108 for schizophrenia to 368 and 61, respectively. In contrast, a larger GWAS of educational attainment shows no residual inflation. Additionally, we find that height has a relatively low polygenicity, with approximately 8k SNPs having causal association, more than an order of magnitude less than has been reported. The residual inflation in GWAS summary statistics can be corrected using the standard genomic control procedure with the estimated residual inflation factor.