Enrichment improves discovery using established methods.

<p>Among three phenotypes, (A) Height, (B) Crohn's Disease, (C) and Schizophrenia, we demonstrate an increased discovery of SNPs at a given FDR when incorporating the enriched genic annotation information into an established stratified false discovery rate (sFDR; red) framework. SNPs declared significant by sFDR also replicate at a higher rate (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003449#pgen.1003449.s012" target="_blank">Figure S12</a>).</p

Independent study replication confirms enrichment in Crohn's disease.

<p>(A). Stratified True Discovery Rate (TDR) plots illustrating the increase in TDR associated with increased enrichment. (B) Cumulative replication plot showing the average rate of replication (p<.05) within sub-studies for a given p-value threshold shows enriched categories replicate at a higher rate in independent samples. The vertical intercept is the overall replication rate per category.</p

Stratified Q-Q plots and true discovery rates show consistency of enrichment.

<p><i>Upper panel:</i> Stratified Q-Q plots illustrating consistent enrichment of genic annotation categories across diverse phenotypes: (A) Height, (B) Schizophrenia (SCZ), and (C) Cigarettes per Day (CPD). All figures are corrected for inflation using intergenic inflation control. Only nominal p-values below the standard genome-wide significance threshold (p<5×10⁻⁸) are shown. <i>Lower panel:</i> Stratified True Discovery Rate (TDR) plots illustrating the increase in TDR associated with increased enrichment in (D) Height, (E) SCZ and (F) CPD. Genic annotation categories were: 5′ untranslated region (5′UTR), Exon, Intron, 3′ untranslated region (3′UTR), All SNPs, in addition to Intergenic.</p