Calculated powers for simulated genome-wide homozygosity association scans.

<p>The simulated genome-wide homozygosity association scans included 2,000 patients and 3,000 controls and used −log₁₀(p)>8 for the threshold of statistical significance. Parameters for the calculations included: The proportion of patients carrying the ROH (<i>δ</i> = 0.1, 0.2, or 0.3) controlled the effective size of a scan. The number of evenly spaced SNPs (<i>L</i> = 100, 150, or 200 SNPs) determined the length of the true disease-associated ROH. The heterozygous interference was defined as the fraction of heterozygous-call SNPs in the true disease-associated ROH (<i>ε</i> = 0, 0.1, or 0.2). <i>W</i> = 100, red solid line, circles; <i>W</i> = 150, blue dashed line, triangles; <i>W</i> = 200, green dotted line, crosses.</p

Gene amplifications and deletions in the MHC region.

<p>The fraction and numbers of RA patients and controls who carried amplifications and deletions in the MHC region are showed. The top and bottom panels show the results for the amplifications and deletions, respectively. In both panels, the results for the RA patients and controls are indicated as red dots and blue crosses, respectively. The fraction of RA patients and controls is shown on the left <i>y</i> axis, and the number of RA patients and controls is shown on the right <i>y</i> axis.</p

Overall analytical strategy.

<p>In step I, 50 co-regulation modules were generated using meta-clustering of gene clusters identified by the “penalized K-medoids” method across 11 transcriptome MDD and matched controls studies. In step II, modules enriched from most of the selected GWAS studies related to MDD, neuropsychiatric disorder and traits, including systemic disease linked to psychiatric disorders were identified. In step III, the biological functions represented by genes included in each module were defined by pathway analysis from 2,334 gene sets of MSigDB (<a href="http://www.broadinstitute.org/gsea/msigdb" target="_blank">www.broadinstitute.org/gsea/msigdb</a>). In step IV, SNPs from the Catalog of GWAS were organized into three categories: cancer GWAS, human body indices GWAS and GWAS for common diseases and medial illnesses unrelated to MDD or other brain function. Three additional categories were defined as non-MDD-related negative control gene sets. (Note: In order to increase the performance of the heatmap in module #35, we first performed the hierarchical clustering with “complete” agglomeration method to aggregated samples with similar expression among all 88 genes, and the genes were sorted by the correlation from high to low of selected genes in the top.).</p

Histograms of the –log₁₀(p) of the Stouffer statistic from 50 modules of meta-analysis of 11 MDD studies and each single study.

<p>Module #35 with 88 genes (red arrow and double-cross) have largest –log₁₀ transformed p-value of Stouffer’s statistic 4.4. The other four blue arrows and double crosses indicated that these four modules in all single studies have more than 14 (15% of the 88 genes in module #35) overlapped with module #35. See detailed description in text.</p

Consistent association of genes in module #35 with MDD-related gene categories.

<p>(<b>a</b>) Heatmap of log₁₀-transformed p-values from Fisher’s exact test for 50 modules obtained from MDD cases and matched controls and 8 MDD related GWAS and 3 negative controls. (<b>b</b>) Heatmap of log₁₀-transformed p-values from Fisher’s exact test for 50 modules obtained from controls and 8 MDD related GWAS and 3 negative controls. The green rectangle identifies module #35.</p

Top 15 enriched pathways in module #35.

<p>Top 15 enriched pathways in module #35.</p

Genome-wide homozygosity association scans.

<p>The values of −log₁₀(p) at the anchor SNPs for the three genome-wide homozygosity association scans, WTCCC_100, WTCCC_150, and WTCCC_200, are displayed. The purple, horizontal reference lines indicate −log₁₀(p) = 8, the cut-off used to test for significance. Two peaks with −log₁₀(p)>8 in the MHC region on chromosome 6p21.3 were found for all three scans. The bottom panel shows an expanded plot containing the region of the two peaks. WTCCC_100, blue line, circles; WTCCC_150, green line, crosses; WTCCC_200, orange line, triangles.</p

Genes and LD structures in the MHC region identified by the homozygosity association scans.

<p>The genes and intermarker LDs in the regions containing ROHs are displayed. The two dotted, red vertical lines demarcate the MHC region from 29,732,804 bp to 33,268,223 bp on chromosome 6p. The regions identified by the WTCCC_100, WTCCC_150, and WTCCC_200 scans are identified by the sky blue, light green, and orange horizontal bars, respectively. The outermost vertical bars denote the first SNP (gray tick) in the first window and the last SNP (gray tick) in the last window. Additionally, the first anchor SNP and the last anchor SNP for regions with −log₁₀(p)>8 are marked using bold ticks. If two regions identified by the same genome scan overlap, the segment containing the overlapping regions is shown in dark blue, green, and orange for WTCCC_100, WTCCC_150, and WTCCC_200, respectively. The names of genes within the annotated regions are given above the bars. The names of genes in the regions identified by the three scans are shown in red, and the names of the genes identified by one or two scans are shown in blue. The location and width of the bars that prefix the gene names reflect the physical position and the size of the genes. LD structures are provided in the lower panels in which the higher intermarker LDs are in red.</p

Description of cohorts in 11 MDD microarray platforms.

<p>ACC, anterior cingulate cortex; AMY, amygdala; DLPFC, dorsolateral prefrontal cortex, OFC, orbital ventral prefrontal cortex.</p

Functional groups of 88 gene in module #35<b>.</b>

<p>Annotations are based on Gene Ontology. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090980#pone-0090980-t003" target="_blank">Table 3</a> for a separate analysis of pathway enrichment.</p