Results of the sensitivity analyses: a comparison of different nominal p-values.

<p><i>Note</i>. Results for variations of the method for the 32 Mbp width region on chromosome 5, 128–160 bp. Nom 0.01: the analysis was performed using p = 0.01 as the cutoff for nominal SNP-wise significance. Nom 0.11: the analysis was performed using p = 0.1 as the cutoff for nominal SNP-wise significance. EIGENSTRAT: the analysis was performed on data corrected for population stratification using the EIGENSTRAT procedure.</p

“Manhattan plot of the top segment located at chromosome 5 (128–136

<p> <b>Mbp)”.</b> This figure shows at the y–axis the p-values of the SNPs located at chromosome 5 (128–136 Mbp). The chromosomes are shown at the x-axis. The red line indicates a p-value of 10-7, the blue line indicates a p-value of 10-5 and the green line indicates a p-value of .05.</p

“Manhattan plot of the 22 autosomal chromosomes”.

<p>This figure shows at the y–axis the p-values of the SNPs in a GWA analysis. The chromosomes are shown at the x-axis. The red line indicates a p-value of 10-7, the blue line indicates a p-value of 10-5 and the green line indicates a p-value of .05.</p

Overview of disease associated genes located within the significantly associated region at chromosome 5 (128–136 Mbp).

<p>Note: The table shows genes that have previously reported to be associated with disease based on the UCSC Genome Bioinformatics site (NCBI36/hg18) (<a href="http://genome.ucsc.edu/" target="_blank">http://genome.ucsc.edu/</a>) and genes previously found to be associated with schizophrenia based on the Schizophrenia Research Forum (<a href="http://www.schizophreniaresearchforum.org" target="_blank">www.schizophreniaresearchforum.org</a>). The final column represents the phenotype and disease associations according to the UCSC Genome Bioinformatics site.</p><p>Set-based tests were performed in Plink to assess the association between SNPs within a particular gene and case-control status. This test uses permutation to determine the significance. The default values were used (r-squared = .5; p-value = .05; maximum number of SNPs within a gene = 5); more details can be found at <a href="http://pngu.mgh.harvard.edu/~purcell/plink" target="_blank">http://pngu.mgh.harvard.edu/~purcell/plink</a>.</p

Metasignificance of segments located in chromosome 5 (128–160 Mbp).

<p><i>Note</i>. Segment width refers to the width of regions over which tests of the number of nominally significant SNPs were tested. The replicable region indicates the location of the segment. The p-values provide the results of permutation based tests.</p