Sample collections.

*<p>Numbers of samples by country of origin are listed in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003270#s3" target="_blank">Methods</a> section.</p><p>Case cohort names represent location of genotyping, and do not reflect country of origin of samples.</p

Association signal at the mapping intervals flanking rs34593439 and rs7553711.

<p>Association scores at 15q25.1 (panel A) and 1q25.1 (panel B). Genotyped (diamonds) and imputed (circles) SNPs are indicated and the top genotyped SNP in the interval is outlined in orange. A SNP in 15q25.1 previously associated with Diabetes is outlined in blue. The degree of red color in each diamond or circle indicates the strength of LD with the top SNP (on a scale shown in the legend at the upper left hand corner of the plot). The X-axis shows the chromosome and physical distance (kb) from the human genome reference sequence (hg19), the left Y-axis shows the negative base ten logarithm of the p-value and the right Y-axis shows recombination rate (cM/Mb) as a navy line. The genome-wide significance threshold (P<5×10⁻⁸) is given by the dashed grey line. Genes in the regions are annotated at the bottom as green arrows. Also indicated in 1q25.1 is a ∼130 kb region with no SNPs on the ImmunoChip.</p

Non-HLA narcolepsy risk variant loci reaching genome-wide significance.

<p>Chr.: Chromosome; BP: position according to NCBI build 36 (Hg18) coordinates; MAF_N: minor allele frequency in narcolepsy (_N) and controls (_C); P: P value according to variance component model (EMMAX). EMMAX does not provide OR (Odds Ratio) or adjusted allele frequencies, therefore MAF, OR, and 95% confidence intervals (CI) were calculated with Plink on subset of 8,474 samples with the greatest PCA homogeneity (see Figure S2; EV 11.21<0.004, EV 4.12<0.01).</p

Manhattan Plot of association statistics.

<p>The significance threshold used (blue line) was P = 5×10⁻⁸; The insets depict plots of 1) association results in a broad region encompassing the HLA locus (chr 6:24,067–35,474 kb) that were excluded from the present analysis (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003270#s3" target="_blank">Methods</a>) and 2) QQ plot of results for 109,777 markers after excluding a 1 Mb window surrounding the associated loci (λ = 1.004). The inflation statistic for all 111,240 tested markers is 1.04.</p