Fine mapping was performed using the ImmunoChip platform in 1,886 individuals with hypocretin-defficiant narcolepsy (cases) and 10,421 controls, all of European ancestry. Genotyping was performed on an Illumina array and genetopyes were called using Illumina GeneExpress. PLINK was used to calculate call rate and HWE. Imputation of genotypes was performed using Beagle v3.3 software against the 1000 genomes integrated dataset (phase 1 release v3). The HLA region was excluded from the analysis. Three loci outside the HLA were found to be significantly associated with narcolepsy (P < 5x10-08), confirming the previous association at the TRA@ loci and reporting two novel loci.
- Call rate ≤ 99%
- Deviation from Hardy-Weinberg equilibrium (P < 10-5)
- MAF < 0.01
- Located around the HLA complex (hg18 - chr6:24,067,000..35,474,000)
- Call rate < 98%
- Related samples (pi hat > 0.2)
GDXHsS00028 meets the following criteria: