Table 1.
Cases before and after QC.
Fig 1.
Genetic substructure of the Combined GWAS dataset.
Two-dimensional scatterplots from multidimensional scaling analyses of the Generation R Study and Behçet collected data together with the three initial Panels form the HapMap Project. Each dot represents an individual in the dataset. Color codes: Grey = Generation R, Black = Behcet Cases, Yellow = Jordan controls. Blue = CEU, Red = YRB, Green = JPT.
Fig 2.
Behçet GWAS results using Genomic Principal Components (GPC) adjustment.
Each dot represents an SNP in the dataset. QQ-plot (left). Associated SNPs deviating from the null hypothesis of no association (identity line). Manhattan plot (right). SNPs showing association with the disease map to chromosome 6 and a singleton in chromosome 18.
Table 2.
GWS SNPs associated with Behçet’s disease susceptibility using GPC and EMMAX approaches.
Fig 3.
Behcet GWAS results using Linear Mixed Models Genomic approach.
Each dot represents an SNP in the dataset. QQ-plot (left). Associated SNPs deviating from the null hypothesis of no association (identity line). Manhattan plot (right). SNPs showing association with the disease map to two different signals in chromosome 6 and a singleton in chromosome 18.
Fig 4.
SNP association plot for Behçet’s susceptibility-associated region of chromosome 6q25.3.
Dots represent GWAS P-values (EMMAX approach) and positions of SNPs found within the 6q25.3 locus. The top SNP, i.e. rs8187722, is denoted by a diamond. Different colours indicate varying degrees of pair-wise linkage disequilibrium (1000 Genomes Nov 2010 CEU) between the top SNP and all other genotyped SNPs. Genetic coordinates are per 1000 Genomes Nov 2010-CEU. Bottom, LD heat map based on D’ values from the combined population under study including all SNPs in the 500Kb region.
Fig 5.
SNP association plot for Behçet’s susceptibility-associated region of Chromosome 18q22.3.
Dots represent GWAS P-values (EMMAX approach) and positions of SNPs found within the 18q22.3 locus. The top SNP, i.e. rs17087141, is denoted by a diamond. Different colours indicate varying degrees of pair-wise linkage disequilibrium (1000Genomes CEU) between the top SNP and all other genotyped SNPs. Genetic coordinates are per 1000 Genomes Nov 2010-CEU. Bottom, LD heat map based on D’ values from the combined population under study including all SNPs in the 500Kb region.
Table 3.
Meta-analysis of leading SNP in IL12A.