DNA samples were genotyped using the Immunochip, an Illumina iSelect HD custom genotyping array. This BeadChip was developed for highly multiplexed SNP genotyping and the SNP content of this array was mainly based on findings in ankylosing spondylitis, autoimmune thyroiditis, Crohn’s disease, celiac disease, IgA deficiency, multiple sclerosis, primary biliary cirrhosis, psoriasis, rheumatoid arthritis, systemic lupus erythematosus, type 1 diabetes and ulcerative colitis. Genotyping was performed according to Illumina protocols with 4μl of genomic DNA samples at 50ng per μl, aliquoted to the corresponding wells of 96-well plates. The NCBI build 36 (hg19) map was used (Illumina manifest file Immuno_BeadChip_11419691_B.bpm) and normalized probe intensities were extracted for all samples passing standard laboratory quality-control thresholds. Genotype calling was performed with Illumina’s GenomeStudio data analysis software, the GenomeStudio GenTrain 2.0 algorithm and the cluster file generated by Trynka et al. (based on the clustering of 2,000 UK samples and subsequent manual readjustment of cluster positions)38 (link).
All CVID cases from Norway, Sweden and Germany were genotyped at the Institute of Clinical Molecular Biology in Kiel, Germany. The USA/UK cases were genotyped at the Center for Applied Genomics, the Children’s Hospital of Philadelphia, USA.
All CVID cases from Norway, Sweden and Germany were genotyped at the Institute of Clinical Molecular Biology in Kiel, Germany. The USA/UK cases were genotyped at the Center for Applied Genomics, the Children’s Hospital of Philadelphia, USA.