The second sample (MRCE) of 950 individuals from 320 families of British descent identified through a proband with atopic dermatitis (eczema) was genotyped using the Illumina Sentrix HumanHap300 Genotyping BeadChip. The genotyped sample contained 487 subjects with atopic dermatitis (and 347 subjects with asthma and 259 subjects with both diseases). Of the 314,552 SNPs with annotation available in the UCSC Genome Browser (hg18, Mar 2006), 8345 with <95% genotyping success rate or deviating from Hardy-Weinberg (P < 10−6) were excluded. We retained 306,207 SNPs and 296,533,535 genotypes (99.1% call rate) for further analyses. There were only 0.204 Mendelian errors per SNP: These genotypes were excluded from subsequent analyses. Expression arrays using Illumina Human 6 BeadChips were available on 550 children (atopic dermatitis probands and their siblings, among them 496 are genotyped). Expression values were estimated using BeadStudio (Illumina), and bead summary data were used for downstream analysis. From the total of 47,293 probes, we excluded 30,806 probes called as “absent” (detection score less than 0.95) in >80% arrays to eliminate noise. We retained 16,487 probes representing 15,576 genes for analysis.
