Global gene expression data were measured by two techniques in two independent samples. The first sample (MRCA) contained 405 children of British descent (Dixon et al. 2007). The 405 children are organized into 206 sibships, including 297 sib pairs and 11 half-sib pairs. The families were identified through a proband with childhood asthma, and siblings were included regardless of disease status. Global gene expression in LCLs was measured using Affymetrix HG-U133 Plus 2.0 chips. LCL cultures were harvested at log phase in the first growth after Epstein-Barr virus (EBV) transformation. Robust multi-array averaging (RMA) (Bolstad et al. 2003; Irizarry et al. 2003) was used for background correction and normalization and to compute expression values. All 405 children and their parents were genotyped using the Illumina Sentrix Human-1 Genotyping BeadChip (ILMN100K, including 105,713 autosomal SNPs), and 378 children were also genotyped using Illumina Sentrix HumanHap300 BeadChip (ILMN300K, including 307,981 autosomal SNPs) according to the manufacturers' instructions (Dixon et al. 2007; Moffatt et al. 2007). Before analysis, we excluded 4050 SNPs with a call rate <95%, 96 SNPs with Hardy-Weinberg equilibrium P-value
