For SNPs with evidence of replication, we investigated their effects on the expression of nearby genes (genes within 100 kb up and downstream from the SNP) in lung samples from the Lung QTL consortium. This includes data on 1,111 individuals undergoing lung surgery, recruited at Laval University (n = 409), University of British Columbia (n = 339) and University of Groningen (n = 363)[24 (link)].
Gene expression and genotyping profiles were obtained using a custom Affymetrix array (GEO platform GPL10379) and the Illumina Human1M-Duo BeadChip array, respectively. Expression values were extracted using the Robust Multichip Average method[25 (link)] implemented in the Affymetrix Power Tools software. Expression values were analysed with a robust regression model adjusted for age, sex and smoking status, using the R statistical package MASS (rlm function).
Genetic associations were performed in PLINK 1.9. A fixed-effect meta-analysis was used to pool the results across the three sites.
Gene expression and genotyping profiles were obtained using a custom Affymetrix array (GEO platform GPL10379) and the Illumina Human1M-Duo BeadChip array, respectively. Expression values were extracted using the Robust Multichip Average method[25 (link)] implemented in the Affymetrix Power Tools software. Expression values were analysed with a robust regression model adjusted for age, sex and smoking status, using the R statistical package MASS (rlm function).
Genetic associations were performed in PLINK 1.9. A fixed-effect meta-analysis was used to pool the results across the three sites.
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