Computational protocol: Association between a Single Donor TARC/CCL17 Promotor Polymorphism and Obstructive Chronic Lung Allograft Dysfunction after Lung Transplantation

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Protocol publication

[…] Six SNPs (rs223895, rs223897, rs223898, rs223899, rs223900, and rs229827) in the promotor region of TARC/CCL17 that are frequent in the western European population were selected from the HapMap (http://hapmap.ncbi.nlm.nih.gov/) and the Ensemble databases (). We also analyzed the configuration of rs229828, which configuration has previously been associated with CCCL17/TARC serum levels (). Samples were genotyped using the Affymetrix “TxArray” (, ) containing 767,203 variants, and stringent quality control (QC) was conducted to remove low-quality SNPs and samples. Samples with a missing rate >3% were removed. We created a subset of high-quality, independent SNPs with missing rate <1%, Hardy–Weinberg p > 0.001, minor allele frequency >0.1, and LD pruning leaving no SNP pairs with r2 > 0.2. Using this subset, we removed samples with heterozygosity >2 SD from the mean of all samples, related samples (keeping only one samples of each pair with proportion of IBD > 0.2), and samples of non-European ancestry [based on principle component analysis using the 1000 Genomes Project (Phase 1) populations as reference ()]. SNPs were removed if they had a missing rate >5%, Hardy–Weinberg p < 0.01, or if they were monomorphic. After QC, 543,637 SNPs and 133 patients and 131 donor samples remained. Untyped SNPs were imputed using a combined reference panel of the 1000 Genomes Project (Phase 3) () and the Genomes of the Netherlands (v5) (). Samples were first phased with SHAPEIT () and then imputed with IMPUTE v2 (). […]

Pipeline specifications

Software tools SHAPEIT, IMPUTE
Application GWAS
Organisms Homo sapiens
Diseases Bronchiolitis Obliterans