Computational protocol: The interaction of genetic variants and DNA methylation of the interleukin-4 receptor gene increase the risk of asthma at age 18 years

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Protocol publication

[…] An efficient genotype tagging scheme was developed that gave priority to variants that 1) showed strong association with asthma in the Isle of Wight birth cohort, and/or 2) have been reported by others to be associated with asthma/allergy, and/or 3) have functional importance. A literature search for IL4R gene plus asthma and allergy was used to identify associated variants (SNPs, indels). Functional variants included those that were non-synonymous, located in conserved DNA, and/or present in DNA regions with gene regulatory potential. Tagger implemented in Haploview 3.2 using Caucasian Hapmap data was used to develop a tagging scheme for the IL4R gene region, including 10 kb upstream and downstream of the gene []. An r2 value of 0.85 was the threshold for tagging and one, two and three SNP marker combination tests were used. The result was an efficient number of genotyped variants (n = 13) that would provide the needed information to statistically support or exclude the gene in its association with asthma outcomes. […]

Pipeline specifications

Software tools Tagger, Haploview
Application GWAS
Organisms Homo sapiens
Diseases Asthma
Chemicals Cytosine, Guanine