Computational protocol: Using spatio-temporal surveillance data to test the infectious environment of children before type 1 diabetes diagnosis

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Protocol publication

[…] In the environmental study, exposures of cases and controls were compared with the conditional logistic regression R-package CLogit. A test was reported as indicative of a possible difference when the median p value computed over the 100 comparisons of the cases with the 100 sets of virtual controls was <0.05. It was reported as significant when the median p value was below the Bonferroni limit p<0.05/N, where N = 76 (total number of exposure variables in ).In the gene-environment study, we used the case-only method as implemented in PLINK []. We first searched for GxE association by using Wald tests based on the linear regression model. Results were visualized using a Manhattan plot (using ggplot2 package in R). Dominant, recessive, and genotypic analyses were performed. A test was considered as indicative of a possible association when p was between 0.05/N and 1/N, and significant when p<0.05/N where N = 7,329,768 (total number of imputed SNPs). […]

Pipeline specifications

Software tools PLINK, Ggplot2
Applications Miscellaneous, GWAS
Organisms Homo sapiens, Viruses
Diseases Autoimmune Diseases, Communicable Diseases, Diabetes Mellitus, Type 1, Infection, Influenza, Human, Sialic Acid Storage Disease