DNA methylation measurements and statistical analyses
DNA was extracted from 72 whole blood and 103 nasal brushing samples.
Genome-wide DNA methylation was determined using Illumina Infinium
HumanMethylation450 BeadChips. After quality control, 72 whole blood
samples and 97 nasal epithelium samples (of in total 103 unique
subjects) with 436,824 CpG sites remained for following steps.
We used robust linear regression to determine the differential
methylation between persistent asthma and asthma remission: 1) PersA
versus ClinR, and 2) PersA versus ComR, in whole blood and nasal
brushing samples, with adjustment for covariates that are known to
affect DNA methylation (age, sex, smoking status, pack years, and
batch). For whole blood samples, we performed adjustment on the
percentage of monocytes, B cells, NK cells, CD4+ T cells, CD8+ T cells,
neutrophils and eosinophils, which were predicted by the
Houseman13 algorithm using minfi14package. For nasal brushing samples, we applied the R package
sva15 to estimate significant surrogate variables
(SVs), representing unknown latent factors that capture heterogeneity in
data, such as cell type composition. Differentially methylated regions
(DMR) were identified using comb-p v0.4816.