Peripheral blood DNA methylation was interrogated using the Illumina HM450k array. Data acquisition, preprocessing, QC, normalisation of methylation data and estimation of relative blood cell type distribution have been described previously.24 (link) Differential DNA methylation for CpG sites at the loci of interest between SLE-ESRD (n=20) and non-renal SLE (n=302) was tested using a linear regression model including age at sampling, sex, blood cell type distribution and HM450k BeadChip as covariates, with significance defined at p<0.0028 after Bonferroni correction for multiple testing (0.05/18 tests).
Yavuz S., Pucholt P., Sandling J.K., Bianchi M., Leonard D., Bolin K., Imgenberg-Kreuz J., Eloranta M.L., Kozyrev S.V., Lanata C.M., Jönsen A., Bengtsson A.A., Sjöwall C., Svenungsson E., Gunnarsson I., Rantapää-Dahlqvist S., Nititham J., Criswell L.A., Lindblad-Toh K, & Rönnblom L. (2022). Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease. Lupus Science & Medicine, 9(1), e000752.
Other organizations :
National Human Genome Research Institute, National Institutes of Health, Skåne University Hospital, Lund University, Linköping University, Karolinska Institutet, Karolinska University Hospital, Umeå University, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Broad Institute
Differential DNA methylation for CpG sites at the loci of interest
control variables
Age at sampling
Blood cell type distribution
HM450k BeadChip
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