Journal: Human Molecular Genetics
Article Title: Risk of childhood asthma is associated with CpG-site polymorphisms, regional DNA methylation and mRNA levels at the GSDMB/ORMDL3 locus
Figure Lengend Snippet: ( A , upper panel) Dot-plot showing the distribution of the 61 CpG sites analyzed in the Swedish Search study ( n = 46) and the P -value after 10 000 permutations of comparing the three groups (healthy controls versus controlled asthma versus severe asthma, Kruskal–Wallis test). Dotted line: significance level at P = 0.05; red line: significance level at P = 0.01; red circles: differentially methylated probes according to asthma; black circle: CpG site excluded as the probe sequence is affected by a SNP; lower panel: DNA methylation levels ( β -values) for the two CpG sites located in ORMDL3 (cg02305874 and cg16638648). HC: healthy controls ( n = 15); CA: controlled asthma ( n = 16); SA: severe asthma ( n = 15). Error bars represent mean and standard deviation. All CpG sites were analyzed in peripheral blood leukocytes using the Infinium 450K assay. ( B ) mRNA expression of ORMDL3 according to disease status in children of the Swedish Search study. HC: healthy controls ( n = 15); CA: controlled asthma ( n = 16); SA: severe asthma ( n = 15). Error bars represent mean and standard deviation. Gene expression was analyzed in peripheral blood leukocytes using the GeneChip Human ST1.0 array from Affymetrix. ( C ) Spearman correlation coefficient for the relation between DNA methylation levels within the asthma-associated CpG sites. Correlation significant at * P = 0.05, ** P = 0.01 level and *** P
Article Snippet: Gene expression In the Swedish Search study, mRNA levels of IKZF3 , ZPBP2 , GSDMB , ORMDL3 and GSDMA in peripheral blood leukocytes were measured by the GeneChip® Human Gene ST1.0 Array (Affymetrix, Santa Clara, CA, USA) as previously described , Gene Expression Omnibus repository; accession no. GSE27011.
Techniques: Methylation, Sequencing, DNA Methylation Assay, Standard Deviation, Expressing