Differential methylation between AA and EA cases among breast cancer subtypes. Differential methylation between AA and EA cases among breast cancer subtypes.

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Differential methylation between AA and EA cases among breast cancer subtypes. Differential methylation between AA and EA cases among breast cancer subtypes. For all methylation loci in all genomic regions (n = 392,591; selected probes when a case count of “NA” for β value was less than 10), β-values of two population groups were compared, and the observed P values were calculated using a t-test (t. test in R) or Mann–Whitney–Wilcox test (wilcox.test in R) based on the data distribution for each methylation site. The normality of β value distributions in EAs and AAs for each methylation site was tested with the Shapiro–Wilk test (shipiro.test in R). The x-axis represents the expected P value: a null distribution. Q–Q plots are shown for the P values of β-value distribution between (A) 101 AA and 520 EA cases for all subtypes, (B) 26 AA and 214 EA cases for the Luminal A subtype, and (C) 18 AA and46 EA cases for the Basal-like subtype. The Q–Q plots depicted in D–F represent the same statistical results for the methylation loci in only intragenic regions (i.e., exon and intron, n = 285,642) for all subtypes, Luminal A, and Basal-like, respectively. Dongwook Kim et al. Mol Cancer Res 2018;16:461-469 ©2018 by American Association for Cancer Research