Recent microarray profiling studies on breast cancer have recognized unique subtypes that are associated with different clinical outcomes. 5/6 and epidermal growth factor receptor. The median methylation levels of and methylation level was significantly higher in basal-like subtype than in luminal subtype. The methylation status of a panel of four SU11274 genes (and and was not detectable in the samples and thus was excluded from your analyses. Statistically significant differences in median methylation levels for at least one pair of the subtypes of breast cancer were found in six genes with the SU11274 exception for and (Table 2 Fig. 2). Overall significant differences in methylation levels were observed for (p = 0.023) (p = 0.005) (p = 0.0002) (p = 0.004) (p < 0.0001) (p = 0.002) (Table 2). In particular as a special case with the GST approach (Table 3) and methylation levels were significantly lower in basal-like subtype compared to luminal (p = 0.006 p < 0.0001 and p = 0.0006 respectively) or HER2 subtypes (p = 0.003 p = 0.048 and p = 0.009 respectively) whereas their methylation levels were found to be comparable between luminal and HER2 subtypes (p > 0.999 p = 0.090 and p = >0.999 respectively). methylation level was significantly higher in basal-like subtype compared to luminal subtype (p = 0.012) and had shown a pattern towards higher methylation levels in basal-like than HER2 tumors even though difference was not statistically significant (p = 0.402). showed a significantly higher methylation level in HER2 tumors than in basal tumors (p = 0.003). methylation levels were significantly higher in HER2 subtype SU11274 compared to luminal subtype (p < 0.0001). Physique 2 Distributions of gene methylation across subtypes. Box plots Tal1 showed distribution of individual gene methylation across three subtypes. The box represents the middle 50% of the data. The ends of the box represent the 25th and 75th percentiles the bars … Table 2 Methylation levels in subtypes of invasive breast carcinoma Table 3 Comparison of methylation levels between subtypes of invasive breast carcinoma In this study none of the genes analyzed showed a correlation of methylation with tumor grade across any of the groups. Only methylation of was found to be negatively associated with patients’ age (p = 0.036). The multivariate GST analysis indicated that this observed differences in methylation among the three subtypes remained significant after adjusting for age and tumor grade except for and where the difference between basal-like and HER2 tumors was no longer statistically significant after adjustment for the above confounding factors (data not shown). The global effect of gene combinations across the subtypes was then explored using the GST approach SU11274 to differentiate difference between groups and meanwhile account for correlations among multiple outcomes in calculation of the estimate of the global effect its variance and the test statistic. The global effect using all the nine genes as a whole suggested a significantly higher methylation levels in HER2 subtypes compared to basal-like subtypes (GE = 0.257 p < 0.0001). Consistent styles were observed towards higher methylation in HER2 tumors compared to luminal tumors in and and and into the 3-gene panel did not improve the global effect on the comparison between methylation status between basal-like and luminal subtypes (data not shown). Overall rate of promoter hypermethylation To further explore the possible use of methylation patterns for breast malignancy classification and whether such cutoff-based methylation patterns were consistent with what we observed using the quantitative methylation values we defined the promoter hypermethylation (positive vs. unfavorable) using the selected cutoff values. The cutoff values were calculated based on the 90 percentile rank of normal values.33 The differences in promoter hypermethylation frequencies among three subtypes of breast cancer were similar to the differences of methylation level among three subtypes (data not shown). For and the methylation frequency observed in basal-like subtype was significantly lower than that of luminal or HER2 subtypes whereas the difference of methylation frequency between luminal and HER2 subtypes was comparable. For and and showed no significant association with the known risk factors (data not shown). We found that tumors at an advanced stage (stage III) exhibit a significantly higher frequency of promoter hypermethylation in and compared to those at the.