For triple-negative breast cancer samples (Fig. 2c), there were no significant metastasis-related methylation changes in either the EBF3 promoter or TBC1D16, but five CpG sites (cg07890827, cg16803064, cg09649486, cg25866634, cg09121772) in the EBF3 gene body showed 12% loss of methylation in primary tumours compared to normal tissue (red vs blue boxplots). Here, TBC1D16 is linked to triple-negative breast carcinoma.