MOESM10 of Global impact of somatic structural variation on the DNA methylome of human cancers

Additional file 10. Related to Fig. 5. SSVs associated with rearrangement of regions with high or low methylation. Using a dataset of DNA methylation of normal tissues, the average DNA methylation represented by the rearranged region (using window of 50 kb) was compared with that of the CGI nearby the gene on the other side of the SSV breakpoint, with the average difference in methylation beta values computed for all SSV-CGI associations, as well as for the subset of SSV-CGI associations involving higher or lower DNA methylation (defined using distance metric FDR < 5% and methylation in cancer sample either > 0.4SD or < − 0.4SD from sample median for the case harboring the breakpoint).

补充文件10：与图5相关。针对高低甲基化区域重排相关的体细胞结构变异（SSVs），本研究采用正常组织DNA甲基化数据集，将以50kb窗口表征的重排区域的平均DNA甲基化水平，与SSV断裂点另一侧基因附近的CpG岛（CGI）的平均甲基化水平进行对比；同时计算所有SSV-CGI关联的甲基化β值平均差值，以及涉及高/低DNA甲基化的SSV-CGI关联子集的平均差值。该子集的筛选标准为：距离指标的错误发现率（FDR）小于5%，且携带该断裂点的病例的癌症样本中，甲基化水平相对于样本中位数的偏差大于0.4倍标准差（SD）或小于-0.4倍标准差（SD）。