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Fig. 1 | Genome Biology

Fig. 1

From: Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs

Fig. 1

ASM is increased in cancers and correlates with global DNA hypomethylation. a Relationship between global DNA methylation and the percentage of SNPs that reveal ASM in each sample, showing a strong inverse correlation between per sample ASM frequencies and global methylation levels. Cancer samples (color-coded in red scale) have higher ASM frequencies than nearly all the non-cancer samples (color-coded in blue scale), except for partial overlap of the GBM ASM frequencies with those of normal placental trophoblast and cultured bladder epithelial cells. When compared to lineage-matched normal cell types, there is a 5- to 9-fold higher frequency of ASM in the cancers. The EBV-immortalized but euploid GM12878 LCL shows global hypomethylation and a high frequency of ASM. b Zoomed-in graph showing an inverse correlation of ASM frequencies with global methylation, even when focusing on the non-cancer samples. p values are from Wilcoxon tests. *EBV-immortalized GM12878 LCL is grouped with the cancers. **Mammary epithelial cell lines (N = 3) and epithelium-rich normal breast tissue (N = 2). ***Includes purified T cells, B cells, and monocytes/macrophages (Additional file 1: Table S1)

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