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Fig. 6 | Genome Biology

Fig. 6

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. 6

Increased allele switching at ASM loci in cancers. a Map of the ASM region tagged by SNP rs11864188 in the PKD1L3 gene. The ASM shows allele switching, with the ALT allele being hyper-methylated in the FL but with an opposite direction of the allelic methylation bias in the DLBCL. No ASM was detected in 23 non-cancer heterozygous samples. The rs11864188 SNP disrupts multiple TF motifs, some of which have opposite allele-specific predicted affinity differences, including MYC and ABF1 motifs with a higher affinity on the ALT allele and RXRA and NR4A2 motifs with a higher affinity on the REF allele. The MYC motif maps to the negative strand and is oriented 3′ to 5′. b Frequency of switching, scored for ASM index SNPs that were heterozygous in > 2 samples, is increased among cancer-only ASM loci (43%) compared to ASM loci found in normal samples (10%). As a control, ASM index SNPs mapping to imprinted regions showed 46% switching, approximating the expected 50% based on parent-of-origin dependent ASM. c Enrichment analyses of CTCF and TF binding motifs among switching vs non-switching ASM loci: in the left panel, polymorphic motifs with strong correlations between ASM magnitude and affinity score differences are found to be depleted among switching compared to non-switching ASM loci. In the right panel, polymorphic TF motifs enriched among ASM but with little or no correlations of predicted binding affinity with ASM magnitude showed little or no depletion among switching ASM loci. The solid vertical lines represent zero (no enrichment or depletion), and the dotted lines show the average values for depletion for each set of motifs

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