Results: 2

1.
Figure 2.

Figure 2. From: Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome.

Allele-specific methylation. (A) Sanger reads from BJ-iPS12 show an extended ASM region in dbSNP 129 rs10846023 indexed region (chr12:14611423–14612359) in the intron of the RAB11FIP1 (also known as FLJ22622) gene. This ASM region includes two CpG dinucleotides that overlap with SNPs, but the ASM is not limited to these sites. (Orange circles) SNPs that overlap with CpG dinucleotides. (B) An allele-specific methylation frequency graph based on aligned Illumina data showing ASM at rs10846023 in BJ-iPS12 (chr12:14611616–14611654). (Y-axis) Methylation frequency, where a value of 1 indicates complete methylation at a CpG dinucleotide; (x-axis) chromosomal coordinates. (C) Sanger sequence data around SNP site rs6061990 (TAF4 intronic region, chr20:60061657–60062273) in PGP9L illustrates an example where ASM is solely dependent on SNPs at CpG dinucleotides. (D) An allele-specific methylation frequency graph based on Illumina data showing ASM at rs6061990 in PGP9L (chr20:60061712–60061895). (Green line) SNP position; (orange triangles) SNPs that overlap with CpG dinucleotides. Note that the Illumina data show ASM at a CpG (chr20:60061784) that is not supported by the Sanger data.

Robert Shoemaker, et al. Genome Res. 2010 July;20(7):883-889.
2.
Figure 1.

Figure 1. From: Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome.

Linkage disequilibrium (LD) analysis of CpG methylation haplotypes. (A) LD diagram of 5′ region of the imprinted gene SNRPN (chr15:22750806–22751314) from Hues63. Each row represents a Sanger sequence and each column represents a CpG dinucleotide. (Filled circles) Methylated CpGs; (open circles) unmethylated CpGs, (dashed lines) methylation state of the CpG could not be determined. Chromosomal coordinates are listed above. This region shows a methylation LD block spanned over 500 bp in Sanger reads. (B,C) CpG pairwise r2-value plots and heatmap for 5′ region of the SNRPN gene. While the majority of CpG pairs have high methylation correlation values (r2 > 0.3), some pairs of CpG sites have little or no correlation (r2 < 0.3). The pairwise distance represents the separation of the CpG dinucleotides used in the r2 calculation. The heatmap colors represent the probe fraction at a given pairwise distance (rounded down to the nearest 50 bp) that has the indicated r2-value. The probe fractions for each pairwise distance sum to one. The color scale saturates at 0.5, so that small probe fraction differences can be distinguished.

Robert Shoemaker, et al. Genome Res. 2010 July;20(7):883-889.

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