Gene expression profiling of colon samples.

<p>Hierarchical clustering and sample-to-sample distance heatmap of the expression of protein coding genes. SSP samples are clustered together, FAP samples also clustered together. Gene expression in TSA-2 that has both APC and BRAF mutation is more similar to the pattern of SSP expression cluster. The gene expression pattern of FAP show about 50% similarity to the gene expression of SSP, although the DNA methylation patterns of these two polyp types differ significantly. Therefore studying the DNA methylation marker can lead to detect SSP more specifically than studying the gene expression.</p

Hierarchical clustering of all CpGs in 450K methyl-array on colon samples.

<p>The SSP samples are clustered together based on DNA methylation. The TSA-2 sample that is mutant for BRAF gene also clustered with SSPs.</p

The biopsy samples.

<p>Mutations known for each sample are listed. SSP-1 to SSP-8 are exome sequenced. Mutations in other samples are tested by OncoCarta3. BRAF-V600E mutation and KRAS codon 12 and 13 mutations are tested by PCR-sequencing in all samples.</p

Global loss of methylation and partial methylation in SSP.

<p><b>(A)</b> Global level of cytosine methylation in SSP, GU and blood. <b>(B)</b> Global level of CpG methylation in SSP, GU and blood. Histogram of fraction methylation in colon SSP, GU and blood <b>(C-E). (C)</b> In normal tissues most of the CpGs are either unmethylated or highly methylated (75–95% methylated). In SSP the very high level of methylation is lost and methylation level shows a more disperse distribution (35–80% methylated). <b>(D)</b> The EMRs show mostly 5–15% methylation in uninvolved colon tissue, while they are 15–45% methylated in SSP. <b>(E)</b> The RMRs in SSP were originally 65–90% methylated in uninvolved colon but this level is reduced to 15–40% in SSP.</p

Global methylation changes in SSP and FAP.

<p><b>(a)</b> Comparison of FAP with normal samples shows only few DNA methylation changes. From 395,899 CpGs tested on the Infinium array, only 52 CpGs show more than 2 fold increase in methylation in FAP compared to normal colon tissue and 6 CpGs show more than 2 fold reduction in methylation (p-value <0.05). <b>(b)</b> In contrast comparison of SSP with normal samples shows significant DNA methylation changes. From 395,899 CpGs tested on the Infinium array, 42,965 (10.85%) show more than 2 fold increase in methylation in SSP compared to normal colon tissue and 19,019 (4.80%) show more than 2 fold reduction in methylation (p-value <0.05).</p

DNA methylation markers for SSP characterization and early diagnosis.

<p>DNA methylation markers for SSP characterization and early diagnosis.</p