Journal: BMC Cancer

Article Title: Prognostication of patients with clear cell renal cell carcinomas based on quantification of DNA methylation levels of CpG island methylator phenotype marker genes

doi: 10.1186/1471-2407-14-772

Figure Lengend Snippet: Average DNA methylation levels at promoter CpG islands in the SLC13A5 (A) and ZNF671 (B) genes in CIMP-negative (n = 88) and CIMP-positive (n = 14) ccRCCs in the learning cohort. DNA methylation levels of each CpG unit were evaluated quantitatively using the MassARRAY system. A . Average DNA methylation levels of all examined 38 CpG units including 68 CpG sites located within 1347 bp 5′ region of the SLC13A5 gene in CIMP-positive ccRCCs (red line) were significantly higher than those in CIMP-negative ccRCCs (blue line). B . Average DNA methylation levels of all examined 21 CpG units including 29 CpG sites located within the 428 bp 5′ region of the ZNF671 gene in CIMP-positive ccRCCs (red line) were significantly higher than those in CIMP-negative ccRCCs (blue line). * P < 0.05 and ** P < 0.01. Exact P values for each CpG unit of the SLC13A5 and ZNF671 genes are summarized in Additional file : Table S5. Error bar: standard error.

Article Snippet: All 14 ccRCCs showing DNA methylation levels higher than the cutoff values listed in Table at 16 or more CpG units based on the present MassARRAY analysis (red bars in Figure B) were CIMP-positive ccRCCs identified by our previous hierarchical clustering based on the Infinium assay.

Techniques: DNA Methylation Assay

Journal: BMC Cancer

Article Title: Prognostication of patients with clear cell renal cell carcinomas based on quantification of DNA methylation levels of CpG island methylator phenotype marker genes

doi: 10.1186/1471-2407-14-772

Figure Lengend Snippet: The criteria for CIMP diagnosis discriminating CIMP-positive from CIMP-negative ccRCCs based on the MassARRAY system. A . Scattergrams of DNA methylation levels of representative CpG units in the learning cohort. Using each CpG unit and its cutoff value (CV) described in Table 1, CIMP-positive ccRCCs were discriminated from CIMP-negative ccRCCs with sufficient sensitivity and specificity. B . Histogram showing the number of CpG units with DNA methylation levels higher than the cutoff values listed in Table 1 in the learning cohort. All 14 ccRCCs (red columns) showing DNA methylation levels higher than the cutoff values at 16 or more CpG units were CIMP-positive ccRCCs, and all 88 ccRCCs (blue columns) showing DNA methylation levels higher than the cutoff values at less than 16 CpG units were CIMP-negative ccRCCs. On the basis of this histogram, we established the following criteria: When the cancerous tissue showed DNA methylation levels higher than the cutoff values at 16 (green bar) or more CpG units, it was judged to be CIMP-positive. The number of CpG units showing higher DNA methylation levels than the cutoff values in CIMP-positive ccRCCs (20.79 ± 0.69) was higher than that of CIMP-negative ccRCCs (2.09 ± 0.32, P = 8.75 × 10 −10 ). C . Histogram showing the number of CpG units with DNA methylation levels higher than the cutoff values listed in Table 1 in the additional 100 ccRCCs comprising the validation cohort. Using the criteria established on the basis of panel B , 5 ccRCCs (black bars) were diagnosed as CIMP-positive ccRCCs, whereas 95 ccRCCs (gray bars) were diagnosed as CIMP-negative ccRCCs. The number of CpG units showing higher DNA methylation levels than the cutoff values in ccRCCs diagnosed as CIMP-positive (18.00 ± 0.84) was higher than that of ccRCCs diagnosed as CIMP-negative (2.73 ± 0.30, P = 1.41 × 10 −4 ).

Article Snippet: All 14 ccRCCs showing DNA methylation levels higher than the cutoff values listed in Table at 16 or more CpG units based on the present MassARRAY analysis (red bars in Figure B) were CIMP-positive ccRCCs identified by our previous hierarchical clustering based on the Infinium assay.

Techniques: Biomarker Discovery, DNA Methylation Assay