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INFINIUM Inc massarray analysis

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 <t>MassARRAY</t> 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.

Massarray Analysis, supplied by INFINIUM Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/massarray-system/massarray+system/pmc04216836-116-25-44
Average 90 stars, based on 1 article reviews

massarray analysis - by Bioz Stars, 2026-10

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1) Product Images from "Prognostication of patients with clear cell renal cell carcinomas based on quantification of DNA methylation levels of CpG island methylator phenotype marker genes"

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

Journal: BMC Cancer

doi: 10.1186/1471-2407-14-772

Figure Legend 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.

Techniques Used: DNA Methylation Assay

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 ).

Figure Legend 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 ).

Techniques Used: Biomarker Discovery, DNA Methylation Assay

DNA Methylation Assay:

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
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. .. All 88 ccRCCs showing DNA methylation levels higher than the cutoff values listed in Table at less than 16 CpG units based on the present MassARRAY analysis (blue bars in Figure B) were CIMP-negative ccRCCs identified by our previous hierarchical clustering based on the Infinium assay.

Article Title: Novel method for DNA methylation analysis using high‐performance liquid chromatography and its clinical application
Article Snippet: .. In our previous study, 14 ccRCC included in the present study were found to be CIMP‐positive using genome‐wide DNA methylation analysis by Infinium assay and DNA methylation quantification of the 7 ccRCC‐specific CIMP marker genes using the MassARRAY system. ..

Article Title: DNA methylation profile distinguishes clear cell sarcoma of the kidney from other pediatric renal tumors.
Article Snippet: .. We analyzed 6 each of RTK, CCSK, ESFT, and NK, the results of MassARRAY were well correlated with those of the Infinium assay, and each type of tumor revealed a specific DNA methylation pattern (Figure S2). ..

Article Title: Prognostic implication of PTPRH hypomethylation in non-small cell lung cancer
Article Snippet: Because investigation of DNA methylation by the MassARRAY system allowed a comprehensive coverage of CpG sites, we assessed DNA methylation levels at the relatively CpG-rich region containing the CpG site cg11261264 in the same LC-C2 samples using the MassARRAY system (Genomic positions of the CpG sites are shown in ). .. DNA methylation levels obtained by the MassARRAY system and Infinium assay correlated well (r=0.952, P=1.44×10 −73 ), confirming the reliability of the latter assay. ..

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
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. .. All 88 ccRCCs showing DNA methylation levels higher than the cutoff values listed in Table at less than 16 CpG units based on the present MassARRAY analysis (blue bars in Figure B) were CIMP-negative ccRCCs identified by our previous hierarchical clustering based on the Infinium assay. ..

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
Article Snippet: Significant correlations between DNA methylation levels determined by our previous Infinium assay [ ] and those determined by the present MassArray analysis were statistically confirmed ( P = 1.25 × 10 −35 , P = 1.98 × 10 −32 , P = 1.31 × 10 −41 , P = 5.30 × 10 −34 , P = 7.91 × 10 −22 and P = 7.61 × 10 −44 , respectively). .. In the present study, our primary intention was to evaluate quantitatively the DNA methylation status of not only the Infinium probe sites but also the entire promoter CpG islands in the ccRCC-specific CIMP marker genes using the MassARRAY system [ ]. ..

Genome Wide:

Marker:

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
Article Snippet: Significant correlations between DNA methylation levels determined by our previous Infinium assay [ ] and those determined by the present MassArray analysis were statistically confirmed ( P = 1.25 × 10 −35 , P = 1.98 × 10 −32 , P = 1.31 × 10 −41 , P = 5.30 × 10 −34 , P = 7.91 × 10 −22 and P = 7.61 × 10 −44 , respectively). .. In the present study, our primary intention was to evaluate quantitatively the DNA methylation status of not only the Infinium probe sites but also the entire promoter CpG islands in the ccRCC-specific CIMP marker genes using the MassARRAY system [ ]. ..

Amplification:

Article Title: How to Translate DNA Methylation Biomarkers Into Clinical Practice
Article Snippet: .. Targeted epigenetic clocks for pyrosequencing, MassArray, ddPCR, or barcoded amplicon sequencing can reach almost similar precision as described for Infinium BeadChip clocks ( ). ..

Sequencing:

other:

Article Title: DNA Methylation Profile Distinguishes Clear Cell Sarcoma of the Kidney from Other Pediatric Renal Tumors
Article Snippet: Genes ALDOC , CREG1, PKN1 , and Thrombospondin-1 ( THBS1) were selected because of their tendency to be hypermethylated in CCSK by the Infinium assay, while ADRA1D was selected because of distinct methylation levels among tumors.

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