mgmt plus kit  (Pyrosequencing Inc)

Journal: Cancer Medicine

Article Title: Molecular Characterization and Clinical Relevance of MGMT ‐Silenced Pancreatic Cancer

doi: 10.1002/cam4.70393

Figure Lengend Snippet: Patients' and tumor characteristics according to MGMT methylation status in the public cohorts.

Article Snippet: MGMT promoter methylation status was assessed by pyrosequencing (via the MGMT plus Diatech Pharmacogenetics [Jesi, Italy] kit), as previously described [ ].

Techniques: Methylation

Journal: Cancer Medicine

Article Title: Molecular Characterization and Clinical Relevance of MGMT ‐Silenced Pancreatic Cancer

doi: 10.1002/cam4.70393

Figure Lengend Snippet: Transcriptomic features of MGMT ‐silenced PAC. (a) Volcano plot of differentially expressed genes in MGMT ‐methylated versus not‐methylated PAC. The vertical dotted lines identify genes with absolute log2FoldChange > 0.58 (i.e., absolute fold change > 1). The horizontal dotted line identifies genes with adjusted p < 0.01. Each point represents a gene, and genes are colored based on up (red) and downregulation (yellow) in MGMT ‐methylated versus not‐methylated groups. (b) Bar plot reporting results of GSEA performed on up‐ and downregulated genes in MGMT ‐methylated versus not‐methylated PAC. The color of the barplot reports the significance of the p value of the hypergeometric tests (after Benjamini–Hochberg multiple test correction). Only pathways with adjusted p < 0.1 are reported. Most pathways show a negative enrichment score, representing a negative enrichment in MGMT ‐methylated tumors. (c) Boxplots comparing ESTIMATE deconvolution scores between MGMT ‐methylated versus not‐methylated PAC. Wilcoxon mean rank‐sum p values are shown. (d) Overlay of PAC cases according to MGMT ‐methylation status (inner ring) with published PAC transcriptomic subtypes (outer rings), according to Moffitt, Collisson, and Bailey classifications. ADEX , Aberrantly Differentiated Endocrine Exocrine; GSEA , Gene Set Enrichment Analysis; MGMT , O 6 ‐methylguanine‐ DNA methyltransferase; PAC , pancreatic cancer.

Article Snippet: MGMT promoter methylation status was assessed by pyrosequencing (via the MGMT plus Diatech Pharmacogenetics [Jesi, Italy] kit), as previously described [ ].

Techniques: Methylation

Journal: Cancer Medicine

Article Title: Molecular Characterization and Clinical Relevance of MGMT ‐Silenced Pancreatic Cancer

doi: 10.1002/cam4.70393

Figure Lengend Snippet: Genomic features of PAC cases according to MGMT methylation status. (a) Oncoprint summarizing somatic SNVs/indels according to MGMT methylation status. The top 20 most frequently mutated genes are presented. Upper bars represent TMB levels. MGMT ‐methylated tumors are shown on the far right. (b) Bar plot reporting results of enrichment analysis of SNVs/indels according to MGMT methylation status. On the x axis, enrichment score is reported as the z‐score scaled‐, natural logarithm‐transformed odds ratio of the comparison between MGMT ‐methylated versus not‐methylated cases. Bars are colored according to the enrichment score and adjusted (after Benjamini–Hochberg multiple test correction) p value as orange (significantly enriched in not‐methylated, enrichment score ≤ 0 and adjusted p ≤ 0.05), yellow (enriched in not‐methylated, enrichment score < 0 and adjusted p value > 0.05), light red (enriched in methylated, enrichment score > 0 and adjusted p > 0.05), and dark red (significantly enriched in methylated, enrichment score > 0 and adjusted p ≤ 0.05). (c, d) Barplots reporting results of oncogenic signaling pathways analysis according to MGMT methylation status. Fraction of each affected pathway (c) and fraction of samples affected (d). The NRF2 pathway is not plotted as it was not affected in any cases. The * identifies the only significant different, as evaluated by Fisher's exact test. Del, Deletion—Ins, Insertion; MGMT , O 6 ‐methylguanine‐ DNA methyltransferase; NRF2 , Nuclear Respiratory Factor 2; TMB , tumor mutational burden.

Article Snippet: MGMT promoter methylation status was assessed by pyrosequencing (via the MGMT plus Diatech Pharmacogenetics [Jesi, Italy] kit), as previously described [ ].

Techniques: Methylation, Transformation Assay, Comparison, Protein-Protein interactions

Journal: Cancer Medicine

Article Title: Molecular Characterization and Clinical Relevance of MGMT ‐Silenced Pancreatic Cancer

doi: 10.1002/cam4.70393

Figure Lengend Snippet: Prognostic impact of MGMT ‐silencing in the public cohorts and in the INT validation cohort. (a) Overall survival represented through Kaplan–Meier curves according to MGMT methylation status in the pooled training cohort. Survival data are missing for one case among non‐methylated patients. (b) Forest plot of multivariable Cox regression analysis for overall survival adjusting for patients' age, sex, tumor histology, and tumor stage at diagnosis. (c) Overall survival represented through Kaplan–Meier curves according to MGMT methylation status in the INT cohort. (d) Forest plot of multivariable Cox regression analysis for overall survival adjusting for patients' age, sex, ECOG PS, and tumor stage at diagnosis. The hazard ratios are shown with 95% confidence intervals, and Wald p values are reported on the far right. Patient with MGMT ‐methylated tumors show better overall survival after adjustment for other covariates. BR , Borderline Resectable; ECOG PS , Eastern Cooperative Oncology Group Performance Status; LAD , Locally Advanced Disease; MGMT , O 6 ‐methylguanine‐ DNA methyltransferase.

Article Snippet: MGMT promoter methylation status was assessed by pyrosequencing (via the MGMT plus Diatech Pharmacogenetics [Jesi, Italy] kit), as previously described [ ].

Techniques: Biomarker Discovery, Methylation

Journal: Cancer Medicine

Article Title: Molecular Characterization and Clinical Relevance of MGMT ‐Silenced Pancreatic Cancer

doi: 10.1002/cam4.70393

Figure Lengend Snippet: Patients' and tumor characteristics according to MGMT status in the INT cohort.

Article Snippet: MGMT promoter methylation status was assessed by pyrosequencing (via the MGMT plus Diatech Pharmacogenetics [Jesi, Italy] kit), as previously described [ ].

Techniques: Biomarker Discovery, Methylation, Expressing