pyrosequencing-based methylation analysis  (Pyrosequencing Inc)

Journal: Neuro-Oncology Advances

Article Title: Clinical value of the MGMT promoter methylation score in IDHmt low-grade glioma for predicting benefit from temozolomide treatment

doi: 10.1093/noajnl/vdae224

Figure Lengend Snippet: Association between progression-free survival (PFS) and the MGMTp methylation score. The association of the MGMTp methylation score, based on the MGMT-STP27 procedure, with progression-free survival (PFS; interval from diagnosis) was evaluated by the hazard ratio (confidence interval at 95%) from the cox regression model. The forest plots in A and B correspond to the PFS reported for patients treated in EORTC-22033 with temozolomide (TMZ) or radiotherapy (RT), respectively. , The MGMT-STP27 score was significant in the TMZ treated patients, but not in the patients with RT. The forest plots in C and D visualize the outcome of the Montpellier patients treated with TMZ, with time to progression defined by the next treatment-free survival (NxtTrtFS), and PFS defined by RANO, respectively. The MGMT-STP27 score was significant in the Montpellier cohort when using NxtTrtFS as outcome measure, a trend was observed when using RANO criteria for PFS. * P <.05; ** P <.01.

Article Snippet: The association between the MGMT-STP27 score and NxtTrtFS was confirmed using a pyrosequencing-based MGMTp methylation score (MGMT-PYROscore) obtained for the same samples ( P = .002, ).

Techniques: Methylation, Biomarker Discovery

Journal: Cancers

Article Title: Impact of Physical Activity on DNA Methylation Signatures in Breast Cancer Patients: A Systematic Review with Bioinformatic Analysis

doi: 10.3390/cancers16173067

Figure Lengend Snippet: Effects of PA on DNA methylation patterns in BC populations. Table summarising the study design and results of interest from all selected articles that evaluated the effects of PA on DNA methylation signatures in BC patients. DNA methylation results are presented using the gene codes of the genes associated and/or affected by the PA-induced methylation changes reported by the original authors.

Article Snippet: The authors also analysed global DNA methylation in white blood cell DNA [ , ] using the luminometric methylation assay (LUMA), a quantitative measurement of genome-wide DNA methylation, as described by Bjornsson et al. [ ], and LINE-1, where four CpG sites in the promoter region of LINE-1 were assessed using a validated pyrosequencing-based methylation assay [ ].

Techniques: DNA Methylation Assay, Methylation, Control

Journal: PLoS ONE

Article Title: DNA Methylation Dynamics in Blood after Hematopoietic Cell Transplant

doi: 10.1371/journal.pone.0056931

Figure Lengend Snippet: (A) Diagram of the experimental design. The differences of the global methylation levels between donors, pre-HCT recipients and post-HCT recipients were assessed by a pyrosequencing based methylation assay of repetitive DNA elements (LINE1 and NBL2) in whole blood. (B) NBL2 ΔMet values between donors, pre-HCT recipients, and 1 month post-HCT recipients. (C) NBL2 ΔMet mean values between donors and recipients up to 12 months post-transplant. The dotted line marks the ΔMet mean value between donors and 1 month post-HCT recipients (ΔMet = 5.8450). During the follow up of the transplant, the mean values barely deviated from the initial post-HCT ΔMet. (D) LINE1 ΔMet values between donors, pre-HCT recipients and 1 month post-HCT recipients. (E) LINE1 ΔMet mean values between donors and recipients up to 12 months post-transplant. The dotted line marked the ΔMet mean value between donors and 1 month post-HCT recipients (ΔMet = 5.383).

Article Snippet: Pyrosequencing-based DNA methylation analysis is relatively inexpensive, is very sensitive, and provides an interesting alternative to protein and mRNA detection in blood samples, allowing the development of novel biomarkers in a large array of human diseases.

Techniques: Methylation

Journal: PLoS ONE

Article Title: DNA Methylation Dynamics in Blood after Hematopoietic Cell Transplant

doi: 10.1371/journal.pone.0056931

Figure Lengend Snippet: Scatter plots showing DNA methylation in donors versus post-transplant recipients 1 month and 6 months post-HCT. Red dots represent CpG sites with methylation values altered more than 20% relative to donor values.

Article Snippet: Pyrosequencing-based DNA methylation analysis is relatively inexpensive, is very sensitive, and provides an interesting alternative to protein and mRNA detection in blood samples, allowing the development of novel biomarkers in a large array of human diseases.

Techniques: DNA Methylation Assay, Methylation

Journal: PLoS ONE

Article Title: Genome-Wide Hypomethylation in Head and Neck Cancer Is More Pronounced in HPV-Negative Tumors and Is Associated with Genomic Instability

doi: 10.1371/journal.pone.0004941

Figure Lengend Snippet: LINE-1 and Alu PMA Assays.

Article Snippet: To assay global methylation levels, we adapted our Pyrosequencing-based Methylation Analysis (PMA) assay to assess methylation of repetitive LINE and SINE ( Alu ) elements, similar to genome-wide methylation assays reported previously .

Techniques: