Journal: Genetics and Molecular Biology

Article Title: Constitutional and somatic methylation status of DMRH19 and KvDMR in Wilms tumor patients

doi: 10.1590/S1415-47572012005000073

Figure Lengend Snippet: Pyrogram showing DMRH19 hypermethylation in blood DNA samples from patients P2 (A) and P35 (B). The average methylation index (MI) for DMRH19 in patients P2 and P35 was 71% and 57%, respectively. Panel (C) shows DMRH19 methylation in blood from healthy controls (average MI = 41.7%). The average MI of all blood samples from healthy controls used in DMRH19 pyrosequencing was 45.4 ± 6.2%. The MI is indicated above peaks (gray columns) corresponding to the CpG islands in this region.

Article Snippet: Pyrosequencing reactions were done with 2 μg of DNA previously modified with bisulfite (EZ DNA Methylation kit, Zymo Research, CA, USA) according to the manufacturer’s instructions.

Techniques: Methylation

Journal: Genetics and Molecular Biology

Article Title: Constitutional and somatic methylation status of DMRH19 and KvDMR in Wilms tumor patients

doi: 10.1590/S1415-47572012005000073

Figure Lengend Snippet: MS-MLPA methylation indices. (A) Peripheral blood DNA from patient P2 showing isolated hypermethylation of DMRH19 (average MI = 84 ± 6%) and normal methylation of KvDMR (average MI = 64 ± 8%). (B) Peripheral blood DNA from patient P42 showing normal methylation of DMRH19 (average MI = 47 ± 6%) and KvDMR (average MI = 51 ± 8%). (C) Fresh tumor DNA (sample A) from patient P19 showing paternal uniparental disomy (average MI for DMRH19 and KvDMR was 70 ± 27% and 22 ± 19%, respectively). Dark gray columns: expected ratios; light gray columns: observed ratios. Each pair of columns corresponds to one of the DMRH19 and KvDMR probes included in the MS-MLPA kit (five probes for DMRH19 and four for KvDMR).

Article Snippet: Pyrosequencing reactions were done with 2 μg of DNA previously modified with bisulfite (EZ DNA Methylation kit, Zymo Research, CA, USA) according to the manufacturer’s instructions.

Techniques: Methylation, Isolation

Journal: Gut

Article Title: Glutathione peroxidase 7 has potential tumor suppressor functions that are silenced by location-specific methylation in oesophageal adenocarcinoma

doi: 10.1136/gutjnl-2013-304612

Figure Lengend Snippet: A) A schematic chart shows GPX7 genomic structure. GPX7 has 3 exons as shown in black boxes. A CpG island with dense CpG sites is present around the transcription start site (TSS); each vertical bar represents one CpG site. Pyrosequencing assays that covered CpG sites from −162 to +138, relative to TSS were designed (Supplementary Table 1). B) Summary of pyrosequencing results in normal oesophageal squamous epithelia (NS), normal gastric mucosa (NG), Barrett’s oesophagus (BO) and oesophageal adenocarcinoma (OAC) (additional details in Table 1). Hypermethylation of CpG sites from +13 to +64 (dash-line square) was only seen in OAC. C) Comparison of the average DNA methylation levels (CpG sites from +13 to +64) in NS, NG, BO, and OAC samples. D) Spearman correlation analysis demonstrated inverse correlation between methylation levels (+13 to +64) and GPX7 mRNA expression fold (r=−0.37, p=0.001).

Article Snippet: DNA bisulfite treatment and pyrosequencing analysis The DNA was bisulfite modified using an EZ DNA Methylation Gold Kit (Zymo Research, Orange, California, USA) according to the manufacturer’s protocol.

Techniques: DNA Methylation Assay, Methylation, Expressing

Journal: Gut

Article Title: Glutathione peroxidase 7 has potential tumor suppressor functions that are silenced by location-specific methylation in oesophageal adenocarcinoma

doi: 10.1136/gutjnl-2013-304612

Figure Lengend Snippet: GPX7 DNA copy number, methylation level, and mRNA expression in oesophageal cell lines and primary tumors

Article Snippet: DNA bisulfite treatment and pyrosequencing analysis The DNA was bisulfite modified using an EZ DNA Methylation Gold Kit (Zymo Research, Orange, California, USA) according to the manufacturer’s protocol.

Techniques: Methylation, Expressing, DNA Methylation Assay

Journal: Clinical Epigenetics

Article Title: Quantitative methodology is critical for assessing DNA methylation and impacts on correlation with patient outcome

doi: 10.1186/1868-7083-6-22

Figure Lengend Snippet: Literature identified hypermethylated loci in head and neck squamous cell carcinomas, according to frequency, methodology and univariate correlation with survival a

Article Snippet: For the RUNX3 pyrosequencing analysis, 83 samples had sufficient bisulfite modified DNA available for assessment.

Techniques: Methylation

Journal: Clinical Epigenetics

Article Title: Quantitative methodology is critical for assessing DNA methylation and impacts on correlation with patient outcome

doi: 10.1186/1868-7083-6-22

Figure Lengend Snippet: Summary of methylation events for each locus assessed by methylation sensitive high resolution melting (MS-HRM), and assessed in the Cancer Genome Atlas (TCGA) cohort a

Article Snippet: For the RUNX3 pyrosequencing analysis, 83 samples had sufficient bisulfite modified DNA available for assessment.

Techniques: Methylation

Journal: Clinical Epigenetics

Article Title: Quantitative methodology is critical for assessing DNA methylation and impacts on correlation with patient outcome

doi: 10.1186/1868-7083-6-22

Figure Lengend Snippet: Pyrosequencing results for all samples demonstrating heterogeneous methylation of RUNX3 when assessed by methylation sensitive high resolution melting (MS-HRM). Each analyzed sample is annotated for the quantity of methylation detected at each CpG site interrogated, and the mean methylation value for all CpG sites analyzed is also provided. This figure demonstrates that the vast majority of samples with heterogeneous methylation for this locus assessed by MS-HRM, had low levels of methylation when quantified by pyrosequencing.

Article Snippet: For the RUNX3 pyrosequencing analysis, 83 samples had sufficient bisulfite modified DNA available for assessment.

Techniques: Methylation