Journal: Frontiers in Oncology

Article Title: Case report: Atypical neurofibromatous neoplasm with uncertain biological potential of the sciatic nerve and a widespread arteriovenous fistula mimicking a malignant peripheral nerve tumor in a young patient with neurofibromatosis type 1

doi: 10.3389/fonc.2024.1391456

Figure Lengend Snippet: Histopathological analysis and copy number variation (CNV) profile. (A-I) Histopathological analysis: H&E stained sections (A-C) showing typical histopathological findings of neurofibroma, including cytologically bland, wavy nuclei, loose matrix architecture with collagen bundles, so-called “shredded carrots” in some regions (A) ; hypercellularity in other regions (B) and nuclear atypia (C) . Necrosis and increased mitotic activity were absent. Immunohistochemistry (D-I) shows that a subset of tumor cells expressed S100 (D) and CD34 (E) , respectively. A small subset of tumor cells in focal small clusters expressed GLUT1. Entrapped neurofilament (NF) positive axon bundles within the tumor (G) . P16, one protein product of the CDKN2A gene, highlights a subset of tumor cells; focal complete loss of p16 was seen (H) . Ki-67 proliferation fraction was around 5%. (J) The CNV profile of the tumor was generated based on DNA methylation analysis by microarray for 850,000 CpG sites (Infinium MethylationEPIC/ 850k analysis). No chromosomal losses or gains were observed. The CNV profile, however, suggested deletion of CDKN2A/B (light blue dot) on chromosome 9.

Article Snippet: DNA methylation analysis by microarray (Infinium MethylationEPIC/850k analysis) assigned this tumor to the methylation class “schwannoma” matching score >0.99 (v12.8) and suggested CDKN2A/B deletion ( ).

Techniques: Staining, Activity Assay, Immunohistochemistry, Generated, DNA Methylation Assay, Microarray

Journal: Scientific Reports

Article Title: Prenatal DEHP exposure predicts neurological disorders via transgenerational epigenetics

doi: 10.1038/s41598-023-34661-3

Figure Lengend Snippet: Infinium methylation microarray analysis of Methylation changes in DEHP-exposed human placenta samples. ( A ) The flowchart shows how the pipeline of raw data was processed. DNA methylation was performed using the high-resolution Infinium MethylationEPIC BeadChip Kit interrogating about 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution. By utilizing a cut-off p-value threshold of greater than 0.05 and an FDR of 10%, a total of 1254 probes displaying a minimum of 10% differential methylation were identified. ( B ) Density of DNA methylation level for 12 human placenta samples exposed to DEHP; blue lines: low DEHP exposure (n = 6), red lines: high DEHP exposure (n = 6). Individual probes with beta (β)-values (range 0–1) are approximate representations of the absolute methylation percentage of specific CpG sites within the sample population. Beta value = 1 indicates complete methylation; beta value = 0 represents no methylation. ( C ) Density of 10% differentially DNA methylated probes of all samples. Hypomethylation was observed in the DEHP high group (red line), as compared to DEHP low group (blue line). ( D ) Heatmap showing the 10% differentially DNA methylated probes; left panel: low DEHP exposure; right panel: high DEHP exposure. Heatmap showing differentially methylated cytosine (DMC) sites across the two different exposure dosages of DEHP. Most of the probes observed were hypomethylation in DEHP (red line: methylated, blue line: unmethylated).

Article Snippet: DNA methylation was performed using the high-resolution Infinium MethylationEPIC BeadChip Kit interrogating about 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution.

Techniques: Methylation, Microarray, DNA Methylation Assay

Journal: Epigenomics

Article Title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

doi: 10.2217/epi.15.114

Figure Lengend Snippet: Venn diagram showing the degree of CpG overlapping (yellow) between the Infinium HumanMethylation450 BeadChip (450K; red) and the MethylationEPIC BeadChip (850K; green) microarrays.

Article Snippet: The MethylationEPIC BeadChip Infinium also interrogates 2880 CNG (C stands for cytosine; N stands for any nucleotide; G stands for guanine) sites that are present in the 450K DNA methylation microarray ( Supplementary Table 4 ), while 211 CNG sites from the 450K microarray are not included in the 850K platform.

Techniques:

Journal: Epigenomics

Article Title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

doi: 10.2217/epi.15.114

Figure Lengend Snippet: Comparison of methylation values from HumanMethylation450 and their corresponding shared CpG sites present on MethylationEPIC microarray (A) for a renal tumor sample (RCC9). Assay reproducibility (B) of methylation measurements when using technical replicates on a normal colon (NC22A) sample. Correlation plot (C) of the methylation values obtained from a FFPE sample (RCC9-FFPE) when compared with its match biopsy of the same tumor that was preserved as FF (RCC9). 5-hmC value representation (D) , where the same sample was treated as per conventional bifsulfite conversion or as per oxBS. Differences on oxBS with bifsulfite conversion are due to the level of 5-hydroxymethylation, where the absence of 5-hmC has been modeled as a discontinue red line. Frequency of hydroxymethylaton values (E) as a result of subtracting the oxBS values (due to 5-mC) from the BS values (due to 5-mC + 5-hmC) for each CpG site included on the 850K array. 5-hmC: 5-hydroxymethylation; FF: Fresh frozen; FFPE: Formalin-fixed paraffin-embedded; oxBS: Oxidative bisulfite conversion.

Article Snippet: The MethylationEPIC BeadChip Infinium also interrogates 2880 CNG (C stands for cytosine; N stands for any nucleotide; G stands for guanine) sites that are present in the 450K DNA methylation microarray ( Supplementary Table 4 ), while 211 CNG sites from the 450K microarray are not included in the 850K platform.

Techniques: Comparison, Methylation, Microarray, Formalin-fixed Paraffin-Embedded

Journal: Epigenomics

Article Title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

doi: 10.2217/epi.15.114

Figure Lengend Snippet: (A) Differentially methylated CpG sites (Δβ ≥0.66 ) on MethylationEPIC BeadChip microarray from a normal colon sample (NC22A), and normal sorted brain neurons (N229). Heatmap representation of differentially methylated CpG sites (left) and methylation values distribution (right) of samples where methylation differences threshold has been denoted as a discontinued red line (Δβ ≥0.66), and those values considered as differentially methylated have been highlighted in blue. (B) Differentially methylated CpG sites (Δβ ≥0.66), among the newly added 413,759 CpG sites of the MethylationEPIC BeadChip microarray, for a normal colon sample (NC22A), and normal sorted brain neurons (N229). Heatmap representation of differentially methylated CpG sites (left) and methylation values distribution (right) of samples where methylation differences threshold has been denoted as a discontinued red line (Δβ ≥0.66), and those values considered as differentially methylated have been highlighted in blue.

Article Snippet: The MethylationEPIC BeadChip Infinium also interrogates 2880 CNG (C stands for cytosine; N stands for any nucleotide; G stands for guanine) sites that are present in the 450K DNA methylation microarray ( Supplementary Table 4 ), while 211 CNG sites from the 450K microarray are not included in the 850K platform.

Techniques: Methylation, Microarray