Journal: Epigenetics

Article Title: Validation of the new EPIC DNA methylation microarray (900K EPIC v2) for high-throughput profiling of the human DNA methylome

doi: 10.1080/15592294.2023.2185742

Figure Lengend Snippet: Comparison of the genomic context of the MethylationEPIC v1.0 (850K) and v2.0 (900K) BeadChip microarrays and the newly added CpG probes. (a) Venn diagram showing the degree of overlap (dark blue) between 850K (light blue) and 900K (deep-dark blue) microarrays. ( b ) CpG density plot of the 22 autosomes, 1 sex chromosome pair and M chromosome of the human genome showing the number of new CpGs in 900K microarray within 1-Mb-sized windows. The horizontal axis represents chromosome length (Mb) and the different colours indicate CpG density. ( c ) Bar plots represent the percentage of CpG for each chromosome pertaining to the 850K and 900K microarrays and the new probes of the 900K microarray. ( d ) Stacked bar plot represent the percentage of the Infinium design chemistry (Infinium I or Infinium II) of the probes in the 850K and 900K microarrays and the new probes of the 900K microarray.

Article Snippet: The recently developed MethylationEPIC BeadChip Infinium microarray v2.0 (900K) annotated to the most recent version of the human genome (GRCh38/h38).

Techniques: Comparison, Microarray

Journal: Epigenetics

Article Title: Validation of the new EPIC DNA methylation microarray (900K EPIC v2) for high-throughput profiling of the human DNA methylome

doi: 10.1080/15592294.2023.2185742

Figure Lengend Snippet: Comparison of the functional context of the MethylationEPIC v1.0 (850K) and v2.0 (900K) BeadChip microarrays and the newly added CpG probes. ( a ) Donut pie plot representing the percentage of CpG probes associated with RNA transcripts according to the GENCODE annotation in the 850K (top) and 900K (middle) microarrays and the new probes from the 900K (bottom) microarray. ( b ) Gene Ontology analysis of the additional transcripts in the 900K compared with the 850K microarray. The pathway name is indicated on the y-axis; the x-axis shows the ratio between observed and expected genes in a GO pathway. Bubble size and colour indicate the false-discovery rate (FDR): large blue and small red represent high and low values, respectively. ( c ) Bar plot representing the number of CpG probes in several annotation features of the microarray manifest: CpG probes in relation to gene (gene distribution) and CpG islands (CpG island distribution), and CpG probes associated with the different chromatin states model (chromatin state dynamics) and with CTCF-binding regions (CTCF-binding sites). Light, dark and deep-dark blue correspond to the 850K and 900K microarray probes and the new probes of the 900K microarray, respectively.

Article Snippet: The recently developed MethylationEPIC BeadChip Infinium microarray v2.0 (900K) annotated to the most recent version of the human genome (GRCh38/h38).

Techniques: Comparison, Functional Assay, Microarray, Binding Assay

Journal: Epigenetics

Article Title: Validation of the new EPIC DNA methylation microarray (900K EPIC v2) for high-throughput profiling of the human DNA methylome

doi: 10.1080/15592294.2023.2185742

Figure Lengend Snippet: Technical and biological validation of the methylation profiles of the same samples hybridized in the MethylationEPIC v1.0 (850K) and v2.0 (900K) BeadChip microarrays. ( a-d ) Correlation plots of the CpG methylation values within ( a ) the same sample hybridized in the 850K and 900K microarrays; (b ) technical replicate of the breast cancer primary sample; ( c ) technical replicate of the blood primary sample; and ( d ) consecutive fresh-frozen and formalin-fixed paraffin-embedded (FFPE) sections of normal endometrium primary tissue. At the bottom and to the left of each correlation graph, density plots show the methylation β-values corresponding to the sample on the x-axis (bottom plot) or the sample on the y-axis (left plot). At the bottom-left edge, density plots show the methylation differences between the two samples. ( e ) Biplot representing principal component (PC) 1 and PC2 of β-values of samples hybridized in the 850K (left) and 900K (middle) microarrays, and for the additional probes in the new 900K microarray (right). Colors represent the different tissues, dots indicate whether samples are primary tissue or cell line samples, and unfilled and filled dots represent healthy and tumoural tissue, respectively. ( f ) Biplot of the t-SNE analysis of samples hybridized in the 850K (left) and 900K (middle) microarrays and for the additional probes in the new 900K microarray (right). Colors represent the different tissues and dots indicate whether samples are primary tissue or cell line samples. ( g ) Unsupervised hierarchical analysis and heatmap for the 43 different samples hybridized in the 850K (left) and 900K (middle) microarrays and for the additional probes in the 900K (right) microarray. Colors indicate whether the sample is from primary tissue (normal or tumoural) and the tissue type, as described in the legend of the heatmap. Methylation β-values range from 0 (green) to 1 (red). ( h ) Dendrogram comparison of 43 samples hybridized in the 850K and 900K microarrays. Bold and coloured branches and lines between dendrograms indicate subtrees common to the two microarrays. Distinct edges in the 850K and 900K microarray dendrograms are shown as dashed branches.

Article Snippet: The recently developed MethylationEPIC BeadChip Infinium microarray v2.0 (900K) annotated to the most recent version of the human genome (GRCh38/h38).

Techniques: Biomarker Discovery, Methylation, CpG Methylation Assay, Formalin-fixed Paraffin-Embedded, Microarray, Comparison

Journal: Epigenetics

Article Title: Validation of the new EPIC DNA methylation microarray (900K EPIC v2) for high-throughput profiling of the human DNA methylome

doi: 10.1080/15592294.2023.2185742

Figure Lengend Snippet: List of samples used for the technical and biological validation of the Human MethylationEPIC v2.0 microarray.

Article Snippet: The recently developed MethylationEPIC BeadChip Infinium microarray v2.0 (900K) annotated to the most recent version of the human genome (GRCh38/h38).

Techniques: Biomarker Discovery, Microarray

Journal: Epigenetics

Article Title: Validation of the new EPIC DNA methylation microarray (900K EPIC v2) for high-throughput profiling of the human DNA methylome

doi: 10.1080/15592294.2023.2185742

Figure Lengend Snippet: Unsupervised hierarchical analysis of methylation profiles of blood and lung sample revealed by the MethylationEPIC v1.0 (850K) and v2.0 (900K) BeadChip microarrays. ( a ) Unsupervised hierarchical analysis and heatmap from the 21 haematological samples hybridized in the 850K (left) and 900K (right) microarrays. Colors indicate whether the sample is from primary tissue (normal or tumoural) and the tissue type, as described in the legend of the heatmap. Methylation β-values range from 0 (green) to 1 (red). ( b ) Dendrogram comparison of 21 haematological samples hybridized in the 850K and 900K microarrays. Bold and coloured branches and lines between dendrograms indicate subtrees common to the two microarrays. Distinct edges to the 850K and 900K microarray dendrograms are shown as dashed branches. ( c ) Unsupervised hierarchical analysis and heatmap from the 15 lung samples hybridized in the 850K (left) and 900K (right) microarrays. Colors indicate whether the sample is from primary tissue (normal or tumoural) and the tissue type, as described in the legend of the heatmap. Methylation β-values range from 0 (green) to 1 (red). ( d ) Dendrogram comparison of 15 lung samples hybridized in the 850K and 900K microarrays. Bold and coloured branches and lines between dendrograms indicate subtrees common to the two microarrays. Distinct edges to the 850K and 900K microarray dendrograms are shown as dashed branches.

Article Snippet: The recently developed MethylationEPIC BeadChip Infinium microarray v2.0 (900K) annotated to the most recent version of the human genome (GRCh38/h38).

Techniques: Methylation, Comparison, Microarray

Journal: Molecular Neurobiology

Article Title: MicroRNA Expression Signatures Determine Prognosis and Survival in Glioblastoma Multiforme—a Systematic Overview

doi: 10.1007/s12035-014-8668-y

Figure Lengend Snippet: The biogenesis of miRNA requires RNA polymerase II/III for the transcription of pri-miRNA. The pri-miRNA product is then cleaved by the Drosha-DGCR8 complex into pre-miRNA. The pre-miRNA is exported to the cytoplasm by Exportin-5 in the presence of Ran-GTP co-factor. Once in the cytoplasm, the pre-miRNA is cleaved by the Dicer-TRBP complex into a miRNA duplex, which is unwound into two products: a guide strand bound to Ago2, which is incorporated into the RISC, and a passenger strand, which is degraded. Finally, the miRNA binds to its target mRNAs resulting in mRNA target cleavage, translational repression, or mRNA decay. A more novel fate of the miRNAs is the selective secretion via microvesicles or exosomes. Ran = Ras-related nuclear protein; GTP = guanosine-5′-triphosphate; TRBP = TAR (HIV-1) RNA binding protein; Ago2 = Argonaute protein 2; RISC = RNA-induced silencing complex

Article Snippet: However, four studies used the Chinese Glioma Genome Atlas (CGGA) ( http://www.cgga.org.cn ), which uses the Illumina Human v2.0 miRNA Expression BeadChip microarray platform [ , – ].

Techniques: RNA Binding Assay

Journal: Molecular Neurobiology

Article Title: MicroRNA Expression Signatures Determine Prognosis and Survival in Glioblastoma Multiforme—a Systematic Overview

doi: 10.1007/s12035-014-8668-y

Figure Lengend Snippet: Studies performed on dataset obtained from public databases

Article Snippet: However, four studies used the Chinese Glioma Genome Atlas (CGGA) ( http://www.cgga.org.cn ), which uses the Illumina Human v2.0 miRNA Expression BeadChip microarray platform [ , – ].

Techniques: Biomarker Discovery, In Vitro, Cell Culture, Activity Assay, Standard Deviation, Expressing, Software, Mutagenesis, Amplification

Journal: Molecular Neurobiology

Article Title: MicroRNA Expression Signatures Determine Prognosis and Survival in Glioblastoma Multiforme—a Systematic Overview

doi: 10.1007/s12035-014-8668-y

Figure Lengend Snippet: Studies performed on independent tissue cohorts

Article Snippet: However, four studies used the Chinese Glioma Genome Atlas (CGGA) ( http://www.cgga.org.cn ), which uses the Illumina Human v2.0 miRNA Expression BeadChip microarray platform [ , – ].

Techniques: Control, Biomarker Discovery, In Situ Hybridization, In Vitro, In Situ, Methylation, Expressing, Invasion Assay, Transfection, Amplification, Migration, Luciferase, Transwell Assay, Wound Healing Assay

Journal: Molecular Neurobiology

Article Title: MicroRNA Expression Signatures Determine Prognosis and Survival in Glioblastoma Multiforme—a Systematic Overview

doi: 10.1007/s12035-014-8668-y

Figure Lengend Snippet: miRNAs reported to be protective or risk-associated

Article Snippet: However, four studies used the Chinese Glioma Genome Atlas (CGGA) ( http://www.cgga.org.cn ), which uses the Illumina Human v2.0 miRNA Expression BeadChip microarray platform [ , – ].

Techniques: Expressing

Journal: Molecular Neurobiology

Article Title: MicroRNA Expression Signatures Determine Prognosis and Survival in Glioblastoma Multiforme—a Systematic Overview

doi: 10.1007/s12035-014-8668-y

Figure Lengend Snippet: miRNA signatures correlating with survival in GBM

Article Snippet: However, four studies used the Chinese Glioma Genome Atlas (CGGA) ( http://www.cgga.org.cn ), which uses the Illumina Human v2.0 miRNA Expression BeadChip microarray platform [ , – ].

Techniques:

Journal: Neuro-Oncology

Article Title: Validation and next-generation update of a DNA methylation–based recurrence predictor for meningioma: A multicenter prospective study

doi: 10.1093/neuonc/noae236

Figure Lengend Snippet: Representative MRI images of 2 sphenoid wing meningiomas in 2 different patients preoperatively, postoperatively following gross total resection in both cases, and at last radiographic follow-up prior to tumor recurrence in Case 1 and interval stability in Case 2. Both cases were clinically graded as WHO grade 2, with mitoses exceeding 4 per 10 high-powered fields, MIB1 of 10-15%, and nearly identical other histopathological features including the presence of hypercellularity, necrosis, sheeting, and prominent nucleoli without brain invasion. The estimated 5-year risk of recurrence for Case 1 was 0.995, whereas for Case 2 the probabilistic risk of recurrence was 0.467 based on its DNA methylation profile alone, agnostic to any clinical features. Notably, when combined with Simpson grade and WHO grade, our molecular nomogram estimates a 4% probability of 5-year recurrence-free survival in Case 1 (therefore a recurrence probability of 96%) and 49% probability of 5-year recurrence free survival in case 2 (therefore a 5-year recurrence probability of 51%), further suggesting that Case 1 is particularly high risk compared with Case 2.

Article Snippet: The aims of this next-generation model were (1) to generate a prognostic DNA methylation–based model that could be cross-compatible with both current generations of Illumina EPIC DNA methylation arrays (850K and v2.0), (2) to utilize a few probes/features as possible for the model in order to move toward translatability using other microarray technology, and (3) to outperform standard-of-care WHO grading.

Techniques: DNA Methylation Assay

Journal: Neuro-Oncology

Article Title: Validation and next-generation update of a DNA methylation–based recurrence predictor for meningioma: A multicenter prospective study

doi: 10.1093/neuonc/noae236

Figure Lengend Snippet: DNA methylation profiling identifies high-risk meningiomas among cases that would traditionally be considered “low risk.” (A) PFS outcomes among WHO grade 1 meningiomas stratified by extent of resection (EOR). This demonstrates that DNA methylation identifies high-risk cases regardless of EOR, even among completely resected WHO grade 1 tumors which are traditionally considered to be cured. (B) PFS outcomes among completely resected WHO grade 2 cases, a cohort associated with significant clinical equipoise, in both the prospective cohort and external grade 2 cohort.

Article Snippet: The aims of this next-generation model were (1) to generate a prognostic DNA methylation–based model that could be cross-compatible with both current generations of Illumina EPIC DNA methylation arrays (850K and v2.0), (2) to utilize a few probes/features as possible for the model in order to move toward translatability using other microarray technology, and (3) to outperform standard-of-care WHO grading.

Techniques: DNA Methylation Assay

Journal: International Journal of Molecular Sciences

Article Title: Non-Coding RNAs in Saliva: Emerging Biomarkers for Molecular Diagnostics

doi: 10.3390/ijms16048676

Figure Lengend Snippet: Salivary ncRNAs as disease-related molecular markers.

Article Snippet: [ ] , Patel et al ., Arch Oral Biol. 2011 , WS , characterization , 20 healthy donors , TaqMan1 Low Density Array Card (TLDA) Human miRNA Panel v2.0 (Applied Biosystems) , miR-223, miR-191, miR-16, miR-203, and miR-24.

Techniques: TaqMan microRNA Assay, Expressing, Methylation, Microarray, Electrophoresis

Journal: Communications Biology

Article Title: The early-life exposome modulates the effect of polymorphic inversions on DNA methylation

doi: 10.1038/s42003-022-03380-2

Figure Lengend Snippet: The first column in the plot panel corresponds to inv-8p23.1, the second to inv-16p11.2, and the third to inv-17q21.31. a – c Manhattan plots for the significance of the associations between the differential methylation of the CpG sites and the inversion genotypes in child blood cells ( N = 1009). The x axes show the chromosome position (±1 Mb between the inversions’ breakpoints). The y axes show the –log 10 ( P -value). The dashed red line indicates Bonferroni’s threshold of significance. Green points are CpG sites with significant associations and those in gray are nonsignificant. The orange block illustrates the inversions’ region. d – f Principal component (PC) analysis for methylation levels of CpG sites within and surrounding the inversions, revealing remarkably distinctive methylation patterns among the different inversion statuses. Blue points illustrate noninverted homozygous (N/N), yellow illustrates heterozygous (N/I), and orange illustrates inverted homozygous (I/I) individuals. In parenthesis, the methylation variance explained by each PC. g – i Manhattan plots of differentially methylated CpG sites, depending on the inversion genotypes in fetal heart DNA ( N = 40).

Article Snippet: For these same children, multi-omics molecular phenotyping was performed, including measurement of blood DNA methylation (450 K, Illumina), blood gene expression (HTA v2.0, Affymetrix), blood miRNA expression (SurePrint Human miRNA rel 21, Agilent), plasma proteins (Luminex), serum metabolites (AbsoluteIDQ p180 kit, Biocrates), urinary metabolites ( 1 H NMR spectroscopy), and DNA microarray (Chemagen kit, Perkin Elmer).

Techniques: Methylation, Blocking Assay

Journal: Database: The Journal of Biological Databases and Curation

Article Title: Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer

doi: 10.1093/database/baz115

Figure Lengend Snippet: A list of CellMiner datasets with their description

Article Snippet: DNA CNV-combined aCGH , Probe intensities combined from four platforms: agilent human genome CGH Microarray 44A, Nimblegen HG19 CGH 385 K WG Tiling v2.0, Affymetrix GeneChip human mapping 500 k array set and Illumina Human1Mv1_C Beadchip.

Techniques: Microarray, Methylation, Expressing, RNA Expression, Quantitative RT-PCR, Amplification, SYBR Green Assay, Sulforhodamine B Assay

Journal: Clinical Epigenetics

Article Title: Combined inhibition of histone deacetylase and cytidine deaminase improves epigenetic potency of decitabine in colorectal adenocarcinomas

doi: 10.1186/s13148-023-01500-1

Figure Lengend Snippet: Human chromosomal maps of decitabine and PBA responsive genes. A Chromosomal locations of up- and downregulated genes following decitabine ( A1 ), PBA ( A2 ) and the combined drug treatment ( A3 ). The histograms provide a quantitative account of the number of responsive genes on each chromosome. B Regulation of the lncRNA XIST and its target genes. Based on the lncRNA–mRNA interaction resource starBase v2.0 and LncRRIsearch, we identified NDRG1 and SEMA6A as target of XIST ( B1 ). B2 The gene expression of XIST, NDRG1 and SEMA6A is significantly repressed in COAD tumor samples when compared to histologically proven adjacent normal tissue. The data refer to 275 patients retrieved from the TCGA public repository. B3 NDRG1 and SEMA6A are hyper-methylated in COAD tumor samples when compared to histologically proven adjacent normal tissue ( B3 ). B4 Regulation of XIST , NDRG1 and SEMA6A in Caco-2 cells following drug treatment. XIST gene expression is highly dependent on the combined decitabine/PBA treatment, whereas NDRG1 and SEMA6A responded to single PBA treatment. B5 Kaplan–Meier survival plots for XIST and SEMA6 in low- and high-expression COAD patients. We retrieved the gene expression data of 275 COAD patients from the TCGA public repository, and although not statistically significant, the data imply better survival in high-expression individuals. C Drug-responsive tumor-suppressor genes and anti-apoptosis genes are linked to chromosomal hotspots of COAD patients

Article Snippet: Based on metal-induced hydrolysis we obtained fragmented cRNA, which we hybridized onto the Affymetrix Gene chip HG-U133 version 2.0 array (human).

Techniques: Expressing, Methylation