infinium® humanmethylation 450k bead chip  (INFINIUM Inc)

Journal: Children

Article Title: The Epigenetic Role of Nutrition Among Children and Adolescents: A Systematic Literature Review

doi: 10.3390/children12020143

Figure Lengend Snippet: Descriptive characteristics of the eligible studies.

Article Snippet: Chen et al. (2018) [ ] , Cross-sectional , African American adolescents (n = 284) , Illumina 450K Bead-Chip. Structured 24-h food surveys , Dietary Fiber Intake , The methylation levels of 3 CpG sites (cg15200711, cg19462022, and cg07035602) in LPCAT1 and RASA3 genes were correlated with fiber intake (FDR < 0.05). The methylation levels of cg07035602 and cg19462022 correlated with visceral adiposity and inflammation..

Techniques: Methylation, Western Blot, DNA Methylation Assay, Multiplex Assay, Mass Spectrometry, Formulation, Genome Wide, Expressing, Metabolic Labelling, Activity Assay

Journal: Epigenomics

Article Title: Differentially methylated regions interrogated for metastable epialleles associate with offspring adiposity

doi: 10.1080/17501911.2024.2359365

Figure Lengend Snippet: Metastable epiallele interrogation on the Illumina 450K and in Cord Blood by Literature Source. Selection of MEs was based upon the following literature sources [ , , ]. ME: Metastable epiallele.

Article Snippet: The use of the lllumina 450K Human Methylation Bead Chip array platform significantly limited our interrogation of MEs reported in the literature and the proximity of the DMRs to MEs identified using the Illumina 450K is inherently dependent upon the array alignment, which is predetermined by the manufacturer.

Techniques: Selection

Journal: Gastro Hep Advances

Article Title: Promoter Methylation Leads to Hepatocyte Nuclear Factor 4A Loss and Pancreatic Cancer Aggressiveness

doi: 10.1016/j.gastha.2024.04.005

Figure Lengend Snippet: HNF4A is methylated and suppressed in pancreatic cancer. (A) Global DNA methylation analysis (Illumina Human Methylation 450K array) in 20 human pancreatic cancer and 11 normal tissues (Stanford University Medical Center, USA). Heatmap of methylation beta values for the top 7242 differentially regulated loci in cancer vs control ( P < .05, FC ≥ 1.5). (B) Venn diagram showing 2717 unique methylation sites identified in our study. (C) Heatmap of methylation beta values across the HNF4A locus. The HNF4A promoter area with increased DNA methylation (high beta values) corresponds to probes covering the proximal promoter area (from −200 nt to −3 nt, TSS200). (D) HNF4A expression as assessed by RT-qPCR, in pancreatic cancer and control tissues. Expression was normalized to GAPDH and β-actin levels and results were expressed as mean ± SEM compared to control tissues (set as 1). (E) Immunohistochemical analysis for HNF4A in normal (N) and pancreatic cancer tissues (red, HNF4A; blue, nuclei staining). Scale bar: 1 mm and 100 μm (left and right panel, respectively).

Article Snippet: We employed the Illumina Human Methylation 450K bead chip, in 20 human pancreatic cancer and 11 uninvolved tissues.

Techniques: Methylation, DNA Methylation Assay, Control, Expressing, Quantitative RT-PCR, Immunohistochemical staining, Staining

Journal: Clinical Epigenetics

Article Title: Predictive value of DNA methylation patterns in AML patients treated with an azacytidine containing induction regimen

doi: 10.1186/s13148-023-01580-z

Figure Lengend Snippet: Analysis overview. A Overview of analysis steps based on DNA isolated from mononuclear cells from each pretreatment bone marrow aspirate from a subset of 155 AML samples derived from the AMLSG 12-09 trial. Global, genome-wide methylation status of a training set was analysed via MCIp followed by NGS-analysis on the HiSeq 2k platform. Differentially methylated regions were derived and ranked according to p -values and effect size. Methylation levels within a set of top regions were validated via 450k analysis at single CpG resolution and used to generate a classifier. B The validation cohort consisted of an independent subset of patients derived from the AMLSG 12-09 collective. Methylation status of the classifier contained CpGs was analysed via MassARRAY assay and used for validation. CR was defined as non-detectability of evidence for disease both cytomorphologically and via immunophenotyping in peripheral blood smear and bone marrow aspirate as well as via molecular genetics. AML acute myeloid leukemia; DMR differentially methylated regions; MCIp methyl-CpG immunoprecipitation; HiSeq 2k the HiSeq next-generation sequencing platform; NGS next generation sequencing; 450k Infinium® HumanMethylation450 Bead Chip; MassARRAY a benchtop multiplex genetic analyzer utilizing Matrix assisted laser desorption/ionization; time-of-flight mass spectrometry; std standard therapy arm; exp experimental therapy arm; CR complete response; RD refractory disease

Article Snippet: Quantitative DNA methylation assessment was performed with the Infinium® HumanMethylation 450k Bead Chip for comprehensive genome-wide coverage of methylation data as described previously [ ].

Techniques: Isolation, Derivative Assay, Genome Wide, Methylation, Biomarker Discovery, Immunoprecipitation, Next-Generation Sequencing, Multiplex Assay, Mass Spectrometry

Journal: Clinical Epigenetics

Article Title: Predictive value of DNA methylation patterns in AML patients treated with an azacytidine containing induction regimen

doi: 10.1186/s13148-023-01580-z

Figure Lengend Snippet: Technical Validation of Differentially Methylated Regions. A Selection of EdgeR-based testing results for differential methylation between responders and non-responders both in EXT and STD arm, prior to validation. B Validation criteria are exemplarily illustrated for the 500 bp region assigned to WNT10A and its corresponding probe cg22587479. For this probe, a strong and distinct correlation between beta values and RPKM exists (Spearman’s rank correlation coefficient > 0.8). Differences in beta regression levels between resp. and non-resp. patients showed statistical significance and overall methylation differences showed congruency in the change between modalities, i.e. hypermethylation in patients with refractory disease both in the MCIp-seq and 450k assay. CR Complete Response; RD Refractory Disease; RPKM Reads per kilobase per million mapped reads

Article Snippet: Quantitative DNA methylation assessment was performed with the Infinium® HumanMethylation 450k Bead Chip for comprehensive genome-wide coverage of methylation data as described previously [ ].

Techniques: Biomarker Discovery, Methylation, Selection