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infinium humanmethylation450 (450k) beadchip array-based platform  (Illumina Inc)


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    Illumina Inc infinium humanmethylation450 (450k) beadchip array-based platform
    Infinium Humanmethylation450 (450k) Beadchip Array Based Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/array-based+infinium+beadchip/illumina+arrays/pmc09514793-235-20-19
    Average 90 stars, based on 1 article reviews
    infinium humanmethylation450 (450k) beadchip array-based platform - by Bioz Stars, 2026-09
    90/100 stars

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    Methylation:

    Article Title: Genomic hypomethylation in cell-free DNA predicts responses to checkpoint blockade in lung and breast cancer.
    Article Snippet: .. Array-based tissue methylation profiling was performed by following the instructions of the Infinium MethylationEPIC BeadChIP Kit (Illumina, WG-317-1002). .. Briefly, 500 ng genomic DNA (gDNA) was used for bisulfite conversion using the EZ DNA methylation kit (Zymo Research, D5001).

    Article Title: Identification of cell-specific epigenetic patterns associated with chondroitin sulfate treatment response in an endemic arthritis, Kashin-Beck disease
    Article Snippet: .. The input methylation data were normalized based on the chromosome position of CpGs in Infinium HumanMethylation450 BeadChip array (Illumina, USA). ..

    Article Title: Construction and evaluation of in-house methylation-sensitive SNaPshot system and three classification prediction models for identifying the tissue origin of body fluid
    Article Snippet: .. We have previously identified eight novel body fluid-specific CpGs based on the Illumina Infinium Methylation EPIC BeadChip array to identify five kinds of body fluids, and verified the consistency of two genotyping results of the SNaPshot system and the pyrosequencing method. ..

    Article Title: Genomic hypomethylation in cell-free DNA predicts responses to checkpoint blockade in lung and breast cancer
    Article Snippet: .. Array-based tissue methylation profiling was performed by following the instructions of the Infinium MethylationEPIC BeadChIP Kit (Illumina, WG-317-1002). .. Briefly, 500 ng genomic DNA (gDNA) was used for bisulfite conversion using the EZ DNA methylation kit (Zymo Research, D5001).

    Derivative Assay:

    Article Title: A cis -regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs
    Article Snippet: .. SNP-array based copy number profiling and analysis of regions of homozygosity using the Infinium Human CytoSNP-850K v1.2 BeadChip (Illumina, San Diego, CA, USA) showed no undesired genomic abnormalities, except for LCLs derived from patient 3, which exhibited a possible low level mosaicism for trisomy 9 (∼10%) and a comparable percentage of mosaicism for a monosomy of chromosome X (∼10%). ..

    other:

    Article Title: A cis -regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs
    Article Snippet: SNP-array based copy number profiling and analysis of regions of homozygosity using the Infinium Human CytoSNP-850K v1.2 BeadChip (Illumina, San Diego, CA, USA) showed several genomic abnormalities in the Jurkat cell lines affecting multiple chromosomes, including a trisomy of chromosome 5.

    Article Title: Tailoring Genomic Selection for Bos taurus indicus : A Comprehensive Review of SNP Arrays and Reference Genomes
    Article Snippet: Another major advancement came in February 2012 with the launch of the GeneSeek Genomic Profiler (GGP) Indicus-specific array, based on the Illumina BovineLD genotyping BeadChip [ ].



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    Validation of the LIFR promoter methylation for cancer specificity and its relationship with the expression of associated genes. (A) DNA methylation levels of target CpGs in public cancer methylome data (Infinium 450K BeadChip array) of four cancer types: colorectal ( n = 313 for cancer samples and n = 38 for normal samples), liver (377 and 50), lung (843 and 74), and stomach (395 and 2) cancers. Infinium CpG identification numbers (IDs) together with the associated gene names are shown; the Infinium IDs cg03723506 and cg11291081 indicate chr5:38557143 and chr3:37033894, respectively, in the Figure . Statistical significance was calculated using Wilcoxon rank sum test. T: tumor samples, N: normal samples. (B) Schematic drawing of COBRA region at the LIFR promoter. Blue arrows, primers. CGI, CpG island (green line). (C) COBRA analysis. Genomic DNA was extracted from each colon cancer cell lines along with a normal control colon cell line (CCD-18co) and subjected to COBRA using the Taq I enzyme to examine the methylation state at the LIFR gene promoter. Arrowhead and arrow indicate the positions of intact and Taq I-digested DNA fragments, respectively. The fraction (% meth) of methylated DNA was measured by band intensity analysis and noted under each cell line. (D) RT-PCR. The same cancer cell lines used in COBRA (C) were subjected to RT-PCR to measure the transcript levels of the LIFR and LIFR-AS genes.

    Journal: Frontiers in Genetics

    Article Title: Simultaneous Methylation-Level Assessment of Hundreds of CpG Sites by Targeted Bisulfite PCR Sequencing (TBPseq)

    doi: 10.3389/fgene.2017.00097

    Figure Lengend Snippet: Validation of the LIFR promoter methylation for cancer specificity and its relationship with the expression of associated genes. (A) DNA methylation levels of target CpGs in public cancer methylome data (Infinium 450K BeadChip array) of four cancer types: colorectal ( n = 313 for cancer samples and n = 38 for normal samples), liver (377 and 50), lung (843 and 74), and stomach (395 and 2) cancers. Infinium CpG identification numbers (IDs) together with the associated gene names are shown; the Infinium IDs cg03723506 and cg11291081 indicate chr5:38557143 and chr3:37033894, respectively, in the Figure . Statistical significance was calculated using Wilcoxon rank sum test. T: tumor samples, N: normal samples. (B) Schematic drawing of COBRA region at the LIFR promoter. Blue arrows, primers. CGI, CpG island (green line). (C) COBRA analysis. Genomic DNA was extracted from each colon cancer cell lines along with a normal control colon cell line (CCD-18co) and subjected to COBRA using the Taq I enzyme to examine the methylation state at the LIFR gene promoter. Arrowhead and arrow indicate the positions of intact and Taq I-digested DNA fragments, respectively. The fraction (% meth) of methylated DNA was measured by band intensity analysis and noted under each cell line. (D) RT-PCR. The same cancer cell lines used in COBRA (C) were subjected to RT-PCR to measure the transcript levels of the LIFR and LIFR-AS genes.

    Article Snippet: The panel composition is highly flexible and can accommodate a variety of experimental designs, a big advantage over other methylation analysis platforms such as the array-based Infinium BeadChip.

    Techniques: Biomarker Discovery, Methylation, Expressing, DNA Methylation Assay, Combined Bisulfite Restriction Analysis Assay, Control, Reverse Transcription Polymerase Chain Reaction

    Potential processes leading to a genetically driven methylation site. Three potential processes can lead to an association of a genetic variant and a trimodal distribution of CpG methylation: (1) “Spillover from a neighboring CpG site” that is deleted by a SNP by processes of local methylation maintenance, (2) SNP-induced changes in gene expression activity may have a feedback effect on DNA methylation due to differences in the translation machinery that leaves methylation marks on the DNA, and (3) SNP-induced changes in gene function may induce different levels of gene expression that are implemented by changes in promoter gene methylation

    Journal: Clinical Epigenetics

    Article Title: Mendelian inheritance of trimodal CpG methylation sites suggests distal cis-acting genetic effects

    doi: 10.1186/s13148-016-0295-1

    Figure Lengend Snippet: Potential processes leading to a genetically driven methylation site. Three potential processes can lead to an association of a genetic variant and a trimodal distribution of CpG methylation: (1) “Spillover from a neighboring CpG site” that is deleted by a SNP by processes of local methylation maintenance, (2) SNP-induced changes in gene expression activity may have a feedback effect on DNA methylation due to differences in the translation machinery that leaves methylation marks on the DNA, and (3) SNP-induced changes in gene function may induce different levels of gene expression that are implemented by changes in promoter gene methylation

    Article Snippet: Array-based DNA methylation data (Infinium HumanMethylation 450 BeadChip platform [ ]) was obtained for these subjects.

    Techniques: Methylation, Variant Assay, CpG Methylation Assay, Expressing, Activity Assay, DNA Methylation Assay