Epic 850k beadchip

Manufactured by Illumina

Sourced in United States

The EPIC/850k BeadChip is a high-density microarray platform designed for genome-wide DNA methylation analysis. It provides comprehensive coverage of CpG sites across the human genome, allowing for the interrogation of DNA methylation patterns at a large scale.

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Lab products found in correlation

Infinium 450k beadchip, by Illumina (2 mentions) Infinium humanmethylation450 450k beadchip, by Illumina (2 mentions) Maxwell 16 ffpe plus lev dna kit, by Promega (1 mentions) Maxwell 16 tissue dna purification kit, by Promega (1 mentions) Infinium humanmethylation450k beadchip, by Illumina (1 mentions)

Close spelling variants of this product

BeadChips (68 citations) EPIC BeadChip (27 citations) Infinium EPIC 850k Human DNA Methylation BeadChips (4 citations) Infinium Human Methylation EPIC 850K BeadChip (3 citations) Methylation EPIC 850k Beadchip (3 citations) Infinium Methylation EPIC BeadChip (850k) array (2 citations) Infinium Methylation 850K/EPIC BeadChip arrays (2 citations) Infinium CytoSNP-850K v1.2 BeadChip array (EPIC 850 K array) (2 citations)

5 protocols using epic 850k beadchip

DNA Methylation Analysis of Tumors

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The tumors were subjected to Illumina Infinium 450 k BeadChip or the successor EPIC/850 k BeadChip (Illumina, San Diego, USA) analysis at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) Heidelberg. DNA-methylation data were normalized by performing background correction and dye bias correction (shifting of negative control probe mean intensity to zero and scaling of normalization control probe mean intensity to 20,000, respectively). Probes targeting sex chromosomes, probes containing multiple single nucleotide polymorphisms and those that could not be uniquely mapped were removed. Probes were excluded if the predecessor Illumina Infinium 450 k BeadChip did not cover them, thereby making data generated by both 450 k and EPIC comparable for subsequent analyses. In total, 438,370 probes were kept for analysis.

Koelsche C., Stichel D., Griewank K.G., Schrimpf D., Reuss D.E., Bewerunge-Hudler M., Vokuhl C., Dinjens W.N., Petersen I., Mittelbronn M., Cuevas-Bourdier A., Buslei R., Pfister S.M., Flucke U., Mechtersheimer G., Mentzel T, & von Deimling A. (2019). Genome-wide methylation profiling and copy number analysis in atypical fibroxanthomas and pleomorphic dermal sarcomas indicate a similar molecular phenotype. Clinical Sarcoma Research, 9, 2.

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Illumina DNA Methylation Profiling

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DNA was also analyzed using the Illumina Infinium HumanMethylation450 (450 k) BeadChip or the EPIC/850k BeadChip (Illumina, San Diego, USA) at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) in Heidelberg. DNA methylation data were normalized by applying background correction and dye bias correction (shifting of negative control probe mean intensity to zero and scaling of normalization control probe mean intensity to 20,000, respectively). Probes targeting sex chromosomes, probes containing multiple single nucleotide polymorphisms, and probes that could not be uniquely mapped were removed.

Kommoss F.K., Stichel D., Mora J., Esteller M., Jones D.T., Pfister S.M., Brack E., Wachtel M., Bode P.K., Sinn H.P., Schmidt D., Mentzel T., Kommoss F., Sahm F., von Deimling A, & Koelsche C. (2021). Clinicopathologic and molecular analysis of embryonal rhabdomyosarcoma of the genitourinary tract: evidence for a distinct DICER1-associated subgroup. Modern Pathology, 34(8), 1558-1569.

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Quantitative DNA Methylation Analysis

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Representative tumor tissue with highest available tumor content was chosen for DNA extraction. The Maxwell® 16 FFPE Plus LEV DNA Kit or the Maxwell® 16 Tissue DNA Purification Kit (for frozen tissue) was applied on the automated Maxwell device (Promega, Madison, WI, USA) according to the manufacturer’s instructions. All tumors had a total amount of >100 ng DNA and were suitable for the array-based DNA methylation analysis. All tumors were subjected to Illumina Infinium HumanMethylation450 (450k) BeadChip or the successor EPIC/850k BeadChip (Illumina, San Diego, USA) analysis at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) Heidelberg. DNA methylation data were normalized by performing background correction and dye bias correction (shifting of negative control probe mean intensity to zero and scaling of normalization control probe mean intensity to 20000, respectively). Probes targeting sex chromosomes, probes containing multiple single nucleotide polymorphisms and those that could not be uniquely mapped were removed. Probes from the EPIC array were excluded if the predecessor Illumina Infinium 450k BeadChip did not cover them, thereby making data generated by both 450k and EPIC feasible for subsequent analyses. In total, 438370 probes were kept for analysis.

Koelsche C., Kriegsmann M., Kommoss F.K., Stichel D., Kriegsmann K., Vokuhl C., Grünewald T.G., Romero-Pérez L., Kirchner T., de Alava E., Diaz-Martin J., Hartmann W., Baumhoer D., Antonescu C.R., Szuhai K., Flucke U., Dirksen U., Pfister S.M., Jones D.T., Mechtersheimer G, & von Deimling A. (2019). DNA methylation profiling distinguishes Ewing-like sarcoma with EWSR1-NFATc2 fusion from Ewing sarcoma. Journal of cancer research and clinical oncology, 145(5), 1273-1281.

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DNA Methylation Profiling with Illumina Arrays

Cited 3 times

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The DNA methylation profiling was based on the Illumina Infinium HumanMethylation450K BeadChip in the FHS and WHI cohort and was based on the Illumina Infinium EPIC 850K BeadChip in the JHS cohort. To ensure future use with EPIC arrays, we focused on the subset of 450,161 CpGs that were present on both platforms. We kept the original normalization methods to ensure consistency with previous publications. The WHI BA23 were normalized using the background correction method implemented in the software GenomeStudio. WHI EMPC were normalized based on BMIQ [57 (link)] for beta-mixture quantile normalization. The JHS data were normalized using the "noob" normalization method implemented in the minfi R package [58 (link),59 (link)].

Lu A.T., Seeboth A., Tsai P.C., Sun D., Quach A., Reiner A.P., Kooperberg C., Ferrucci L., Hou L., Baccarelli A.A., Li Y., Harris S.E., Corley J., Taylor A., Deary I.J., Stewart J.D., Whitsel E.A., Assimes T.L., Chen W., Li S., Mangino M., Bell J.T., Wilson J.G., Aviv A., Marioni R.E., Raj K, & Horvath S. (2019). DNA methylation-based estimator of telomere length. Aging (Albany NY), 11(16), 5895-5923.

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Genome-Wide Molecular Profiling

Cited 1 time

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DNA and RNA isolation, as well as whole-genome, whole-exome, and RNA sequencing, were performed as published previously.^{31 (link)} DNA methylation analysis using the EPIC (850k) BeadChip (Illumina, San Diego, USA) was performed as published previously.^{33 (link)}

Krausert S., Brabetz S., Mack N.L., Schmitt-Hoffner F., Schwalm B., Peterziel H., Mangang A., Holland-Letz T., Sieber L., Korshunov A., Oehme I., Jäger N., Witt O., Pfister S.M, & Kool M. (2022). Predictive modeling of resistance to SMO inhibition in a patient-derived orthotopic xenograft model of SHH medulloblastoma. Neuro-oncology Advances, 4(1), vdac026.

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