High density DNA methylation array with single CpG site resolution.

By M. Bibikova, B. Barnes, C. Tsan, Vincent Ho, Brandy Klotzle, Jennie M. Le, David Delano, Lu Zhang, Gary P. Schroth, Kevin L. Gunderson and 2 more. Genomics, 2011

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We have developed a new generation of genome-wide DNA methylation BeadChip which allows high-throughput methylation profiling of the human genome. The new high density BeadChip can assay over 480K CpG sites and analyze twelve samples in parallel. The innovative content includes coverage of 99% of RefSeq genes with multiple probes per gene, 96% of CpG islands from the UCSC database, CpG island shores and additional content selected from whole-genome bisulfite sequencing data and input from DNA methylation experts. The well-characterized Infinium® Assay is used for analysis of CpG methylation using bisulfite-converted genomic DNA. We applied this technology to analyze DNA methylation in normal and tumor DNA samples and compared results with whole-genome bisulfite sequencing (WGBS) data obtained for the same samples. Highly comparable DNA methylation profiles were generated by the array and sequencing methods (average R2 of 0.95). The ability to determine genome-wide methylation patterns will rapidly advance methylation research.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b86d7c1cdc1533182fd76eb45af1e0dc5d081dac

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Citations in the corpus

RnBeads 2.0: comprehensive analysis of DNA methylation data (2019, methodology): “Finally, the microarray-based Infinium DNA methylation assays—including the MethylationEPIC BeadChip (EPIC) and its predecessor, the HumanMethylation450 BeadChip (450k)—facilitate standardized, high-throughput DNA methylation profiling of a pre-defined subset of CpGs in large sample cohorts [11, 12]”
Comprehensive molecular characterization of gastric adenocarcinoma (2014, positive): “2 (7) FGFR2 (1) CD44 (7) CCND1(7) KRAS (2) MDM2 (14) 13q22.”
eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data (2016, methodology): “The 450k array Illumina annotation (Bibikova et al., 2011) was used to create these data categories (Tables S1 and S2).”
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data (2012, methodology): “A key statistical issue with the Illumina 450k beadchip is that probes come in two different designs, which causes the methylation values derived from these two designs to exhibit widely different distributions (Dedeurwaerder et al., 2011).”
Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. (2018, methodology): “DNA Methylation Sample Preparation and Hybridization The Illumina Infinium HM450 array (Bibikova et al., 2011) was used with standard protocols.”
SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips (2012, background): “[20] demonstrated that the Infinium II probes could have up to three CpG sites underlying their 50 bp probe body without affecting data quality.”
Distinct DNA methylomes of newborns and centenarians (2012, methodology): “We used a newly developed DNA methylation microarray that assays the DNA methylation status of 450,000 CpG sites (28, 29).”
Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases (2016, methodology): “The 450K chip offers accurate and reproducible performance (Bibikova et al., 2011; Sandoval et al., 2011) with known but adjustable bias between Infinium I and II assays (Dedeurwaerder et al., 2011).”
Analysing and interpreting DNA methylation data (2012, methodology): “The genomic coverage of the Infinium assay is more limited than that of most bisulphite‑sequencing protocols (1.5% of CpGs in the human genome are present on the Infinium 450k micro‑ array), but the compatibility with existing genotyping pipelines makes it an attractive assay for measuring DNA methy”
A data-driven approach to preprocessing Illumina 450K methylation array data (2013, methodology): “The 450K BeadChip [2,3] achieves increased coverage by utilising two different probe types on each array: Infinium I (n=135,501) and Infinium II (n=350,076) probes.”