High density DNA methylation array with single CpG site resolution

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 Re...

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Veröffentlicht in:	Genomics (San Diego, Calif.) Jg. 98; H. 4; S. 288 - 295
Hauptverfasser:	Bibikova, Marina, Barnes, Bret, Tsan, Chan, Ho, Vincent, Klotzle, Brandy, Le, Jennie M., Delano, David, Zhang, Lu, Schroth, Gary P., Gunderson, Kevin L., Fan, Jian-Bing, Shen, Richard
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	United States Elsevier Inc 01.10.2011
Schlagworte:	Array chemistry CpG Islands CpG Islands - genetics DNA DNA Methylation Epigenetics Epigenomics experts Gene Expression Profiling genes genetics Genome, Human Genome-wide genomic islands Humans Infinium methods Methylation profiling Oligonucleotide Array Sequence Analysis Oligonucleotide Array Sequence Analysis - methods Sequence Analysis, DNA Sequence Analysis, DNA - methods Sulfites Sulfites - chemistry Array DNA methylation Epigenetics Genome-wide Infinium Methylation profiling
ISSN:	0888-7543, 1089-8646, 1089-8646
Online-Zugang:	Volltext
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Abstract	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. ► New-generation high-throughput DNA methylation platform provides a true genome-wide coverage of over 485K sites. ► Content selected with guidance of a Consortium comprised of 22 methylation experts from 19 institutions worldwide. ► Coverage distributed across gene regions, including promoter, 5' UTR, first exon, gene body and 3' UTR. ► Broad coverage includes CpG islands, regulatory and differentially methylated regions, DHS sites, non-CpG loci and other content. ► Methylation profiles highly correlated with whole-genome bisulfite sequencing data.
AbstractList	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. 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 registered 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. 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. ► New-generation high-throughput DNA methylation platform provides a true genome-wide coverage of over 485K sites. ► Content selected with guidance of a Consortium comprised of 22 methylation experts from 19 institutions worldwide. ► Coverage distributed across gene regions, including promoter, 5' UTR, first exon, gene body and 3' UTR. ► Broad coverage includes CpG islands, regulatory and differentially methylated regions, DHS sites, non-CpG loci and other content. ► Methylation profiles highly correlated with whole-genome bisulfite sequencing data. 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. 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.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.
Author	Fan, Jian-Bing Bibikova, Marina Shen, Richard Zhang, Lu Gunderson, Kevin L. Barnes, Bret Tsan, Chan Ho, Vincent Klotzle, Brandy Schroth, Gary P. Le, Jennie M. Delano, David
Author_xml	– sequence: 1 givenname: Marina surname: Bibikova fullname: Bibikova, Marina email: mbibikova@illumina.com – sequence: 2 givenname: Bret surname: Barnes fullname: Barnes, Bret – sequence: 3 givenname: Chan surname: Tsan fullname: Tsan, Chan – sequence: 4 givenname: Vincent surname: Ho fullname: Ho, Vincent – sequence: 5 givenname: Brandy surname: Klotzle fullname: Klotzle, Brandy – sequence: 6 givenname: Jennie M. surname: Le fullname: Le, Jennie M. – sequence: 7 givenname: David surname: Delano fullname: Delano, David – sequence: 8 givenname: Lu surname: Zhang fullname: Zhang, Lu – sequence: 9 givenname: Gary P. surname: Schroth fullname: Schroth, Gary P. – sequence: 10 givenname: Kevin L. surname: Gunderson fullname: Gunderson, Kevin L. – sequence: 11 givenname: Jian-Bing surname: Fan fullname: Fan, Jian-Bing – sequence: 12 givenname: Richard surname: Shen fullname: Shen, Richard
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/21839163$$D View this record in MEDLINE/PubMed
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ContentType	Journal Article
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Snippet	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...
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SubjectTerms	Array chemistry CpG Islands CpG Islands - genetics DNA DNA Methylation Epigenetics Epigenomics experts Gene Expression Profiling genes genetics Genome, Human Genome-wide genomic islands Humans Infinium methods Methylation profiling Oligonucleotide Array Sequence Analysis Oligonucleotide Array Sequence Analysis - methods Sequence Analysis, DNA Sequence Analysis, DNA - methods Sulfites Sulfites - chemistry
Title	High density DNA methylation array with single CpG site resolution
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