High-throughput DNA methylation profiling using universal bead arrays. 2006

Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
Illumina, Inc., San Diego, California 92121, USA.

We have developed a high-throughput method for analyzing the methylation status of hundreds of preselected genes simultaneously and have applied it to the discovery of methylation signatures that distinguish normal from cancer tissue samples. Through an adaptation of the GoldenGate genotyping assay implemented on a BeadArray platform, the methylation state of 1536 specific CpG sites in 371 genes (one to nine CpG sites per gene) was measured in a single reaction by multiplexed genotyping of 200 ng of bisulfite-treated genomic DNA. The assay was used to obtain a quantitative measure of the methylation level at each CpG site. After validating the assay in cell lines and normal tissues, we analyzed a panel of lung cancer biopsy samples (N = 22) and identified a panel of methylation markers that distinguished lung adenocarcinomas from normal lung tissues with high specificity. These markers were validated in a second sample set (N = 24). These results demonstrate the effectiveness of the method for reliably profiling many CpG sites in parallel for the discovery of informative methylation markers. The technology should prove useful for DNA methylation analyses in large populations, with potential application to the classification and diagnosis of a broad range of cancers and other diseases.

UI MeSH Term Description Entries
D008175 Lung Neoplasms Tumors or cancer of the LUNG. Cancer of Lung,Lung Cancer,Pulmonary Cancer,Pulmonary Neoplasms,Cancer of the Lung,Neoplasms, Lung,Neoplasms, Pulmonary,Cancer, Lung,Cancer, Pulmonary,Cancers, Lung,Cancers, Pulmonary,Lung Cancers,Lung Neoplasm,Neoplasm, Lung,Neoplasm, Pulmonary,Pulmonary Cancers,Pulmonary Neoplasm
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D001483 Base Sequence The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D013447 Sulfites Inorganic salts of sulfurous acid. Sulfite,Sulfites, Inorganic,Inorganic Sulfites
D015203 Reproducibility of Results The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results. Reliability and Validity,Reliability of Result,Reproducibility Of Result,Reproducibility of Finding,Validity of Result,Validity of Results,Face Validity,Reliability (Epidemiology),Reliability of Results,Reproducibility of Findings,Test-Retest Reliability,Validity (Epidemiology),Finding Reproducibilities,Finding Reproducibility,Of Result, Reproducibility,Of Results, Reproducibility,Reliabilities, Test-Retest,Reliability, Test-Retest,Result Reliabilities,Result Reliability,Result Validities,Result Validity,Result, Reproducibility Of,Results, Reproducibility Of,Test Retest Reliability,Validity and Reliability,Validity, Face
D015972 Gene Expression Regulation, Neoplastic Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue. Neoplastic Gene Expression Regulation,Regulation of Gene Expression, Neoplastic,Regulation, Gene Expression, Neoplastic
D016172 DNA Fingerprinting A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population. DNA Fingerprints,DNA Profiling,DNA Typing,Genetic Fingerprinting,DNA Fingerprint,DNA Fingerprintings,DNA Profilings,DNA Typings,Fingerprint, DNA,Fingerprinting, DNA,Fingerprinting, Genetic,Fingerprintings, DNA,Fingerprintings, Genetic,Fingerprints, DNA,Genetic Fingerprintings,Profiling, DNA,Typing, DNA,Typings, DNA
D018899 CpG Islands Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes. CpG Clusters,CpG-Rich Islands,Cluster, CpG,Clusters, CpG,CpG Cluster,CpG Island,CpG Rich Islands,CpG-Rich Island,Island, CpG,Island, CpG-Rich,Islands, CpG,Islands, CpG-Rich
D019175 DNA Methylation Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor. DNA Methylations,Methylation, DNA,Methylations, DNA

Related Publications

Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
June 2005, Mutation research,
Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
October 2010, Oncology reports,
Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
January 2006, Methods in enzymology,
Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
November 2004, The American journal of pathology,
Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
September 2015, Langmuir : the ACS journal of surfaces and colloids,
Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
January 2012, Molecular ecology resources,
Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
December 2022, Nature communications,
Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
July 2001, Genome research,
Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
May 2008, Genome research,
Marina Bibikova, and Zhenwu Lin, and Lixin Zhou, and Eugene Chudin, and Eliza Wickham Garcia, and Bonnie Wu, and Dennis Doucet, and Neal J Thomas, and Yunhua Wang, and Ekkehard Vollmer, and Torsten Goldmann, and Carola Seifart, and Wei Jiang, and David L Barker, and Mark S Chee, and Joanna Floros, and Jian-Bing Fan
April 2010, Current protocols in human genetics,
Copied contents to your clipboard!