Home LiteratureArticle Details
PMID: 16449502 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

High-throughput DNA methylation profiling using universal bead arrays.

Genome research ·Vol. 16 ·No. 3 ·2006-03-00 ·Pages 383-93

Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, Wu B, Doucet D, Thomas NJ, Wang Y, Vollmer E, Goldmann T, Seifart C, Jiang W, Barker DL, Chee MS, Floros J, Fan JB

Abstract

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.

MeSH Terms
Base Sequence Chromosomes, Human, X/metabolism CpG Islands/genetics DNA Fingerprinting DNA Methylation Gene Expression Regulation, Neoplastic Humans Lung Neoplasms/genetics Molecular Sequence Data Oligonucleotide Array Sequence Analysis/methods Polymorphism, Single Nucleotide Reproducibility of Results Sulfites/metabolism
Chemicals
Sulfites hydrogen sulfite
Authors & Affiliations
17 authors, click to expand affiliations / ORCID
Bibikova Marina
Illumina, Inc., San Diego, California 92121, USA.
Lin Zhenwu
Zhou Lixin
Chudin Eugene
Garcia Eliza Wickham
Wu Bonnie
Doucet Dennis
Thomas Neal J
Wang Yunhua
Vollmer Ekkehard
Goldmann Torsten
Seifart Carola
Jiang Wei
Barker David L
Chee Mark S
Floros Joanna
Fan Jian-Bing
References (54)
54 references, click to expand
  1. The genetics and genomics of cancer.
    Nat Genet. 2003 Mar;33 Suppl:238-44 PMID: 12610533
  2. DNA Methylation Database "MethDB": a user guide.
    J Nutr. 2002 Aug;132(8 Suppl):2435S-2439S PMID: 12163707
  3. A systematic profile of DNA methylation in human cancer cell lines.
    Cancer Res. 2003 Mar 1;63(5):1114-21 PMID: 12615730
  4. Loss of IGF2 imprinting: a potential marker of colorectal cancer risk.
    Science. 2003 Mar 14;299(5613):1753-5 PMID: 12637750
  5. Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry.
    Nucleic Acids Res. 2003 May 1;31(9):e50 PMID: 12711695
  6. Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes.
    Am J Pathol. 2003 Jul;163(1):37-45 PMID: 12819009
  7. Automatic registration of microarray images. II. Hexagonal grid.
    Bioinformatics. 2003 Sep 22;19(14):1832-6 PMID: 14512355
  8. Gene silencing in cancer in association with promoter hypermethylation.
    N Engl J Med. 2003 Nov 20;349(21):2042-54 PMID: 14627790
  9. Transcriptional silencing of the RUNX3 gene by CpG hypermethylation is associated with lung cancer.
    Biochem Biophys Res Commun. 2004 Jan 30;314(1):223-8 PMID: 14715269
  10. A real-time PCR assay for DNA-methylation using methylation-specific blockers.
    Nucleic Acids Res. 2004;32(1):e10 PMID: 14722226
  11. The history of cancer epigenetics.
    Nat Rev Cancer. 2004 Feb;4(2):143-53 PMID: 14732866
  12. Methylation status of TP73 in meningiomas.
    Cancer Genet Cytogenet. 2004 Jan 15;148(2):148-51 PMID: 14734228
  13. Methylation status and expression of human telomerase reverse transcriptase in ovarian and cervical cancer.
    Gynecol Oncol. 2004 May;93(2):407-16 PMID: 15099954
  14. Decoding randomly ordered DNA arrays.
    Genome Res. 2004 May;14(5):870-7 PMID: 15078854
  15. Epigenetics in human disease and prospects for epigenetic therapy.
    Nature. 2004 May 27;429(6990):457-63 PMID: 15164071
  16. Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen.
    Cancer Res. 2004 Jun 1;64(11):3807-13 PMID: 15172987
  17. Epigenetic regulation of human telomerase reverse transcriptase promoter activity during cellular differentiation.
    Genes Chromosomes Cancer. 2004 Sep;41(1):26-37 PMID: 15236314
  18. Prevalent hyper-methylation of the CDH13 gene promoter in malignant B cell lymphomas.
    Int J Oncol. 2004 Sep;25(3):685-91 PMID: 15289870
  19. Clustering of gene hypermethylation associated with clinical risk groups in neuroblastoma.
    J Natl Cancer Inst. 2004 Aug 18;96(16):1208-19 PMID: 15316056
  20. Highly parallel SNP genotyping.
    Cold Spring Harb Symp Quant Biol. 2003;68:69-78 PMID: 15338605
  21. De novo quantitative bisulfite sequencing using the pyrosequencing technology.
    Anal Biochem. 2004 Oct 1;333(1):119-27 PMID: 15351288
  22. A quantitative HpaII-PCR assay to measure methylation of DNA from a small number of cells.
    Nucleic Acids Res. 1990 Feb 11;18(3):687 PMID: 1689825
  23. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
    Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1827-31 PMID: 1542678
  24. bcl-2 gene hypomethylation and high-level expression in B-cell chronic lymphocytic leukemia.
    Blood. 1993 Sep 15;82(6):1820-8 PMID: 8104532
  25. Role for DNA methylation in genomic imprinting.
    Nature. 1993 Nov 25;366(6453):362-5 PMID: 8247133
  26. Comparison of DNA methylation patterns among mouse cell lines by restriction landmark genomic scanning.
    Mol Cell Biol. 1994 Nov;14(11):7421-7 PMID: 7935456
  27. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands.
    Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9821-6 PMID: 8790415
  28. The role of DNA methylation in cancer genetic and epigenetics.
    Annu Rev Genet. 1996;30:441-64 PMID: 8982461
  29. Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE).
    Nucleic Acids Res. 1997 Jun 15;25(12):2529-31 PMID: 9171109
  30. Restriction landmark genomic scanning (RLGS-M)-based genome-wide scanning of mouse liver tumors for alterations in DNA methylation status.
    Cancer Res. 1997 Aug 1;57(15):3294-9 PMID: 9242463
  31. Gene silencing. Methylation meets acetylation.
    Nature. 1998 May 28;393(6683):311-2 PMID: 9620794
  32. CpG methylation, chromatin structure and gene silencing-a three-way connection.
    EMBO J. 1998 Sep 1;17(17):4905-8 PMID: 9724627
  33. Methylation profiling of CpG islands in human breast cancer cells.
    Hum Mol Genet. 1999 Mar;8(3):459-70 PMID: 9949205
  34. Cancer epigenetics comes of age.
    Nat Genet. 1999 Feb;21(2):163-7 PMID: 9988266
  35. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.
    PLoS Biol. 2004 Dec;2(12):e405 PMID: 15550986
  36. X-inactivation profile reveals extensive variability in X-linked gene expression in females.
    Nature. 2005 Mar 17;434(7031):400-4 PMID: 15772666
  37. Loss of imprinting of Igf2 alters intestinal maturation and tumorigenesis in mice.
    Science. 2005 Mar 25;307(5717):1976-8 PMID: 15731405
  38. Association of DNA methylation of phosphoserine aminotransferase with response to endocrine therapy in patients with recurrent breast cancer.
    Cancer Res. 2005 May 15;65(10):4101-17 PMID: 15899800
  39. MSRE-PCR for analysis of gene-specific DNA methylation.
    Nucleic Acids Res. 2005;33(10):e93 PMID: 15944447
  40. A novel real-time PCR assay for quantitative analysis of methylated alleles (QAMA): analysis of the retinoblastoma locus.
    Nucleic Acids Res. 2004;32(16):e125 PMID: 15353561
  41. Epistatic interaction between beta2-adrenergic receptor and neuropeptide Y genes influences LDL-cholesterol in hypertension.
    Hypertension. 2004 Nov;44(5):689-94 PMID: 15364898
  42. Comparison of bisulfite modification of 5-methyldeoxycytidine and deoxycytidine residues.
    Nucleic Acids Res. 1980 Oct 24;8(20):4777-90 PMID: 7443525
  43. Hypomethylation distinguishes genes of some human cancers from their normal counterparts.
    Nature. 1983 Jan 6;301(5895):89-92 PMID: 6185846
  44. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns.
    Nat Genet. 2000 Feb;24(2):132-8 PMID: 10655057
  45. DNA hypermethylation in tumorigenesis: epigenetics joins genetics.
    Trends Genet. 2000 Apr;16(4):168-74 PMID: 10729832
  46. MethyLight: a high-throughput assay to measure DNA methylation.
    Nucleic Acids Res. 2000 Apr 15;28(8):E32 PMID: 10734209
  47. Loss of expression and aberrant methylation of the CDH13 (H-cadherin) gene in breast and lung carcinomas.
    Cancer Res. 2001 Jun 1;61(11):4556-60 PMID: 11389090
  48. Cytosine methylation represses glutathione S-transferase P1 (GSTP1) gene expression in human prostate cancer cells.
    Cancer Res. 2001 Jun 15;61(12):4820-6 PMID: 11406558
  49. DNA methylation patterns and epigenetic memory.
    Genes Dev. 2002 Jan 1;16(1):6-21 PMID: 11782440
  50. Tumour class prediction and discovery by microarray-based DNA methylation analysis.
    Nucleic Acids Res. 2002 Mar 1;30(5):e21 PMID: 11861926
  51. The fundamental role of epigenetic events in cancer.
    Nat Rev Genet. 2002 Jun;3(6):415-28 PMID: 12042769
  52. CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future.
    Oncogene. 2002 Aug 12;21(35):5427-40 PMID: 12154405
  53. DNA methylation analysis: a powerful new tool for lung cancer diagnosis.
    Oncogene. 2002 Aug 12;21(35):5450-61 PMID: 12154407
  54. Epigenetics and disease: Altered states.
    Nature. 2003 Feb 13;421(6924):686-8 PMID: 12610592
Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.4410706
Published
2006-03-00
Epub
2006-00-31
Pages
383-93
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC1415217
Subset
IM
Grants
NCI NIH HHS · R44 CA097851 · United States
NCI NIH HHS · 2 R44 CA097851-02 · United States
PHS HHS · R37 NL-34788 · United States
External Links
PubMed source DOI: 10.1101/gr.4410706 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2