MS-qFRET: A quantum dot-based method for analysis of DNA methylation

Vasudev J. Bailey, Hariharan Easwaran, Yi Zhang, Elizabeth Griffiths, Steven A. Belinsky, James G. Herman, Stephen B Baylin, Hetty E. Carraway, Tza Huei Wang

Research output: Contribution to journalArticle

Abstract

DNA methylation contributes to carcinogenesis by silencing key tumor suppressor genes. Here we report an ultrasensitive and reliable nanotechnology assay, MS-qFRET, for detection and quantification of DNA methylation. Bisulfite-modified DNA is subjected to PCR amplification with primers that would differentiate between methylated and unmethylated DNA. Quantum dots are then used to capture PCR amplicons and determine the methylation status via fluorescence resonance energy transfer (FRET). Key features of MS-qFRET include its low intrinsic background noise, high resolution, and high sensitivity. This approach detects as little as 15 pg of methylated DNA in the presence of a 10,000-fold excess of unmethylated alleles, enables reduced use of PCR (as low as eight cycles), and allows for multiplexed analyses. The high sensitivity of MS-qFRET enables one-step detection of methylation at PYCARD, CDKN2B, and CDKN2A genes in patient sputum samples that contain low concentrations of methylated DNA, which normally would require a nested PCR approach. The direct application of MS-qFRET on clinical samples offers great promise for its translational use in early cancer diagnosis, prognostic assessment of tumor behavior, as well as monitoring response to therapeutic agents.

Original languageEnglish (US)
Pages (from-to)1455-1461
Number of pages7
JournalGenome Research
Volume19
Issue number8
DOIs
StatePublished - Aug 2009

Fingerprint

Quantum Dots
DNA Methylation
Polymerase Chain Reaction
DNA
Methylation
p16 Genes
Fluorescence Resonance Energy Transfer
Nanotechnology
Tumor Suppressor Genes
Sputum
Early Detection of Cancer
Noise
Carcinogenesis
Alleles
Neoplasms
Therapeutics

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Bailey, V. J., Easwaran, H., Zhang, Y., Griffiths, E., Belinsky, S. A., Herman, J. G., ... Wang, T. H. (2009). MS-qFRET: A quantum dot-based method for analysis of DNA methylation. Genome Research, 19(8), 1455-1461. https://doi.org/10.1101/gr.088831.108

MS-qFRET : A quantum dot-based method for analysis of DNA methylation. / Bailey, Vasudev J.; Easwaran, Hariharan; Zhang, Yi; Griffiths, Elizabeth; Belinsky, Steven A.; Herman, James G.; Baylin, Stephen B; Carraway, Hetty E.; Wang, Tza Huei.

In: Genome Research, Vol. 19, No. 8, 08.2009, p. 1455-1461.

Research output: Contribution to journalArticle

Bailey, VJ, Easwaran, H, Zhang, Y, Griffiths, E, Belinsky, SA, Herman, JG, Baylin, SB, Carraway, HE & Wang, TH 2009, 'MS-qFRET: A quantum dot-based method for analysis of DNA methylation', Genome Research, vol. 19, no. 8, pp. 1455-1461. https://doi.org/10.1101/gr.088831.108
Bailey VJ, Easwaran H, Zhang Y, Griffiths E, Belinsky SA, Herman JG et al. MS-qFRET: A quantum dot-based method for analysis of DNA methylation. Genome Research. 2009 Aug;19(8):1455-1461. https://doi.org/10.1101/gr.088831.108
Bailey, Vasudev J. ; Easwaran, Hariharan ; Zhang, Yi ; Griffiths, Elizabeth ; Belinsky, Steven A. ; Herman, James G. ; Baylin, Stephen B ; Carraway, Hetty E. ; Wang, Tza Huei. / MS-qFRET : A quantum dot-based method for analysis of DNA methylation. In: Genome Research. 2009 ; Vol. 19, No. 8. pp. 1455-1461.
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