Parallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays

Robert P. Balog; Y. Emi Ponce De Souza; Hue M. Tang; Gina M. DeMasellis; Boning Gao; Adrian Avila; Desmond J. Gaban; David Mittelman; John D. Minna; Kevin J. Luebke; Harold R. Garner

doi:10.1016/S0003-2697(02)00294-4

Parallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays

Robert P. Balog, Y. Emi Ponce De Souza, Hue M. Tang, Gina M. DeMasellis, Boning Gao, Adrian Avila, Desmond J. Gaban, David Mittelman, John D. Minna, Kevin J. Luebke, Harold R. Garner

Research output: Contribution to journal › Article › peer-review

32 Scopus citations

Abstract

We have developed a method for the parallel analysis of multiple CpG sites in genomic DNA for their state of methylation. Hypermethylation of CpG islands within the promoters and 5′ exons of genes has been found to be a mechanism of transcriptional inactivation associated with a variety of tumors. The method that we developed relies on the differential reactivity of methylated and unmethylated cytosines with sodium bisulfite, which exclusively converts unmethylated cytosines to deoxyuracils. The resulting sequence changes are determined with single-nucleotide resolution by hybridization to an oligonucleotide array. Cohybridization with a reference sample containing a different label provides an internal standard for assessment of methylation state. This method provides advantages in parallelism over existing methods of methylation analysis. We have demonstrated this technique with a region from the promoter of the tumor suppressor gene p16, which is hypermethylated in many cancers.

Original language	English (US)
Pages (from-to)	301-310
Number of pages	10
Journal	Analytical biochemistry
Volume	309
Issue number	2
DOIs	https://doi.org/10.1016/S0003-2697(02)00294-4
State	Published - Oct 15 2002

Keywords

CpG island
Hypermethylation
Oligonucleotide array
Sodium bisulfite
Tumor suppressor

ASJC Scopus subject areas

Biophysics
Biochemistry
Molecular Biology
Cell Biology

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10.1016/S0003-2697(02)00294-4

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title = "Parallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays",

abstract = "We have developed a method for the parallel analysis of multiple CpG sites in genomic DNA for their state of methylation. Hypermethylation of CpG islands within the promoters and 5′ exons of genes has been found to be a mechanism of transcriptional inactivation associated with a variety of tumors. The method that we developed relies on the differential reactivity of methylated and unmethylated cytosines with sodium bisulfite, which exclusively converts unmethylated cytosines to deoxyuracils. The resulting sequence changes are determined with single-nucleotide resolution by hybridization to an oligonucleotide array. Cohybridization with a reference sample containing a different label provides an internal standard for assessment of methylation state. This method provides advantages in parallelism over existing methods of methylation analysis. We have demonstrated this technique with a region from the promoter of the tumor suppressor gene p16, which is hypermethylated in many cancers.",

keywords = "CpG island, Hypermethylation, Oligonucleotide array, Sodium bisulfite, Tumor suppressor",

author = "Balog, {Robert P.} and {De Souza}, {Y. Emi Ponce} and Tang, {Hue M.} and DeMasellis, {Gina M.} and Boning Gao and Adrian Avila and Gaban, {Desmond J.} and David Mittelman and Minna, {John D.} and Luebke, {Kevin J.} and Garner, {Harold R.}",

note = "Funding Information: This work was supported by Grants, P50 CA70907 and R33 CA81656 from the National Cancer Institute (NCI) and by a grant from the Donald W. Reynolds Foundation. R.P.B. was supported by a McDermott Center Human Genomics training grant. We are grateful to Yuan Qi for computational analysis of CpG island occurrence and Glenn McGall of Affymetrix for generously supplying phosphoramidites.",

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AU - Balog, Robert P.

AU - De Souza, Y. Emi Ponce

AU - Tang, Hue M.

AU - DeMasellis, Gina M.

AU - Gao, Boning

AU - Avila, Adrian

AU - Gaban, Desmond J.

AU - Mittelman, David

AU - Minna, John D.

AU - Luebke, Kevin J.

AU - Garner, Harold R.

N1 - Funding Information: This work was supported by Grants, P50 CA70907 and R33 CA81656 from the National Cancer Institute (NCI) and by a grant from the Donald W. Reynolds Foundation. R.P.B. was supported by a McDermott Center Human Genomics training grant. We are grateful to Yuan Qi for computational analysis of CpG island occurrence and Glenn McGall of Affymetrix for generously supplying phosphoramidites.

PY - 2002/10/15

Y1 - 2002/10/15

N2 - We have developed a method for the parallel analysis of multiple CpG sites in genomic DNA for their state of methylation. Hypermethylation of CpG islands within the promoters and 5′ exons of genes has been found to be a mechanism of transcriptional inactivation associated with a variety of tumors. The method that we developed relies on the differential reactivity of methylated and unmethylated cytosines with sodium bisulfite, which exclusively converts unmethylated cytosines to deoxyuracils. The resulting sequence changes are determined with single-nucleotide resolution by hybridization to an oligonucleotide array. Cohybridization with a reference sample containing a different label provides an internal standard for assessment of methylation state. This method provides advantages in parallelism over existing methods of methylation analysis. We have demonstrated this technique with a region from the promoter of the tumor suppressor gene p16, which is hypermethylated in many cancers.

AB - We have developed a method for the parallel analysis of multiple CpG sites in genomic DNA for their state of methylation. Hypermethylation of CpG islands within the promoters and 5′ exons of genes has been found to be a mechanism of transcriptional inactivation associated with a variety of tumors. The method that we developed relies on the differential reactivity of methylated and unmethylated cytosines with sodium bisulfite, which exclusively converts unmethylated cytosines to deoxyuracils. The resulting sequence changes are determined with single-nucleotide resolution by hybridization to an oligonucleotide array. Cohybridization with a reference sample containing a different label provides an internal standard for assessment of methylation state. This method provides advantages in parallelism over existing methods of methylation analysis. We have demonstrated this technique with a region from the promoter of the tumor suppressor gene p16, which is hypermethylated in many cancers.

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KW - Hypermethylation

KW - Oligonucleotide array

KW - Sodium bisulfite

KW - Tumor suppressor

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Parallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays

Abstract

Keywords

ASJC Scopus subject areas

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