DNA methylation profiling was previously accomplished using the Illumina GoldenGate Cancer Panel I methylation bead array [39 (link)]. Sodium bisulfite modification of FFPE breast tumor DNA was performed using the EZ DNA Methylation Gold kit according to the manufacturer’s protocol. Bisulfite-converted tumor DNA was analyzed for methylation using the Cancer Panel I array in the Mammalian Genotyping Core facility at UNC. The Cancer Panel I array measures methylation at CpG sites in the promoter (P) or first exon (E) of cancer-related genes, including tumor suppressor genes, oncogenes, DNA repair genes, and others. Array probe names are comprised of the gene symbol followed by the position of the CpG in the P or E upstream from the transcription start site. The methylation level at each CpG site is represented by the beta (β) value, which ranged from 0 (completely unmethylated) to 1.0 (fully methylated). Probes reported to overlap a single-nucleotide polymorphism (SNP) or repeat [41 (link)] were excluded. After quality control filtering as described previously [39 (link)], methylation analysis was completed on 517 breast tumors and included 933 CpG loci in 609 genes.
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DNA Methylation Profiling of Breast Tumors
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Bisulfite
Breast tumors
Cancer
Dna methylation
Dna repair
Exon
Gene
Genes cancer
Genes loci
Gold
Mammalian
Methylation
Oncogenes
Single nucleotide polymorphism
Sodium bisulfite
Transcription start site
Tumor dna
Tumor suppressor genes
Corresponding Organization :
Other organizations : University of North Carolina at Chapel Hill, Virginia Commonwealth University, Emory University, Stony Brook University
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Variable analysis
independent variables
- Sodium bisulfite modification of FFPE breast tumor DNA
- Methylation level at each CpG site represented by the beta (β) value, which ranged from 0 (completely unmethylated) to 1.0 (fully methylated)
- Probes reported to overlap a single-nucleotide polymorphism (SNP) or repeat were excluded
- No positive or negative controls were explicitly mentioned in the provided information.
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