Sensitive and quantitative universal Pyrosequencing™ methylation analysis of CpG sites

Abstract

DNA methylation is implicated inmultiple normal cellular processes, in-cluding the regulation of tissue- and de-velopment-specific gene expression,imprinting, X-chromosome inactiva-tion, DNA repair, and the suppressionof parasitic DNA sequences. Aberrantgene promoter methylation and result-ing altered gene expression have beenassociated with cancers (1,2). Alteredmethylation patterns have been de-scribed in human sporadic cancers:genome-wide hypomethylation and lo-calized hypermethylation have been ob-served, and both alterations can be pre-sent in the same tumor (3). Togetherwith loss-of-heterozygosity and genemutations, transcriptional silencing bymethylation has been shown to be a ma-jor inactivating event of tumor suppres-sor genes in accordance with Knud-son’s two-hit hypothesis (4). Geneinactivation by promoter hypermethyla-tion and resulting loss of function havebeen shown for several cancer genesinvolved in DNA repair, cell cycle con-trol, apoptosis, angiogenesis, differenti-ation, metastasis/invasion, transcrip-tion, and signal transduction (1).A wide range of methods exists todetect genomic DNA methylation, in-cluding approaches to detect genome-wide and gene-specific methylation lev-els (5). Most methods used to analyzethe methylation status of a specific se-quence are based on bisulfite modifica-tion of the DNA. Following the treat-ment, the methylation status can beassessed as a sequence difference by se-quencing, methylation-specific PCR,methylation-sensitive single-strandedconformational polymorphism, methy-lation-sensitive single nucleotide primerextension (Ms-SNuPE), or restrictionenzyme digestion. Recently, high-throughput methods to detect site-spe-cific methylation have been developedusing the TaqMan