Abstract B50: Large scale DNA methylation profiling and high-resolution comparative genomic hybridization of preneoplastic and invasive esophageal squamous cell carcinoma: Discovery of early detection markers

Esophageal cancer causes > 350,000 deaths/year in the world. Clinically useful early detection methods must identify these cancers and their precursor lesions at more curable stages. We conducted genome-wide methylation profiling and comparative genomic hybridization analyses of preneoplastic and invasive esophageal squamous cell carcinoma to look for methylation or gene copy number patterns that might be useful as early detection markers.

DNA was extracted from esophageal biopsies and surgical resections from 94 esophageal tissues spanning a spectrum from normal to invasive tumor. Bisulfite genotyping for 800 genes (Illumina GoldenGate methylation BeadArray), was used to measure CpG methylation of 1505 targets. High-resolution microarray based comparative genomic hybridization (Agilent) was used to measure regions of chromosomal gain or loss.

Analysis of methylation beadarray data identified targets that are differentially methylated between normal and high-grade squamous dysplasia. Chromosome number aberrations were identified that involve several chromosomes, occur early in the neoplastic process, and progress with disease severity.

Genome-wide methylation profiling and comparative genomic hybridization identify patterns of gene methylation and chromosome number aberrations, respectively, that may distinguish patients with and without high-grade squamous dysplasia or cancer.

Citation Information: Cancer Prev Res 2008;1(7 Suppl):B50.