Cancer Research: Large-Scale Profiling of Archival Lymph Nodes Reveals Pervasive Remodeling of the Follicular Lymphoma Methylome

J. Keith KillianSven BilkeSean DavisRobert L. WalkerM. Scott KillianErich B. JaegerYidong ChenJason HippStefania PittalugaMark RaffeldRobert CornelisonWilliam I. Smith, Jr.Marina BibikovaJian-Bing FanMichael R. Emmert-BuckElaine S. Jaffe and Paul S. Meltzer

Abstract

Emerging technologies allow broad profiling of the cancer genome for differential DNA methylation relative to benign cells. Herein, bisulfite-modified DNA from lymph nodes with either reactive hyperplasia or follicular lymphoma (FL) were analyzed using a commercial C/UpG genotyping assay. Two hundred fifty-nine differentially methylated targets (DMT) distributed among 183 unique genes were identified in FL. Comparison of matched formalin-fixed, paraffin-embedded, and frozen surgical pathology replicates showed the complete preservation of the cancer methylome among differently archived tissue specimens. Analysis of the DMT profile is consistent with a pervasive epigenomic remodeling process in FL that affects predominantly nonlymphoid genes. [Cancer Res 2009;69(3):758–64]

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