title: Identification and validation of colorectal neoplasia-specific methylation markers for accurate classification of disease.
abstract: Aberrant DNA methylation occurs early in oncogenesis, is stable, and can be assayed in tissues and body fluids. Therefore, genes with aberrant methylation can provide clues for understanding tumor pathways and are attractive candidates for detection of early neoplastic events. Identification of sequences that optimally discriminate cancer from other diseased and healthy tissues is needed to advance both approaches. Using well-characterized specimens, genome-wide methylation techniques were used to identify candidate markers specific for colorectal neoplasia. To further validate 30 of these candidates from genome-wide analysis and 13 literature-derived genes, including genes involved in cancer and others with unknown functions, a high-throughput methylation-specific oligonucleotide microarray was used. The arrays were probed with bisulfite-converted DNA from 89 colorectal adenocarcinomas, 55 colorectal polyps, 31 inflammatory bowel disease, 115 extracolonic cancers, and 67 healthy tissues. The 20 most discriminating markers were highly methylated in colorectal neoplasia (area under the receiver operating characteristic curve > 0.8; P < 0.0001). Normal epithelium and extracolonic cancers revealed significantly lower methylation. Real-time PCR assays developed for 11 markers were tested on an independent set of 149 samples from colorectal adenocarcinomas, other diseases, and healthy tissues. Microarray results could be reproduced for 10 of 11 marker assays, including eight of the most discriminating markers (area under the receiver operating characteristic curve > 0.72; P < 0.009). The markers with high specificity for colorectal cancer have potential as blood-based screening markers whereas markers that are specific for multiple cancers could potentially be used as prognostic indicators, as biomarkers for therapeutic response monitoring or other diagnostic applications, compelling further investigation into their use in clinical testing and overall roles in tumorigenesis.
authors.affiliation: Epigenomics, Inc., Suite 300, 1000 Seneca Street, Seattle, WA 98101, USA.
authors.forename: Fabian
authors.initials: F
authors.lastname: Model
authors.forename: Neal
authors.initials: N
authors.lastname: Osborn
authors.forename: David
authors.initials: D
authors.lastname: Ahlquist
authors.forename: Robert
authors.initials: R
authors.lastname: Gruetzmann
authors.forename: Bela
authors.initials: B
authors.lastname: Molnar
authors.forename: Ferenc
authors.initials: F
authors.lastname: Sipos
authors.forename: Orsolya
authors.initials: O
authors.lastname: Galamb
authors.forename: Christian
authors.initials: C
authors.lastname: Pilarsky
authors.forename: Hans-Detlev
authors.initials: HD
authors.lastname: Saeger
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Tulassay
authors.forename: Kari
authors.initials: K
authors.lastname: Hale
authors.forename: Suzanne
authors.initials: S
authors.lastname: Mooney
authors.forename: Joseph
authors.initials: J
authors.lastname: Lograsso
authors.forename: Peter
authors.initials: P
authors.lastname: Adorjan
authors.forename: Ralf
authors.initials: R
authors.lastname: Lesche
authors.forename: Andreas
authors.initials: A
authors.lastname: Dessauer
authors.forename: Joerg
authors.initials: J
authors.lastname: Kleiber
authors.forename: Baerbel
authors.initials: B
authors.lastname: Porstmann
authors.forename: Andrew
authors.initials: A
authors.lastname: Sledziewski
authors.forename: Catherine
authors.initials: C
authors.lastname: Lofton-Day
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis*; D016000:Cluster Analysis; D015179:Colorectal Neoplasms / Q000145:classification / Q000378:metabolism*; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000378:metabolism*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm