Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

Genome-wide methylation in paired lung tumor/non-tumor samples using the HELP assay


ABSTRACT: In lung cancer, hypermethylation of specific gene promoters has been found during the progressive carcinogenesis. The identification of common methylation events will aid in the understanding of molecular events during neoplastic transformation and help develop biomarkers for cancer with high predictive and diagnostic value. To explore common methylation events on a genome-wide scale in lung cancer, we analyzed the methylation profiles of paired NSCLC tumor and far adjacent non-tumor samples using the HELP-microarray assay, which yields information on 1.2 million fragments throughout the genome. In this study, 24 pairs of tumor and adjacent non-tumor samples were analyzed using the HELP assay. At p = 5E-6, we identified 26,138 differentially methylated fragments (corresponding to 2 CpG sites each) in tumor versus non-tumor. The overall trend was consistent with genome-wide hypomethylation and locus specific hypermethylation (localized to CG-island containing promoters). We could identify both known and novel regions of the genome as well as specific gene-promoters that are hypermethylated in tumor versus non-tumor. The HELPassay: HpaII tiny fragment enrichment by ligation-mediated polymerase chain reaction [PCR] assay 24 pairs of NSCLC subjects, tumor and paired non-tumor samples from each subject were analyzed. Individual HpaII restriction digest profiles were compared to an internal MspI digest control, to yield differentially methylated fragments for every sample. Samples were compared intra-subject between tumor and adjacent non-tumor for these differential methylation profiles and the overall significant changes across 24 subjects were identified.

ORGANISM(S): Homo sapiens

SUBMITTER: Miao Shi 

PROVIDER: E-GEOD-35520 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

Similar Datasets

2012-04-01 | GSE35520 | GEO
2015-01-18 | E-GEOD-59200 | biostudies-arrayexpress
2012-12-05 | E-GEOD-42721 | biostudies-arrayexpress
2015-05-20 | E-GEOD-60233 | biostudies-arrayexpress
2010-04-12 | E-GEOD-19937 | biostudies-arrayexpress
2015-09-10 | E-GEOD-51680 | biostudies-arrayexpress
2009-12-08 | GSE19363 | GEO
2019-06-06 | GSE82288 | GEO
2015-09-08 | GSE66296 | GEO
2017-07-10 | GSE75496 | GEO