Similar Datasets
Project description:Lung adenocarcinoma’s genomic alterations exhibit vast variation. Lung adenocarcinoma also has previously described intrinsic gene expression subtypes (Hayes et al. 2006, PMID: 17075127). This study detect global methylation differences among gene expression subtypes. These specimens were also assayed for genomewide transcription in GSE26939 and copy number in GSE36363.
2012-05-17 | GSE36438 | GEO
Project description:The aim of this study is to identify the gene affected carcinogenesis by DNA methylation in early lung adenocarcinoma
2016-12-31 | GSE83842 | GEO
Project description:Genome wide DNA methylation profiling of tumor samples with lung adenocarcinoma patients. The Illumina HumanMethylation27 BeadChip array was used to obtain DNA methylation profiles across approximately 27,578 CpGs in lung cancer samples. Samples included tumor samples with lung adenocarcinoma.
2017-02-09 | GSE83845 | GEO
Project description:Pathologic differentiation of tissue of origin in tumors found in the lung can be challenging, with differentiation of mesothelioma and lung adenocarcinoma emblematic of this problem. Indeed, proper classification is essential for determination of treatment regimen for these diseases, making accurate and early diagnosis critical. Here we investigate the potential of epigenetic profiles of lung adenocarcinoma, mesothelioma, and non-malignant pulmonary tissues (n=285) as differentiation markers in an analysis of DNA methylation at 1413 autosomal CpG loci associated with 773 cancer-related genes. Using an unsupervised recursively-partitioned mixture modeling technique for all samples, the derived methylation profile classes were significantly associated with sample type (P < 0.0001). In a similar analysis restricted to tumors, methylation profile classes significantly predicted tumor type (P < 0.0001). Random forests classification of CpG methylation of tumors - which splits the data into training and test sets - accurately differentiated MPM from lung adenocarcinoma over 99% of the time (P < 0.0001). In a locus-by-locus comparison of CpG methylation between tumor types, 1266 CpG loci had significantly different methylation between tumors following correction for multiple comparisons (Q < 0.05); 61% had higher methylation in adenocarcinoma. Using the CpG loci with significant differential methylation in a pathways analysis revealed significant enrichment of methylated gene-loci in Cell Cycle Regulation, DNA Damage Response, PTEN Signaling, and Apoptosis Signaling pathways in lung adenocarcinoma when compared to mesothelioma. Methylation-profile-based differentiation of lung adenocarcinoma and mesothelioma is highly accurate, informs on the distinct etiologies of these diseases, and holds promise for clinical application.
2009-07-28 | GSE16559 | GEO
Project description:Genome wide DNA methylation profiling of normal and adenocarcinoma lung tissues. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in lung adenocarcinoma samples.
2016-12-31 | GSE49996 | GEO
Project description:Pathologic differentiation of tissue of origin in tumors found in the lung can be challenging, with differentiation of mesothelioma and lung adenocarcinoma emblematic of this problem. Indeed, proper classification is essential for determination of treatment regimen for these diseases, making accurate and early diagnosis critical. Here we investigate the potential of epigenetic profiles of lung adenocarcinoma, mesothelioma, and non-malignant pulmonary tissues (n=285) as differentiation markers in an analysis of DNA methylation at 1413 autosomal CpG loci associated with 773 cancer-related genes. Using an unsupervised recursively-partitioned mixture modeling technique for all samples, the derived methylation profile classes were significantly associated with sample type (P < 0.0001). In a similar analysis restricted to tumors, methylation profile classes significantly predicted tumor type (P < 0.0001). Random forests classification of CpG methylation of tumors - which splits the data into training and test sets - accurately differentiated MPM from lung adenocarcinoma over 99% of the time (P < 0.0001). In a locus-by-locus comparison of CpG methylation between tumor types, 1266 CpG loci had significantly different methylation between tumors following correction for multiple comparisons (Q < 0.05); 61% had higher methylation in adenocarcinoma. Using the CpG loci with significant differential methylation in a pathways analysis revealed significant enrichment of methylated gene-loci in Cell Cycle Regulation, DNA Damage Response, PTEN Signaling, and Apoptosis Signaling pathways in lung adenocarcinoma when compared to mesothelioma. Methylation-profile-based differentiation of lung adenocarcinoma and mesothelioma is highly accurate, informs on the distinct etiologies of these diseases, and holds promise for clinical application. Mesotheliomas (n=158) and grossly non-tumorigenic parietal pleura (n=18) were obtained following surgical resection at Brigham and Womenâ??s Hospital through the International Mesothelioma Program from a pilot study conducted in 2002 (n=70) and an incident case series beginning in 2005 (n=88) with a participation rate of 85%. We used biopsy specimens from patients treated for NSCLC at the Massachusetts General Hospital from 1992 â?? 1996 (18) including lung adenocarcinomas (n=57) and non-malignant pulmonary tissues (n=48) (of which 22 (39%) were taken from the adenocarcinoma patients) (18). Additional normal lung tissues were obtained from the National Disease Research Interchange from donors free of lung malignancy (n=4).
2010-06-25 | E-GEOD-16559 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of lung adenocarcinoma samples. Illumina Infinium 450K(n=61) and EPIC (n=27) arrays were used to obtain DNA methylation data.
2021-07-16 | GSE180060 | GEO
Project description:Lung adenocarcinoma’s genomic alterations exhibit vast variation. Lung adenocarcinoma also has previously described intrinsic gene expression subtypes (Hayes et al. 2006, PMID: 17075127). This study detect global methylation differences among gene expression subtypes. These specimens were also assayed for genomewide transcription in GSE26939 and copy number in GSE36363. 33 tumor samples and 10 normal samples were quantified for DNA methylation by MSNP (Yuan et al, PMID: 16585166) using Affymetrix SNP 250K_StyI microarrays.
2012-05-16 | E-GEOD-36438 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of lung adenocarcinoma and non-tumor adjacent tissues. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles. Samples included eight lung cancer and adjacent non-tumor tissues excised from a cohort of 8 patients with lung adenocarcinoma.
2016-12-01 | GSE85845 | GEO
Project description:Genome-wide DNA methylation profiling of normal and lung adenocarcinoma fresh tissue samples. The Illumina Infinium MethylationEPIC BeadChip (850K) was used to obtain DNA methylation profiles across 860,000 CpGs in fresh tissue of lung adenocarcinoma and adjacent histological normal lung tissue samples. Samples included 30 paired tumor-normal driver gene-negative lung adenocarcinoma tissues and 35 paired tumor-normal EGFR-mutation positive lung adenocarcinoma tissues.
2024-05-28 | GSE235414 | GEO