DNA extraction and bisulfite conversion were performed as described previously27 (link). DNA samples were processed and run on HumanMethylation450 (HM450) arrays following the manufacturer’s instructions (Illumina Inc.). Raw intensity data was read, preprocessed and batch corrected in R (v3.2.2). After subsequent filtering, 426,718 probes were left for analysis. Additional HM450 array datasets include: Level 1 HM450 array data from 87 EAC and 11 adjacent normal tissue samples obtained from TCGA on 11/13/2015 (https://tcga-data.nci.nih.gov/tcga/ ), and 125 EAC samples from the Gene Expression Omnibus (study ID: GSE72872) 23 (link).
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Epigenetic profiling of esophageal adenocarcinoma
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Corresponding Organization : Fred Hutch Cancer Center
Other organizations : Brigham and Women's Hospital, Harvard University, Dana-Farber Cancer Institute, University of Washington, VA Puget Sound Health Care System, Eli and Edythe Broad Foundation, Broad Institute, Case Western Reserve University, University Hospitals of Cleveland
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Variable analysis
independent variables
- DNA extraction and bisulfite conversion were performed as described previously
- DNA samples were processed and run on HumanMethylation450 (HM450) arrays following the manufacturer's instructions (Illumina Inc.)
- Methylation profiles of 426,718 probes
- Raw intensity data was read, preprocessed and batch corrected in R (v3.2.2)
- No positive or negative controls were explicitly mentioned.
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