Genome-Wide DNA Methylation Analysis

Independent breast tissue samples were available from the National Disease Research Interchange (NDRI, GSE74214, n = 18) and The Cancer Genome Atlas Database (TCGA, n = 97) [16 (link)]. Raw intensity data (IDAT) files were available for both studies and DNA methylation data were processed and normalized using the same methods described above. Likewise, raw DNA methylation IDAT files were accessed and processed using the same methods outlined above for both ductal carcinoma in situ (n = 55, GSE66313) and invasive ductal carcinoma (n = 749, TCGA) to compare DNA methylation differences between normal-adjacent tissue and pre-invasive or invasive lesions [8 (link)].

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Johnson K.C., Houseman E.A., King J.E, & Christensen B.C. (2017). Normal breast tissue DNA methylation differences at regulatory elements are associated with the cancer risk factor age. Breast Cancer Research : BCR, 19, 81.

Publication 2017

Breast Cancer Dna methylation Ductal carcinoma in situ Genome Invasive ductal carcinoma Normal tissue

Corresponding Organization :

Other organizations : Dartmouth College, Oregon State University

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Variable analysis

independent variables

Tissue type (normal-adjacent, ductal carcinoma in situ, invasive ductal carcinoma)

dependent variables

DNA methylation

control variables

Processing and normalization methods for DNA methylation data were the same across studies

controls

No positive or negative controls were explicitly mentioned in the input.

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