Abstract: This invention provides a system and method for use of a library for reference-based deconvolution of breast tissue and/or breast milk DNA methylation data assayed using the Illumina Infinium MethylationEPIC BeadChip. A library is accessed, containing information related to an estimate of relative proportions of epithelial cells, endothelial cells, fibroblasts, adipocytes, B cells, CD4+ T cells, CD8+ T cells, NK cells, monocytes, and neutrophils associated with the breast tissue and/or breast milk. The library is applied to diagnosis and treatment of a medical condition based upon patient information obtained from a sample of patient breast tissue and/or breast milk.