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Breast cancer is the most common cancer in women worldwide. 10% of cancers are known to be caused from genetic predisposition with inherited germline mutations. Using the CellRaft Array, hTERT-IMEC cell populations were seeded for generating clonal lines. Once monoclonal lines were established, cells were again seeded on a CellRaft Array for single cell collection. Using PCR strip tubes, CellRafts containing a single elongated cell were isolated and frozen at -80°C until further use. Single primary and immortalized mammary epithelial cells were whole genome amplification using single cell multiple displacement amplification method. Variants were identified and demonstrated a small statistically significant increase in mutation frequency in mammary epithelial cells isolated from the breast of mutation carriers as compared with those obtained from age-matched controls with no genetically increased risk for breast cancer.