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Researchers from Sweden compared lifestyle factors and coffee consumption between women with breast cancer and age-matched women without. They found that coffee drinkers had a lower incidence of breast cancer than women who rarely drank coffee. However they also found that several lifestyle factors affected breast cancer rates, such as age at menopause, exercise, weight, education, and a family history of breast cancer. Once they had adjusted their data to account for these other factors they found that the protective effect of coffee on breast cancer was only measurable for ER-negative breast cancer.
The group from Karolinska Institutet explained that, "There is often conflicting information about the beneficial effects of coffee – when we compared our results to that of a German study we discovered that their data showed the same trend, but the relationship was much weaker. We suggest that this may have something to do with the way the coffee was prepared, or the type of bean preferred. It is unlikely that the protective effect is due to phytoestrogens present in coffee since there was no reduction in the incidence of ER-positive cancer in this study."
So while it is evident that coffee may have beneficial effects in protecting women from ER negative breast cancer the exact mechanism and compounds involved are not yet clear and not all types of coffee are the same.
(Coffee consumption modifies risk of estrogen-receptor negative breast cancer - Jingmei Li, Petra Seibold, Jenny Chang-Claude, Dieter Flesch-Janys, Jianjun Liu, Kamila Czene, Keith Humphreys and Per Hall - Breast Cancer Research)