I get this question almost daily from my breast cancer patients. People are understandably confused. As is the case with other foods, as research evolves, there are changing messages disseminated about their impact on health matters.
So, what information compels you to make decisions in life? The story about soy is the story about the evolution of knowledge about diet and cancer in general, as they say, and here is the rest of the story.
The earliest studies in the '70s and '80s indicated that Asian women had lower breast cancer risk than European and American women.    It turns out that many things about the life and culture of Asian women are different beyond their diets. The early thinking about possible connections to lower cancer risk focused on low fat intake and soy. Many in the research community advocated lowering dietary fat and increasing soy intake to reduce breast cancer risk and improve survival. Thus was born a wave of enthusiasm for all things soy.
As better research surfaced, it turned out that lower dietary fat had minimal effect on overall breast cancer risk.  
As is typical of Western science, soy was dissected and found to contain a variety of nutrients with potential cancer effects. One series of compounds, isoflavones, were found to possess estrogen-like effects, albeit far weaker than human estrogen compounds. Laboratory research subsequently indicated a potential adverse risk with an increase in breast cancer growth with exposure to isoflavones compounds typically consumed through diet or with supplementation.   This started the shift in attitudes suggesting a potential risk rather than benefit for soy consumption.
Other studies in animals as well as long-term human studies supported the idea that any benefit of soy only occurred when consumed prior to puberty.    This would alter the later risk of developing breast cancer through favorable changes during maturation of the breast. There remained concern, however, that consuming soy at high doses in adulthood might increase breast cancer risk and, in breast cancer survivors, impact survival through possible higher recurrence risk. There was also concern that soy might impair the effectiveness of hormone therapies, such as tamoxifen, prescribed to patients at higher risk of getting breast cancer or recurrence. As more and more women were using powdered soy protein or isoflavone supplements, this was particularly worrisome.
I am particularly interested in one critical piece of evidence, which is what happens to large groups (many thousands) of women with breast cancer who consume soy at varying levels. Do they show greater recurrence risk of breast cancer? Unfortunately, these studies are expensive, take years and often decades to complete but provide the best and most reliable evidence of risk, short of a very large "randomized control trial" in breast cancer survivors.
Despite the fears, the result of higher levels of soy intake shows no clear evidence of risk. In fact, several studies showed that the higher the soy intake there appeared to be a lower risk of breast cancer recurrence and mortality.     Surprisingly, this effect was noted in both estrogen receptor negative and positive women. Remembering all the press from earlier pronouncements, which were based on inadequate and limited studies, many women are leery and find this hard to believe. Beliefs are hard to dislodge once they become part of the accepted wisdom (wisdom, indeed!).
The bottom line is: What happens to women who eat soy? And the answer in my opinion is that it is safe in regard to breast cancer recurrence risk.
Are you still worried about eating soy? Rest assured, the current thinking on soy among cancer nutritionists and the American dietetic community has changed based on these new larger and reassuring studies. As the field has evolved, better research on long-term outcomes in very large populations of breast cancer patients confirms that soy is NOT bad and has no adverse impact. It may even be beneficial as part of a healthy, prudent plant-based diet.
The safety of soy and breast cancer risk is separate from the question of GMO (genetically modified) soy. These studies didn't separate sources of dietary soy. They included all soy products, presumably both GMO and non-GMO, suggesting that may not be an issue for breast recurrence. With the high use of genetically-modified soy in U.S. products, this remains a very controversial area.
GMO soy is in widespread use in the U.S. and has been recognized as safe by the FDA as well as international organizations. Nonetheless, there remain many unanswered questions, from impact on long-term human health to the risk to native plant populations that acquire these genes (as is inevitable) and the ecologic and evolutionary consequences.
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