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This is may not be entirely technical question but rather a academic question. But the technique behind the application is within the scope of bioinformatics. So I would try to ask here that:

In each cancer type, there have been tons of papers that describe RNA-Seq based subtyping resulting in molecularly distinct subgroups with survival difference. However, only very few of them gained acceptance at clinical setting, such as breast cancer (luminal subtype A, luminal subtype B, normal breast-like subtype, HER-2 overexpression subtype and basal-like subtype).

My question is: why did this molecular subtyping of breast cancer gain much acceptance but not others? Did this one own some advantages that other did not?

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In two words: incidence and funding

I'm not an expert on this topic, but I assume it has something to do with the incidence of breast cancer itself:

Breast cancer is the most common cancer in American women, except for skin cancers. Currently, the average risk of a woman in the United States developing breast cancer sometime in her life is about 13%. This means there is a 1 in 8 chance she will develop breast cancer. This also means there is a 7 in 8 chance she will never have the disease.

This incidence most likely amplifies how big of a problem society/funders/governments consider breast cancer to be. For example, a study performed by Northwestern University’s Feinberg School of Medicine and Robert H. Lurie Comprehensive Cancer Center showed that breast cancer research is by and large one of the most well-funded areas of cancer research.

How common breast cancer is has likely affected how much funding it gets

This higher amount of funding leads to more and better resources and research into every aspect of breast cancer, from identification to treatment. I would wager better funding has had the effect of increasing the level of research performed in the usage of sub-typing for identifying people at risk of getting breast cancer. Given positive results and lots of literature backing up such a method as useful, its levels of acceptance in clinical settings increased.

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