This may not be technically related to bioinformatics. 

Using bioinformatics method, lots of biomarker (methylation; microRNA; mRNA; etc...) based classifiers (for benign / malignant tumor; tumor early detection; tumor subtype; etc) have been published and claim to have good performance. However, it seems that few of them have been used in clinical setting. I can only guess that all these classifiers have some kind of shared issue that forbid them being used in clinical setting. Can anyone please share some opinions on this matter? 

Hey, thanks for posting. Other opinions than mine are very welcome.

Some issues that I have identified over the years:

1,  lack of reproducibility of results
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This is compounded by poor study design, which itself relates to any number of things:

 - no statistical power
 - imbalanced sample groups
 - failure to control for sources of bias, including age, gender, sampling time, ethnicity, *et cetera*
 - untested software that contains bugs

I could add here the fact that every instrument that we use has windows of specification in which the instrument is meant to be operated, and they also have error rates. No NGS instrument, for example, can faithfully sequence any sample of DNA - error will always exist.

2, lack of appreciation of biological variability and how to best capture this
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This is mainly for expression, ChIP, metabolomic, and proteomic studies


3, slow and costly clinical trials
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Clinical trials are very costly and take many years to conduct. Most go nowhere.




4, No 'translational' mechanisms in place
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In most cases, there are no official mechanisms / systems in place such that data from a research setting can be readily used in a clinical environment, or, if one exists, validation obviously has to take place, and this may be governed by national and / or international law. If something new is introduced, I notice that it is usually a 'local' change to the health system, i.e., in a hospital unit / department, and not something that is global.


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On a side note, I have noticed research change even in the time during which I have been in it (or maybe it is that I have changed). I notice researchers exhibiting greater signs of stress and with less focus on the end goal of the very research that they are conducting. Most do not ponder on what their results could do in terms of improving a health service. Many are also focused intensely on publications and winning the next grant to simply stay in the job. This is a vicious cycle that is ultimately eroding quality research.


I should finally add that I believe more tests will be produced in the next few years. In fact, in certain countries (e.g. Brazil) where there is less regulation, many tests are enrolled straight into practice from research settings. This may prove dangerous, though.


Kevin

