Is miRNA microarray better than NGS for circulating miRNA quantification?

Question

[alexandru.floares]

It is clear that miRNA are informative molecules for cancer diagnosis, and there is a desire for non-invasive tests. It is also clear that NGS is a real progress. However, the known advantages of miRNA NGS vs microarray are not important for my study, as I do not want to discover new miRNAs or isoforms. I want just to discriminate, with the highest possible accuracy, between cancer and normal, using advanced Artificial Intelligence (AI) methods. Preliminary results suggest that microRNA data are better than NGS. Moreover, microarray profiling is cheaper. Searching the literature, I found some papers corroborating this idea: microarray is a better choice if you are interested in miRNA quantification. What is your opinion? Thank you!

[alexandru.floares]

Thank you. I am developing a non-invasive multi-cancer diagnostic test - a classification problem, without any interest in discovering new miRNAs/isoforms. Most of the miRNA TCGA data are NGS (tissue miRNA), preprocessed data (mapped and quantified). While TCGA data are not good for a diagnostic test, being tissue data, they were very useful for AI experiments. Usually, I obtained either similar accuracy for both array and NGS or better for microarray data. If the accuracy is similar, NGS has a bigger cost and generate huge files. So, for my problem, microarray seems to be a better solution.

Answer 1

[Björn]

It all depends on your research question. For targeted approach, microarray will be better and cheaper than NGS. You mentioned that you are using advanced AI, then probably you can try TCGA data.