How to get the most out of your biobank

For years, clinicians and researchers have gathered enormous collections of samples coming from different patients. These samples enable retrospective studies in order to better understand the mechanisms underlying a variety of diseases, helping to find novel biomarkers for early diagnosis, prognosis or evaluate the response to treatment.

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Example of analysis of miRNA from FFPE samples (A) Reproducibility of experiment (mouse cerebellum RNA), (B) Comparison with quantitative PT-PCR (expression ratios of miR-21 in tumor lesion and normal region in stomach cancer FFPE tissue), (C) Survival curves of stomach cancer FFPE in an miR-21 high expression group and a low expression group.

These samples, collected in repositories or biobanks, are an invaluable source of information. However, they can have some limitations when studied with “omics” technologies, as they are mostly FFPE samples. Permeabilisation / fixation techniques can interfere in downstream analysis, and FFPE blocks are prone to RNA degradation.

miRNAs seems to emerge as key disease-related biomarkers, but their use with FFPE samples can be tricky. Some recently developed technologies have been used to analyse FFPE samples in biobanks to find novel miRNA biomarkers in retrospective studies. One example is a publication by Osawa and co-workers, who found that miR-21 is a prognostic marker for stomach cancer. In order to be able to analyse the FFPE samples they had in hand, they used methodologies allowing them to both extract high quality RNA as well as analysing expression with ultra-sensitive methods.

For RNA extraction, it is important to use methods that allow to extract RNA of a useable quality without introducing bias that could compromise the whole analysis. As for the miRNA analysis itself, the downstream technology should not be influenced by the presence of degraded RNA, that may bias or inhibit later amplification steps.

So if you want to unravel all the wealth of information in your FFPE samples, just leave your comments below!