Abstract
MiRNAs are important regulators of gene expression and are frequently deregulated under pathologic conditions. They are highly stable in bodily fluids which makes them feasible candidates to become minimally invasive biomarkers. In fact, several studies already proposed circulating miRNA-based biomarkers for different types of neoplastic, cardiovascular and degenerative diseases. However, many of these studies rely on small RNA sequencing experiments that are based on different RNA extraction and processing protocols, rendering results incomparable. We generated liqDB, a database for liquid biopsy small RNA sequencing profiles that provides users with meaningful information to guide their small RNA liquid biopsy research and to overcome technical and conceptual problems. By means of a user-friendly web interface, miRNA expression profiles from 1607 manually annotated samples can be queried and explored at different levels. Result pages include downloadable expression matrices, differential expression analysis, most stably expressed miRNAs, cluster analysis and relevant visualizations by means of boxplots and heatmaps. We anticipate that liqDB will be a useful tool in liquid biopsy research as it provides a consistently annotated large compilation of experiments together with tools for reproducible analysis, comparison and hypothesis generation. LiqDB is available at http://bioinfo5.ugr.es/liqdb.
Highlights
Despite the well-established usage of blood and urine in disease detection and diagnosis, the term liquid biopsy does not appear in PubMed until 2011 in a work where breast cancer patients response to trastuzumab was monitored using circulating epithelial tumour cells (CETC) [1]
Genotypes and methylation states of extracted DNA molecules or the abundance of RNA molecules can be screened to search for non-invasive biomarkers that allow for early diagnosis, treatment monitoring, tumour staging, relapse risk assessment and prognosis [2]
In order to help to overcome the problems described above we developed liqDB, a database for small RNA expression profiles in bodily fluids
Summary
Despite the well-established usage of blood and urine in disease detection and diagnosis, the term liquid biopsy does not appear in PubMed until 2011 in a work where breast cancer patients response to trastuzumab was monitored using circulating epithelial tumour cells (CETC) [1]. Liquid biopsy has become a rapidly growing research field based on the extraction of non-solid biological material such as blood, saliva, urine or cerebrospinal fluid that can be sampled in a minimally invasive way. From this material can be extracted, among others: protein-bound RNA molecules, vesicles such as exosomes, cell-free DNA (cfDNA), circulating tumour cells (CTC) and platelets that can be used for clinical purposes. The job IDs can be used as input as well as relevant query variables to generate a standard result page including differential expression between database and uploaded samples
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