New public database gives clinical laboratory researchers a single, searchable source for non-coding RNA data, thus aiding development of new diagnostic assays

Clinical laboratories involved in next-generation gene sequencing have a new single searchable database for RNA. Experts say that this database should help research and development of medical laboratory tests for clinical purposes.

The launch of RNAcentral now provides RNA biologists and other researchers with an open resource that offers integrated access to a comprehensive, up-to-date set of non-coding RNA sequences. This is a first step to building a repository of information for non-coding RNAs that is similar to the Universal Protein Resource (UniProt) database for proteins.

RNAcentral is the brainchildof the RNAcentral Consortium, a large international collaboration of more than 30 expert databases that specialize in different types of non-coding RNAs. So far, 12 of these databases have been integrated into RNAcentral. The project is hosted by the European Bioinformatics Institute and funded by a United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) grant.

The RNAcentral portal provides access to approximately 8 million sequences, with data accessible via sequence and keyword search. The site also provides a defined identifier space for individual sequences. In the second phase of development, these reference data will be used to provide annotation for genome sequences from across the taxonomic space.

Until now, scientists accessing non-coding RNA data for their research had to search multiple websites in order to gather information on each subtype of non-coding RNAs. Two such databases are miRBase for microRNAs and HAVANA for lncRNA.

Kalorama Information published the 2014 report “miRNA Research and Diagnostic Markets” that outlined the market opportunity for testing using microRNAs. Its researchers believe RNAcentral will be a boon to both small biotechnology companies and big pharmaceutical companies working in the field of microRNA diagnostics.

“RNAcentral should be able to save you a lot of time and potentially save you a lot of grief because you don’t want to be out there re-inventing the wheel,” said K. John Morrow, Ph.D., President/CEO Newport Biotech, and an Information analyst for Kalorama, in an exclusive Dark Daily interview. “That is what these databases are particularly appropriate for. You go in and find out what has been done, or what is available, so you don’t waste time repeating information that is already out there.”

K. John Morrow, Ph.D

K. John Morrow, Ph.D., completed his training in the field of genetics at the University of Washington, Seattle. He did post doctoral study at the Istituto di Geneticà, Universitá di Pavia, Italy, and the Fox Chase Cancer Center, Philadelphia PA. Dr. Morrow has extensive experience in the academic community, including faculty positions at the University of Kansas, and the Texas Tech University Health Sciences Center. He has authored over 60 peer-reviewed publications reporting original research in genetics, immunology, developmental biology, evolution, cancer biology, and animal science. (Photograph and caption copyright Newport Biotechnology Consultants)

Non-coding RNA molecules, particularly micro-RNA, are a factor in cancers and other diseases. Researchers believe microRNA diagnostic technologies offer the promise of cheaper, faster, and non-invasive screening tests for some types of cancer and could trigger improvements to anti-cancer drugs.

Nitin Baliga, Ph.D., is Senior Vice President and Director of the Institute of Systems Biology, in Seattle. Dr. Baliga expects RNAcentral to have an impact across a wide range of research, from health and infectious diseases to environmental sustainability programs.

Nitin Baliga, Ph.D

Nitin Baliga, Ph.D., develops predictive models of biological networks that catalyze strategies for personalized medicine, and a sustainable environment. Dr. Baliga is also actively engaged in HS education, bringing innovative inquiry-based curriculum on current science concepts throughout the United States. His contributions to HS education have been recognized internationally and have won awards including the Alvin J. Thompson award. (Picture and caption copyright the Institute for Systems Biology.)

 

“All organisms have an important role in non-coding RNAs, from humans to mice and plants,” Baliga told Dark Daily. “There’s broad coverage so you will see a lot of benefit to people who work directly on these organisms. It has broad applicability.”

Anton Petrov, Ph.D., bioinformatician/web developer at the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), expects RNAcentral to not only benefit biologists and bioinformaticians who study non-coding RNAs, but also other scientists.

In a Dark Daily interview, Petrov stated that researchers who are not specialists in RNA can use the website to quickly learn about various types of non-coding RNAs and integrate that information into their own work.

Anton Petrov, Ph.D

Anton Petrov, Ph.D., Bioinformatician/Web developer, Kersey team: Non-vertebrate genomics at EMBL-EBI, was a collaborator in the publication of “RNAcentral: an international database of ncRNA sequences,” published online at Europe PubMed Central (PMID: 25352543). (Picture copyright EMBL-EBI.)

“Genomes and genomic annotations are instrumental for development of anti-cancer tests and therapies, because by seeing the information about the molecules in genomic context, scientists can begin to understand the function of various non-coding RNAs,” said Petrov, who authored a paper describing RNAcentral’s tools and features that appeared in the 2015 journal Nucleic Acids Research.

RNAcentral is an offshoot of the first RNAcentral workshop that took place at the Wellcome Trust Genome Campus near Cambridge, England, in September 2011. It outlined the vision for an international database of RNA sequences.

The public launch of RNAcentral in September 2014 was followed last month by RNAcentral 2.0, which added the PDBe (Protein Data Bank Europe) and snOPY (snoRNA Orthological Gene) expert databases as well as more than 330,000 new non-coding RNA sequences and 500,000 additional cross-references. In addition, the website was upgraded to include the ability to export search results and search species-specific IDs.

As RNAcentral evolves and expands, Petrov expects the database to accelerate the understanding of the importance of RNA’s role in living organisms.

“The growth of the RNAcentral database reflects the efforts of the scientific community aimed at unraveling the biological function of non-coding RNA,” Petrov said. “Every new experiment brings some new information or reinforces that what is already known, and RNAcentral will maintain the record of this progress. In addition, the strength of RNAcentral lies in the ability to compare the data from different resources, which can provide important biological insights and lead to new discoveries.”

The availability of the open resource RNAcentral database shows how quickly “big data” is moving forward to create large pools of accessible healthcare data that can be quickly accessed, quickly searched, then analyzed with ever-more sophisticated, analytical tools that are being developed. Similar databases for DNA and proteins will undoubtedly aid pathologists and medical laboratory scientists who are developing new assays that can detect diseases at an earlier stage and with more accuracy than existing clinical laboratory assays.

—Andrea Downing Peck

Related Information:

RNAcentral Consortium Unveils Public RNA Data Resource 

RNAcentral release 1.0 

RNAcentral: An International Database of ncRNA Sequences

RNAcentral Release 2 

Researchers Produce First Map of Human Proteome, Generating Promise for Developing Novel Medical Laboratory Tests and New Therapeutics