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The first bioinformatics tool to analyze mass transcriptomic data in real time

The company Sequentia Biotech, a start-up that originated in the Center for Research in Agricultural Genomics (CRAG) and that has since relocated to the facilities of the Barcelona Science Park  and the Autonomous University of Barcelona Research Park, has developed the first bioinformatic tool capable of analyzing mass transcriptomic data in real time. The cloud computing platform has been launched with the name AIR (Artificial Intelligence RNAseq). “There is a data analysis bottleneck in genomics: on one hand vast amounts of data are generated with NGS (Next Generation Sequencing) technologies, but there is no simple and effective way to store, manage and analyze that amount of data,” said Walter Sanseverino, CEO and co-founder of Sequentia Biotech, in remarks to Biocores.

The researcher and entrepreneur went further to say that, since bioinformatics is a “relatively new discipline, it has high demand but few people specialized in it,”. This is where the need arises for tools that scientists can use without bioinformatic support. “We wanted to respond to this need, specifically in the area of transcriptomics, where RNA sequencing is the leading method for the type of analysis that AIR is meant to perform,” says Sanseverino. The software currently uses a database of 45,000 genomes, and is available in the cloud thanks to SaaS (Software as a Service) technology. Thanks to this bioinformatic prediction tool, researchers can study transcriptomic data linked to the RNA genome of any species, which in turn are attained through massive sequencing technology (NGS). 

A tool for any researcher who analyzes transcriptomic data

The  transcriptome can offer highly valuable information on the genes being expressed in a cell at any given time; therefore, the development of techniques such as RNA-Seq have made it possible to advance in the study of gene expression dynamics, and their impact on biological processes and the onset of diseases such as cancer. Sanseverino underscores the simplicity, quickness and low cost of the bioinformatics tool developed by Sequentia Biotech. “In just three steps it takes you from the FastQ to the complete DEG (Differential Gene Expression) and GEOA (Gene Expression Annotation) reports. On another note, it is extremely quick, as the analysis is automatic, and the results can be exported to a pdf or Excel file. You can even create a private link to share them with the rest of the research group or Principal Investigator,” Sanseverino told Biocores.

The advantage offered by the Sequentia Biotech tool is that it is the first RNA-Seq platform worldwide that overcomes three key challenges. On one hand, the AIR platform performs the automatic analysis and comparison of RNA samples, and interprets the data in the same package. On another, the bioinformatics prediction tool works with the sequenced genome of any species; therefore it is not limited to model organisms. Sequentia Biotech has designed this program using the latest algorithms and published bioinformatics methods. AIR is updated in step with these tools, and is also scalable. In other words, an unlimited number of users can connect to the platform.

Source: Science Park of Barcelona

According to the company, the analysis will cost some two or three dollars per sample. First-time users have access to 6 samples for free, and after that samples start at 3,50€ per sample per year. “That makes for major savings when you consider that a standard analysis of the same quality costs around 100 dollars,” says Sanseverino. In other words, the cost of the analysis performed with the AIR system is fifty times less than with other comparable methods. Another major advancement brought by this transcriptomic data analysis tool is that it is an automated system. In other words, scientists only have to upload the data and define the species reference genome. This makes it possible for any user, even if they are not experts in bioinformatics, to use this cloud computing service. The software is also fast and user-friendly. Users just have to follow three steps, and the first reports can be obtained in less than two hours.

In Sanseverino’s opinion, the AIR platform can be used by “anyone who wants to analyze RNA sequencing data.” As he told Biocores, the system “is aimed at researchers, people whose bioinformatic knowledge is not in-depth enough to work with a pipeline, and don’t have time to study algorithms, or who may be doing their first RNA analysis. But even bioinformatics specialists will find value in this tool. It is very complete, no matter how you look at it,” he adds. According to Sanseverino, the AIR tool “also lets users make changes and get results in real time. For example, if the user identifies an anomalous result, they can eliminate it from the PCA chart and see the updated results, both in the PCA and the annexed results (quality parameters, differentially expressed genes and GEOA).”

The AIR platform was presented some weeks ago at the Plant and Animal Genome XXV Conference (PAG), the world’s premier agricultural genomics meeting, where over 3,000 experts who work in the molecular biology of plants and animal genetics come together every year. Sequentia Biotech tells Biocores that AIR is now in its beta version, and if everything goes according to plan, the final version will be ready in early April, with its pricing defined, as well as updates to regularly offer new functions and analysis. With the development and marketing of AIR, the company, which took its first steps in the consortium formed by the CSIC, IRTA, the University of Barcelona and the Autonomous University of Barcelona, meets one of the goals for which it was created. In the end, Walter Sanseverino and Riccardo Aise, founders of Sequentia Biotech, have improved access to the data obtained through next generation sequencing, in a way that is effective and affordable.