From the left, Vicente Arnau, Wladimiro Díaz, Carmen Ivorra

The EOSAL project of the biotechnology company Sequencing Multiplex (Seqplexing) and the Institute of Integrative Systems Biology (I2SysBio), both in the Science Park of the University of Valencia, has been selected by the CHALLENGES-COLABORATION program of the Ministry of Science and Innovation. The team will apply a company patent for the detection of genetic alterations for the diagnosis of non-hereditary cancers, mainly.

Copy number variations (CNVs) can affect different regions of the genome, contributing to the development of diseases such as some cancers or certain metabolic disorders such as familial hypercholesterolemia.

Despite their importance, it is not easy to have maps and databases of copy number variants in the genome, since their identification generally depends on slow and sophisticated procedures. However, Seqplexing has marketed products, based on its own patent generated five years ago, that allow the detection of genetic alterations that cause hereditary diseases through a capillary sequencing technique – quick, simple and effective – that will soon be incorporated into hospital analysis systems. of this technique – which incorporates new software for the almost instantaneous interpretation of the data generated by EOSAL – and its application is aimed this time at the analysis, through next-generation sequencing, of CNVs and somatic mutations in more complex samples, such as those of non-hereditary cancers, a field of great importance for precision medicine.

“This technique allows the obtaining, identification and analysis of a high number of fragments of interest designed according to the needs of the study. The simplicity of the protocol, which is carried out in a single step, allows for reduced handling and analysis times – the entire process lasts just over two hours; It facilitates laboratory work in hospitals and reduces the probability of error,” comments Carmen Ivorra, scientific director of Seqplexing and co-author of an article published in Clinical Chemistry (Clin Chem. 2020 Feb 18) that supports the idea. that EOSAL technology is an alternative to MLPA, a traditional technique for the study and characterization of CNVs.

To carry out the project, the company will work in cooperation with the Theory, Bioinformatics and Computing Group (TBC) of I²SysBio, a joint center of the Universitat de València and the CSIC, both holders of the award for the program CHALLENGES-COLABORATION.

The university group will approach the project from bioinformatics in a double aspect. On the one hand, it will develop a computer program aimed at facilitating the experimental design of the new kits. On the other hand, it will create a web application for the processing and interpretation of the sequencing data generated by EOSAL. “This is a working model technologically linked to the 'Garnatxa' supercomputer of the I²SysBio, a machine for bioinformatics capable of providing almost immediate and highly reliable results,” indicates Vicente Arnau, professor at the Department of Computer Science at the University of Valencia and head of the project at the I²SysBio. According to Wladimiro Díaz, head of the same department and also a member of the group at the Institute, "it is a multicomputer cluster designed expressly for bioinformatics and computational biology. The equipment is structured around a globally distributed file system of 3.2 Pb capacity, has a RAM memory of more than 17 Tb and a computing power of 648 cores." Acquired with FEDER Funds, the supercomputer is available to both the scientific community and biotechnology-based companies.

The objective of the RETOS call, which occurs within the framework of the State R&D&I Plan, is the financing of cooperation projects between companies and research organizations, in order to promote the development of new technologies and the business application of new ideas and techniques, as well as contribute to the creation of new products and services.

The Theory, Bioinformatics and Computing (TBC) group's fundamental objective is the analysis of bioinformatics data. He works on metagenomic and genomic data, interaction networks and, in general, on the application of mathematical methods with high-performance computers for the analysis of large volumes of data. Its main line of research is metagenomics.

Seqplexing is a firm focused on the design of quality solutions for carrying out genetic studies. The company stands out for the development of products that are very easy to use and implement in different types of genetic studies applicable to both research and clinical practice.