The diagnosis, treatment and identification of a person’s predisposition to certain diseases will be facilitated by the development of a computer system for managing genomics data.
Innovation Objectives and Opportunities (Motivation)
The new generation of massive sequencing platforms such as Roche 454, Solexa-Illumina or SOLiD-Applied Biosystems allows for obtaining the genome sequence of any individual at cost and time rates more increasingly attractive.
These technologies are creating conditions so that in the near future we can have a large amount of genomics and molecular data, which can be exploited in the prediction, diagnosis and treatment of certain diseases following ad-hoc approaches, that is, through strategies for personalized medicine.
The innovative project has the following objectives:
- Develop a computer system to help manage and interpret the vast amount of genomics and genetic data generated by these platforms.
- Have an appropriate tool that allows for both the processing and integrating high volume data such as obtaining useful information about (predisposition to) the pathology and clinical characteristics of interest about the patient.
- Generate concise information to facilitate decision making by experts addressing a diagnosis or treatment that meets the specific needs of any individual.
The final project will comprise 5 modules:
Organiser for any collection of genomics and clinical data.
Genomics data analyser integrated with various different methods.
Identifier for functional impairment.
Identifier for gene-disease relationship.
Display for data and results.
Tecnología de base
El proyecto parte del desarrollo de un sistema de integración de datos genómicos relacionados con el cáncer (IntOGen: Integrative OncoGenomics, www.intogen.org) y un sistema (funcSTAR) para identificar SNPs (Single Nucleotide Polymorphisms) con una posible implicación funcional para el proyecto del mapa de haplotipos de la rata. El grupo también tiene una amplia experiencia en la utilización de bases de datos médicas como OMIM, lo que en su conjunto deber servir de base para el desarrollo de la nueva tecnología propuesta.
The project takes off from the development of an integrated system for genomics data related to cancer (IntOGen: Integrative OncoGenomics, www.intogen.org) and a system (funcSTAR) that identifies single nucleotide polymorphisms (SNP) with potential functional implications for the haplotype mapping project of the rat. The group also has extensive experience in using medical databases such as OMIM, which all together forms the basis for the development of the new proposed technology.
The University Pompeu Fabra (UPF) gives the Institute for Medical and Molecular Genetics (IGEM) an exclusive license for use over the background for developing the project, which is limited to its application in personalized medicine.
Partners Involved in the Project
A research group at UPF, composed of biologists, bioinformaticians and software engineers with experience in identifying the genetic basis for diseases such as cancer, is involved in the implementation of this project. The main participants are:
Nuria Lopez-Bigas: PhD in medical genetics—molecular basis for hereditary deafness—carried out her postdoctoral at the European Bioinformatics Institute (Cambridge, UK) and CRG (Barcelona), and was responsible for a study for the computational characterisation and gene prediction involved in hereditary diseases.
- Christian Perez-Llamas: senior computer engineer with experience in bioinformatics and medicine has led the software development for the GiTools and IntOGen projects and will be responsible for overseeing the software development.
- Roderic Guigo: serves as an external project consultant for his recognized expertise in data analysis of next-generation sequencing.
To the UPF’s core technology, the extensive experience of IGEM in R&D projects with these characteristics must be added
Entity that Assumes the Project
The project is assumed by the IGEM, which is located in Valencia. It is entirely owned by Sistemas Genómicos, which is widely recognized and experienced in research, development and commercialization of analytical applications based on DNA and RNA techniques, and in the provision of medical services in genetic counselling for hereditary diseases.
IGEM is aware that some clinicians are reluctant to approach treatment protocols based on molecular data. However, the institute is convinced that the scenario is changing and that the future lies in patterns of personalized medicine. Therefore, it foresees with this collaboration obtaining an effective, useful and simple product to offer clinicians.
IGEM’s objective with this collaboration is marketing bioinformatics developments of excellence that will be obtained by the research group at UPF, which is a partner of this project.
InnoCash Programme Funding Framework
The InnoCash programme approved funding for the project is 500,000 €, in addition to IGEM’s 1,500,000 € contribution that it promised to undertake as a private investment entity and as a direct beneficiary of the results.
The main purpose of the funding will be used for developing the personalized medicine service and market approach during the first two years, and the three years after will be dedicated to the exploitation of results and marketing services.
The reasons why the funding was approved by the InnoCash programme are: 1) the scientific-technology proposal was robust; 2) the business partner has a recognized expertise in the development and commercialization of applications in genomics; 3) possibility to market a bioinformatics solution of international excellence.