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Health depends on big data, a dynamic environment with handicaps in Catalonia

Experts and professionals shared ideas on the challenges facing bioinformatics in the future and the need for change at the governmental level at the last session of Lessons Learned in 2015

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10.12.2015

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Big data is already being used in human health and should lead to more predictive, more personalized and more participative medicine. This is a topic that concerns researchers, companies, the medical community and patients. To tackle it, the CataloniaBio association of companies and Biocat held the Lessons Learned session Big Data en salut: futurs reptes de la bioinformàtica per a les empreses on 24 November at the Barcelona Science Park (PCB).

In order to tackle future challenges and achieve an efficient process, experts recommend a change in methodology, computing tools (more use of cloud computing) and facilities in Catalonia. The strategy includes much greater levels of interaction among institutions and setting up shared, accessible computing facilities and data centers. “They have it in London, so it’s feasible. It’s just a political decision. Currently the cost is unsustainable,” said Ana Ripoll, executive manager of Bioinformatics Barcelona (BIB) and moderator for the session. “We have to provide service for all stakeholders. We’re excellent, but we are repeating ourselves. It’s a challenge we have to tackle as a country,” said the former rector of the Autonomous University of Barcelona.

Training in bioinformatics

Throughout the big data value chain, different professional profiles are needed: bioinformatics specialists, computational chemists, biologists, doctors, etc. Ana Ripoll stressed that there aren’t specific training programs to cover the current and future needs of hospitals, companies and research groups in this country. “Bioinformatics specialists are self taught or trained abroad. We need professionals with access to both of these disciplines,” she said. Catalan universities don’t offer a specific degree, nor do those in the rest of Spain, although “there are five masters, but they aren’t enough.” To this end, BIB has launched a professional training plan for the 2016-2017 school year with a degree in bioinformatics. They are also working to offer the first interuniversity degree.

Carles Ferrer-Costa, head of bioinformatics at Gendiag, thinks it’s positive that more and more doctors are specializing in medical genetics, helping to address this clinical need. Spain is one of the few countries in Europe where students can study a university degree in this field.

Technology obsolete in the near future

From the point of view of a business that develops diagnostic products like Gendiag, created in 2006 with Ferrer In Code as a sales partner, one of the main hurdles is technological obsolescence. In fact, this is what brought about the company’s bioinformatics department. In late 2010, “we began a series of tests and saw that technology changed every three months,” explained Carles Ferrer-Costa. Finding the right technology is one of the lessons learned: in 2012, they made the decision to go for the Illumina HiSeq and “the following year we ended adding the Illumina MiSeq. Both were very good decisions.”

From 2003 to 2015, numerous types of competing technology have come out, drastically cutting the cost of sequencing, each with its own characteristics. The latest data published confirms that there are 144 million variants of the human genome, and this number will continue to rise. “What’s our recipe? High-quality dNGS, ongoing validation of protocols and exploring new technology,” says Ferrer-Costa. He also recommends opting for open source and standardizing pipeline protocols, especially for diagnostics, regulatory and quality certification and, above all, feedback between diagnostics/research and clinical interpretation.

Another experience shared at the session was that of Roche Spain, which has a software development center with 300 workers in Sant Cugat del Vallès, which serves the multinational corporation worldwide. Bioinformatics Project Manager Josep Gregori explained, “Our strategy is based on advancing in personalized medicine.” In 2016, they will launch a latest generation sequencing technology platform in the Vall d'Hebron Research Institute (VHIR) clinical setting that will allow for the development of protocols to prepare samples and data analysis tools adapted to specific diagnostic needs.

A lack of public data center

Another expert, qGenomics CEO Lluís Armengol, believes that technology is expensive and that “access to public facilities is limited for SMEs, which puts us at a disadvantage in terms of competitiveness compared to public research centers.”

qGenomics is a spin-off of the Center for Genomic Regulation and the Pompeu Fabra University that operates at the interface of research and clinical care, above all in rare diseases. Its aim is to transfer knowledge generated in research environments as quickly as possible to clinical applications using mass sequencing techniques and microarrays. “Bioinformatics allows you to produce and analyze information, but not to interpret it and answer the medical question. Here is where the art of doctors, IT specialists and biologists comes in,” says Armengol.

Family histories and population data are key genetic tools. “If we have a database for our population, in most cases we can eliminate a lot of background noise in the analyses. But one of the problems is that there isn't a joint public database for Spain or the Mediterranean area,” complained Lluís Armengol. In the United States, for example, there are several collective repositories with data on more than 65,000 individuals The CEO of qGenomics believes, “All the data generated through public mass sequencing projects should also be part of public repositories.”

Where does data from apps go?

Mobile applications or apps that patients use for diseases like diabetes, heart disease, and others, generate endless amounts of valuable information “that is collected and left in the hands of app developers. This is data that we are losing for public health,” reflected Lluís del Haro, Healthcare Business Consultant at engineering company IN2.

A doctor specializing in internal medicine and former director of operations for implementing the Argos project in hospitals run by the Catalan Institute of Health, Lluís del Haro believes apps should be accredited for safety and usability. To solve this in Catalonia, IN2 and the Tic Salut Foundation are working on a marketplace pilot program that will certify and manage data from mobile devices to later be used and integrated into current health systems. This initiative falls under the framework of the Digital Health project promoted by the Catalan Ministry of Health.

Legal framework

Resolving the ethical conflict that arises from using this data is another challenge that everyone has an opinion on. “Data can only be used with consent,” clarifies Malcolm Bain, partner at ID Law Partners. We have to distinguish between regulated data and unregulated data. “The majority of data is coded at some point to link it to one individual and thus give it value, so it is protected by the LOPD,” argued the lawyer.

“The law speaks of layers or scope of consent: the first is for medical diagnosis of a patient; the second, for research in a specific project; and the third for any use,” explained Bain. He also explained, answering a question from the audience, that it isn't legal to use social media to share health data.

With regard to managing big data, Spanish law established very high safety measures, much stricter than those in Finland and Germany, for example. We’re not talking only about computer processes, but also “the training of personnel, as that is where the biggest security breaches are often found,” admitted Malcolm Bain.

The most important lesson learned so far? “To think about how an application will be designed, its lifespan and how data can be used from the very beginning,” concluded Bain.

Watch the video of the Lessons Learned sessions.

 

See you in 2016 to hear about new lessons learned!

 

Report on the previous Lessons Learned:

Lessons Learned sobre bigdata

From left to right: Josep Gregori, Carles Ferrer-Costa, Ana Ripoll, Lluís de Haro, Malcolm Bain and Lluís Armengol.

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