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European Project Awarded €10M to Build Biobank, Run GWAS for Sudden Cardiac Arrest


NEW YORK (GenomeWeb) – A new consortium headed by scientists at the University of Amsterdam aims to assemble within the next five years one of the largest genomic databases devoted exclusively to the study of sudden cardiac arrest.

The European Union recently awarded the project, called ESCAPE-NET, €10 million ($10.8 million) to build the biobank, which will eventually include 20,000 DNA samples from SCA patients. Investigators intend to genotype the biorepository using Illumina arrays with the aim of identifying markers that can be used to inform treatment development and prevention efforts.

The project officially commenced in January and is slated to run through December 2021. It has been funded through the EU's Horizon 2020 program.

BC Platforms, a Helsinki, Finland-based bioinformatics company, has been tapped to develop the infrastructure that will enable the sharing of data across the 16 institutions and companies taking part in the project. Participants hope to maintain the database after the effort concludes in 2021.

"I do believe that we can make inroads into solving this problem for the simple reason that SCA is a very difficult phenotype to collect," said Hanno Tan, a cardiologist at the Academic Medical Center of the University of Amsterdam who is leading the project. "There aren't that many groups around the world that have dedicated themselves to studying this," Tan said. "The mere fact that we have collected within Europe the centers that matter is already a big advantage, and I am convinced that we are going to be able to contribute something important."

Tan's work at AMC has provided the basis for ESCAPE-NET. For the past decade, he has amassed a registry of 12,000 DNA samples obtained from SCA patients in the Dutch province of North-Holland, collected from both blood and incubation tubes. North-Holland surrounds Amsterdam and has about 2.5 million inhabitants.

"I collaborate with emergency medical services and collect information on all the sudden cardiac arrests occurring there, and because of that the coverage is about 100 percent," said Tan of the registry, which is called ARREST. "From these people who suffer cardiac arrest, I collect clinical information, medical history, medication use, and DNA," he said. "The purpose of this is to understand the factors that contribute to sudden cardiac arrest in the community."

The purpose of ESCAPE-NET is much the same, as Tan aims to build a European-wide database that will give investigators sufficient power and phenotypic information to run informative genome-wide association studies. "On one hand, we want to look at the factors that lead to the occurrence of sudden cardiac arrest," said Tan, [but] "we also want to look at new treatment options."

According to Tan, SCA causes about a fifth of all deaths in Europe annually, and survival rates are only between 5 and 20 percent. While there is a "large unmet medical need" to investigate the genetics of SCA, he said that efforts to date have been stalled by the lack of such a database, as SCA is by definition sudden and unpredictable, and so obtaining DNA samples and quality phenotypic information has been a challenge. Definitions of what constitutes SCA also vary, which is why ESCAPE-NET's database may eventually house about 100,000 samples, yet only a fifth of those will likely be genotyped.

"We don't have all the same information," said Tan. "Some centers do not have DNA, some centers do not have other information, there is variability in the consortium."

Within the next two years though, ESCAPE-NET will genotype about 20,000 samples using Illumina's Global Screening Array, which the San Diego-based vendor launched last year. Customers can screen 24 samples on each array, each of which contains 660,000 markers covering 26 populations, including about 50,000 markers specific to clinical research. Users can also add up to 50,000 other markers relevant to their studies.

The chip has already been adopted by a number of other biobank projects. For instance, in December the Estonian Genome Center announced plans to screen its 35,000-sample biorepository using the GSA.

The German research institution Helmholtz Zentrum München will be responsible for genotyping the ESCAPE-NET samples, according to Tan. In addition to the genotyping, consortium members will conduct epigenetic profiling on a select group of cohorts. Tan said the project will carry out the GWAS and epigenetic profiling within the next two years, as the data is necessary to realize other aims of the project, such as designing a risk-score prediction model.

Tan also hopes to have the ESCAPE-NET database up and running within a year to support the aims of the group, and consortium member BC Platforms is already working toward that goal, according to its CTO Timo Kanninen. Kanninen said in an interview that BC Platforms will set up the biobank infrastructure for the entire project, providing its existing BC|Genome platform to ESCAPE-NET participants while developing a new data-sharing infrastructure specifically for the project, which it calls BC|Rquest.

"The business model is that we will give our existing products to this project free of charge," Kanninen said. "Our logic is to develop new features off of our platform with this funding," he said. "It's always a product development exercise for us."

BC Platforms has participated in no fewer than nine EU projects to date as a software developer, designing tools for data integration and sharing. BC|Genome, one of the 20-year-old firm's core offerings, provides a scalable platform for complex genomic analyses. It contains multiple modules for various data types and can serve as a hub for diverse resources as well as clinical databases and electronic health records.  

According to Kanninen, BC Platforms will use this product as a foundation for ESCAPE-NET, enabling the group to build and manage its joint database and establish a prediction model for SCA predisposition based on a variety of risk factors. It will enable the researchers to produce evidenced-based advice report describing the optimal first-response treatment strategy and associated infrastructure.

"We will develop data-harmonization tools and distribute data analysis features for this kind of biobank network," Kanninen said. "We will determine how to integrate, how to harmonize, how to best analyze this data." BC Platforms is developing its BC|Rquest tool specifically for linking biobanks together. He said the company will launch BC|Rquest as a product later this year.

"We are already developing the technology and this will be a new product," said Kanninen. "This is our business model: to obtain EU funding to develop new products," he said. He noted that by participating in ESCAPE-NET, the firm will benefit from the ability to collaborate with "top scientists in Europe, get their feedback, and understand what features they would like to have."

BC Platforms will receive €349,500 for its role in the project.

In addition to the University of Amsterdam, BC Platforms, and Helmholtz Zentrum München, other ESCAPE-NET participants include Dutch firms Panaxea and Drug Discovery Factory; the Karolinska Institute in Sweden; the European Resuscitation Council based in Belgium; Université Paris Descartes; the University of Pavia, the Mario Negri Institute for Pharmacological Research, and Istituto Auxologico Italiano, all located in Italy; the Capital Region of Denmark; VU University Medical Center Amsterdam; the European Society of Cardiology; and the Medical Rescue Service for the Hradec Kralove Region in the Czech Republic.

Tan said that in addition to accomplishing the goals of ESCAPE-NET, he would like to see the consortium continue after the project wraps up in 2021."It's valuable that all of these people have come together," he said. "It would be a big shame if after five years everyone goes on their own way again."

Both Tan and BC Platforms' Kanninen said that the group is evaluating ways of maintaining the database after the end of the project.