To start the new year on a positive note, ESPACE hosted the webinar ‘New IT approaches in genome analysis’ together with EUCANCan, another Horizon 2020-funded health research project, on January 11. The event was moderated by Christian Lawerenz (Steinbeis).
The three-hour-long webinar began with a brief introduction of EUCANCan and ESPACE by David Torrents (Barcelona Supercomputing Center/EUCANCan Coordinator) and Christian Conrad (Berlin Institute of Health), respectively.
Thereafter, Sven Twardziok (Charité Berlin) presented an open sharing platform that is compliant with GA4GH standards. Five keynotes by representatives of Dell, Illumina, SVA, Intel, and Institute Curie followed Twardziok’s presentation.
This article provides a summary of the key topics discussed during the webinar.
About EUCANCan
Presenter: David Torrents (BSC/ EUCANCan Coordinator)
EUCANCan aims to support and enhance modern oncology by implementing a cultural, technological, and legal integrated framework across Europe and Canada. The framework will facilitate efficient analysis, management, and sharing of cancer genomic data within and between the project’s nodes.
David Torrents of Barcelona Supercomputing Center coordinates EUCANCan. The project is funded by the European Commission through the Horizon 2020 programme on the European side and the Canadian Institute of Health Research (CIHR) on the Canadian side.
About ESPACE
Presenter: Christian Conrad (Berlin Institute of Health)
ESPACE, an acronym for Expression and Spatial analysis Pancreas Atlas Consortium Europe, is part of the Human Cell Atlas (HCA), a global mission that aims to create comprehensive reference maps of all human cells to better understand human health and diagnosing, monitoring, and treating disease. The ESPACE consortium will build a first version of the HCA of the pancreas.
The project is coordinated by Roland Eils of Charité – Universitätsmedizin Berlin and has received funding through Horizon 2020.
A walkthrough of the GA4GH platform
Presenter: Sven Twardziok (Charité Berlin)
The first attempt to sequence a whole human genome took over a decade. Today, this same feat can be accomplished in a single day. By 2025, it is estimated that over 60 million patients will have their genome sequenced in a healthcare context.
This development offers plentiful opportunities for science. However, managing these large volumes of data effectively and securely is a considerable challenge – a challenge that the GA4GH is trying to tackle with its open sharing platform.
The GA4GH is a policy-framing and technical standards organization which aims to make the large amounts of life science data collected in healthcare and research institutions around the globe more easily accessible to researchers. The platform takes a low-tech approach where users can, for example, query an individual beacon to determine if the associated dataset contains information about a given genetic variant. If there is a match, the user can access the anonymized data through a computing cloud located near the protected source data.
For this type of platform to function properly, standards for how data should be stored, categorize, authorized, etcetera, must be in place.
5 presentations by representatives from leading industry partners
Industry-academia partnerships are becoming more and more important to research.
EUCANCan and ESPACE’s webinar aimed to offer a platform for business and academia representatives to meet and engage on common issues. To this purpose, the webinar included five keynote presentations by industry representatives, each followed by a short Q&A session.
Dell: Cloud technologies and the potentials for research
Marten Neubauer
Opening with a story about when he visited the Broad Institute of MIT and Harvard two years ago, Marten Neubauer told how he was first surprised to learn that most of the Broad Genomics Platform’s data was not saved on local servers but on Google Cloud. Since then, more and more researchers and businesses have adopted cloud storage in some capacity.
In his presentation, Neubauer talked about some of the key advantages of storing data in the cloud and explained how Dell can help their partners to, among other things, generate, store, analyze, and archiving data.
Illumina: Expand Your Understanding of Biology with Illumina Single-Cell & Spatial Sequencing
Pawel Zajac
Single-cell sequencing examines the sequence information from individual cells with optimized next-generation sequencing (NGS) technologies, a method of analysis that can help improve human understanding of biological health and disease.
Illumina develop, manufacture, and market the type of NGS technologies required for single-cell sequencing studies. In his presentation, Pawel Zajac showcased how Illumina’s technology can be used in science, focusing on the technology’s cancer research application.
SVA: Automation of analysis processes in genomics
Giscard Venn
Giscard Venn began his presentation by reminding the audience that much data analysis was still done with paper and pen only a few decades ago. Illustrating how things have changed in recent years, he showed a crowded slide with hundreds of logos of current Big Data and AI tooling providers.
The abundance of tools available today makes setting up efficient workflows between different systems increasingly difficult and time-consuming. Giscard Venn presented several examples of how smart integrations allow people working in life science to conduct more efficient data analyses. He also provided examples of how SVA can help companies and universities integrate their different systems.
Intel: A discussion about the use of Artificial Intelligence (AI) in genomics
Michael McManus
Today, there is a severe shortage of genetic counselors in the U.S. Only around 15,000 genetic counselors are currently working in the country, though over two million people in the country are being actively sequenced in government projects. At the same time, tons of sequencing is also undertaken in the medical sector.
As more and more people are having their genomes sequenced, the demand for new or improved digital methods of analysis is increasing. In his presentation, Michael McManus provided examples of how Artificial Intelligence can help speed up the interpretation process. He also showcased how Intel works to ramp up large-scale sequencing and analysis.
Institut Curie: Alignment and sorting HTS data with Message Passing Interface
Frederic Jarlier
In his presentation, Fredric Jarlier talked about how high-performance computing and parallelization tools can compress delivery time in the early processes of high-throughput sequencing data.
Emphasizing that a one-size-fits-all approach to patient care is no longer enough, he provided examples of how high-throughput screening data analysis can be used to advance precision medicine.
Conclusion
The ESPACE and EUCANCan consortia direct a huge ‘thank you’ to all presenters and participants in the webinar.
The advanced information technology solutions presented in this webinar are essential for today’s complex analytical requirements of molecular and medical research and application.
Therefore, we believe that active partnerships between research projects and industry partners are imperative to move science forward. To this end, we consider events like this webinar where members of industry and academia can meet and discuss joint opportunities and challenges very important. We are therefore thankful for the great interest we received from numerous attendees of the webinar.
Please feel free to contact us by sending an e-mail to ESPACE’s project management team if you have any questions regarding ESPACE or the topics covered in this week’s webinar.