Analyze Genomes – Hasso Plattner Institute

R&D

Organisation Hasso Plattner Institute

Prof.-Dr.-Helmert-Str. 2-3 | 14482 Potsdam | www.hpi.de

»Analyze Genomes: A Federated In-Memory Database Enabling Precision Medicine«

http://we.analyzegenomes.com

Dr.-Ing. Matthieu-P. Schapranow | Program Manager E-Health & Life Sciences +49 (331) 55 09 -1331 | +49 (160) 90 82 25 60 | schapranow@hpi.de

R&D

activities Analyze Genomes: A Federated In-Memory Database Enabling Precision Medicine In an increasing number of cases, medical experts discover roots of complex diseases, such as cancer, within the human genome. Therefore, analyses of the individual genetic code of each patient are the foundation of the innovative precision medicine. For example, the genetic profile of a tumor sample can provide insights about the efficiency of available chemotherapies. However, the acquisition of the genetic profile is still time-consuming, e.g. due to the number of individual processing steps, the sheer amount of data, and the use of arbitrary data formats. The »Analyze Genomes« platform of the Hasso Plattner Institute (HPI) in Potsdam built upon latest in-memory technology enables new perspectives for precision medicine in the clinical routine. For the first time, it enables the analysis of big medical data and their combination with global medical knowledge in real time. As a result, medical experts are able to discover and assess available therapy options in a much faster way to initiate the best one for each patient individually.

Together with experts from life sciences, such as medical experts, biologists, and geneticists, researcher of the HPI under the management of Dr. Matthieu-P. Schapranow have developed the cloud platform ↗Analyze Genomes (↗Figure 4). It enables experts from various disciplines to perform real-time analysis of genome data on their own without the need for dedicated IT personnel. The in-memory technology researched at the chair of HPI founder Prof. Dr. Hasso Plattner provides the technology foundation for the rapid data processing and analysis.

In the »Medical Knowledge Cockpit« doctors as well as patients obtain together a holistic view on individual genetic variants, biological connections, and links to worldwide available clinical trials. A time-consuming search in the Internet by medical doctors is no longer necessary as worldwide databases containing medical knowledge are searched automatically and relevant results are filtered on the patient’s individual anamnesis.

Clinicians can use the »Drug Response Analysis« to incorporate insights from documented historic cases to predict the efficiency of chemotherapies for actual patient cases. Through corresponding laboratory tests, these predictions can be validated to extend the knowledge about pharmaceuticals and their efficiency.

Researchers can explore and assess individual changes within the DNA using the »Genome Browser« in freely selectable level of detail to identify sources of pathogenic changes. In addition to individuals, data of patient cohorts can be examined using the »Cohort Analysis«, e.g. to verify responder or non-responder for a specific medical treatment interactively.

Translating biological connections and affected cell functions in the »Pathway Topology Analysis« helps to assess the impact of, e.g. of a specific tumor disease on the human body.

Together with a team of cardiologic experts and researchers, we design in the »SMART«

consortium specific software applications to establish a systems medicine approach for heart failure. For the first time, all individual sources of patient data, e.g. genome, proteome, and hemodynamics data, are combined in a single software system. This enables the combination and real-time analysis of patient-specific data to predict the outcome of alternative therapy options. As a result, clinicians and medical experts are supported in deriving the best patient-specific treatment option from the beginning.

Furthermore, health researchers, public authorities, as well as small and medium-sized enterprises can explore distributed health care data using the real-time analysis functions developed in the »SAHRA« consortium. Thus, they get more detailed insights into regional health care structures using existing and regularly acquired public health care data.

The »Analyze Genomes« platform enables a completely new way of working. Medical experts and researchers are no longer slowed down by long-running data processing. Instead they can test and verify their hypotheses directly. Through the integration and combination with worldwide sources of medical knowledge manual and time-consuming searches in the Internet are omitted. As a result, precise treatment decisions can be made always on the basis of the latest available, worldwide medical knowledge for the patient’s sake.

R&D cooperation

◼ Stanford University

◼ Massachusetts Institute of Technology (MIT)

◼ German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT)

◼ Charité University Medicine Berlin

◼ Max Delbrueck Center for Molecular Medicine (MDC) Cooperation

with partners in industry

◼ SAP SE, healthcare and life sciences

◼ Intel Corp., life sciences research

◼ Bayer Healthcare, life sciences

◼ U.S. Department of Veteran Affairs Additional

Information Amongst others, the German Federal Ministry of Education and Research and the German Federal Ministry for Economic Affairs and Energy, generously support our research.

Our life sciences activities are combined in the cloud platform »Analyze Genomes«, which was honored by, amongst others, the 2015 Personalized Medicine Award, the 2014 European Life Science Award for Top 3 Most Innovative New Services, and the 2012 Innovation Award of the German Capital Region. Furthermore, our research results are published in international journals and selected work is transferred to industry partners, who are responsible for commercialization. As a result, our findings support precision medicine to become a worldwide clinical routine.

Figure 4: Cloud platform »Analyze Genomes«

4.1.10 Geoinformatics – GFZ German Research Center for GeoSciences – GeoMultiSens

R&D

Organisation GeoMultiSens – Scalable Analysis of Big Remote Sensing Data http://www.geomultisens.gfz-potsdam.de/

Dr. Mike Sips | Coordinator | GFZ German Research Centre for Geosciences | sips@gfz-potsdam.de R&D

activities For more than 40 years, remote sensing satellite missions are globally scanning the earth´s surface. A comprehensive analysis of this data has the potential to support solutions to major global challenges related to climate change, population growth, water scarcity, or loss of biodiversity. This analysis is a challenging task since

◼ there is a lack of Big Data-adapted analysis tools and

◼ available data will increase significantly over the next years due to new satellite missions that will allow to measure data at higher spatial, spectral, and temporal resolutions than ever before.

GeoMultiSens enables comprehensive analysis and, hence, understanding of earth surface processes on a global scale.

R&D cooperation

◼ Helmholtz-Zentrum Potsdam Deutsches GeoForschungsZentrum GFZ,

◼ Humboldt-Universität zu Berlin,

◼ Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB).

The consortium aims to develop an integrated processing chain comprising:

◼ data acquisition,

◼ pre-processing and homogenization,

◼ data storage,

◼ remote sensing analysis, and

◼ visual exploration.

It will demonstrate its effectiveness on various remote sensing application scenarios.

The consortium focuses on developing a scalable and modular open source Big Data system.

Additional Information

A Big Data Programme project of the Federal Ministry of Education and Research.