Project

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Fast Pathogen detection through embedded genomics in resource limited conditions

English title Fast Pathogen detection through embedded genomics in resource limited conditions
Applicant Bezati Endri
Number 177282
Funding scheme Bridge - Proof of Concept
Research institution
Institution of higher education Swiss Institute of Bioinformatics - SIB
Main discipline Genetics
Start/End 01.09.2017 - 31.08.2018
Approved amount 130'000.00
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All Disciplines (2)

Discipline
Genetics
Electrical Engineering

Keywords (5)

Embedded Systems; Genomics; FPGA; Low Power; In the field analysis

Lay Summary (German)

Lead
In unserer globalen Welt, in der Menschen und Güter innerhalb kürzester Zeit von einem Kontinent zum andere transportiert werden können, ist die Überwachung von Epidemien zu einer grossen Herausforderung geworden. Der Ausbruch von H5N1, EBOLA und ZIKA sind nur drei jüngste Beispiele einer wirtschaftlichen und humanen Katastrophe, die viele Leben gekostet hat und die die betroffenen Länder noch lange beeinflussen wird. Um künftig Regierungen und Gesundheitsorganisationen bei der Vorbeugung und Eindämmung der Epidemien zu unterstützen, widmet sich dieses Projekt der Entwicklung eines tragbaren Gerätes, das die Erkennung und Überwachung von Krankheiten ermöglicht.
Lay summary
Inhalt und Ziele

Wir haben uns das Ziel gesetzt, ein tragbares Gerät mit geringem Leistungsverbrauch zu erstellen, das auch ohne Internetverbindung mit hoher Bandbreite und teurer Computer Cluster direkt vor Ort über 250 Krankheitserreger gleichzeitig erkennen kann. Genauer gesagt möchten wir die Erkennung von Pathogenen bei Menschen und Tieren, einfacher, schneller und günstiger gestalten. Es handelt sich hierbei um ein Überwachung-System für Erreger in Echtzeit, das insbesondere an Orten der Welt verwendet werden kann, an denen die hochwertige Ausrüstung der entwickelten Länder nicht zur Verfügung steht, weil die nötigen Mittel fehlen und somit die medizinische Versorgung der lokalen Bevölkerung nicht immer gewährleistet werden kann. 

Sozialer und wissenschaftlicher Kontext

Das Endprodukt unserer Arbeit wird ein tragbares Gerät mit geringem Leistungsverbrauch sein, das direkt im betroffenen Gebiet angewendet werden kann. Durch rasche Routineuntersuchungen und -überwachungen, kann der Ursprung von Infektionen schnell gefunden werden. Die darauffolgenden Gegenmassnahmen werden nicht nur die Verbreitung der Krankheit in dem betroffenen Land eindämmen und somit die Übertragung der Epidemie in Nachbarländer und entfernte Nationen vermeiden können, sondern auch die allgemeinen medizinischen Behandlungskosten reduzieren und vor allem Leben retten.


Das Resultat dieses Projektes ist die Gründung von Streamgenomics GmbH, um das Produkt auf den Markt zu bringen.
Direct link to Lay Summary Last update: 27.03.2019

Lay Summary (French)

Lead
Dans notre monde globalisé, régit par des milliers d’échanges de personnes et de marchandises, la surveillance des épidémies est une nécessité toujours plus difficile. Les virus H5N1, EBOLA et ZIKA sont trois exemples récents qui ont couté la vie à de nombreuses personnes et impacté l’économie présente et future des pays touchés.Dans le but d'aider les autorités et les organismes de santé mondiale à gérer ces épidémies, nous voulons construire un dispositif portable, capable de détecter et de surveiller un grand nombre de maladies indépendamment du lieu.
Lay summary

Sujet et objectif

Notre objectif principal est de permettre la détection dans le terrain de plus de 250 agents pathogènes. Plus précisément, nous souhaitons rendre plus facile, rapide et moins chère la détection de ces agents autant pour les humains que les animaux. Nous voulons offrir un système de surveillance en temps réel dans des régions du monde qui n'ont ni les ressources ni l’équipement nécessaires pour médicalement diagnostiquer leur population comme dans les économies avancées.

Contexte social et scientifique du projet de recherche

Le résultat de notre travail est un dispositif portable de faible consommation qui peut facilement fonctionner sur le terrain. Car rendre accessible à tous une surveillance de routine efficace, c’est permettre des mesures rapides pour soigner ainsi que pour prévenir et endiguer la propagation de ces maladies. Dans tous les cas, c’est surtout sauver des vies.

Streamgenomics sarl a été créée pour amener le produit sur le marché.

Direct link to Lay Summary Last update: 27.03.2019

Lay Summary (English)

Lead
Surveilling epidemics in a globalized world is a tough task, given the thousands of exchanges through the transport of people and goods. H5N1, EBOLA and ZIKA viruses are three recent examples of outbreaks where many people lost their lives and whose consequences will have a huge impact on the affected countries. In order to assist and help authorities and health organizations to enclose such epidemics, this project aims to build a portable device that can detect and surveil such diseases whenever they first occur.
Lay summary

Subject and Objective

Our main objective is to create a low-power portable device which is able to detect 250 or more pathogens in parallel at the point of care without the need of high-bandwidth internet connection and expensive computer clusters. More precisely, we want to make the detection of pathogens for both humans and animals easy, fast and cheaper. We want to offer a real-time surveillance system for detecting pathogens in areas of the world that do not have the necessary means to medically check the local populations with the same high-end equipment as in advanced economies. 

Social and Scientific context

The result of our work is a low-power portable device that can easily be operated in the field. By enabling a swift routine surveillance, an early detection of the infection loci is ensured. This will help taking rapid counter-measures not only to prevent the spread of diseases in limited-resource countries and to avoid epidemics to reach near and far nations but also to reduce the overall medical costs and most importantly to save lives.

As an output of this project, Streamgenomics sarl was created to bring the product in the market.

Direct link to Lay Summary Last update: 27.03.2019

Responsible applicant and co-applicants

Employees

Publications

Publication
Towards in the field fast pathogens detection using FPGAs
Casale Brunet Simone, Schuepbach Thierry, Guex Nicolas, Iseli Christian, Bridge Alan, Kuznetsov Dmitry, Sigrist Christian, Lemercier Lemercier, Xenarios Ioannis, Bezati Endri, Towards in the field fast pathogens detection using FPGAs, in 2018 28th International Conference on Field Programmable Logic and Applications (FPL), 0.

Collaboration

Group / person Country
Types of collaboration
Faculté de biologie et médecine CHUV / Claie Bertelli Lombardo Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
REDS HEIG-VD / Dr. Romuald Mosqueron Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
SIB Days 2018 Poster Embedded fast pathogen detection in resource limited conditions 26.06.2018 Bern, Switzerland Bezati Endri;


Communication with the public

Communication Title Media Place Year
Media relations: print media, online media A BRIDGE over troubled water Laborjournal International 2018
Talks/events/exhibitions Data science to support progress in biological research and health German-speaking Switzerland 2018

Use-inspired outputs


Start-ups

Name Year

Abstract

The rapid detection and identification of infectious pathogens are a critical need for healthcare in both developed and developing countries. Remarkable progress has been made in using genomic information to prevent and manage viral outbreaks. However, more than one billion people in resource-limited developing countries still suffer from one or more neglected infectious diseases, most of which are found in Africa and Southeast Asian countries. Infectious disease diagnostics and epidemiological surveillance systems in many of these countries are not as advanced as in developed economies, where continuous power, strong communication infrastructure, laboratory infrastructure, trained personnel and conventional sequencing technologies are available. This disparity has many consequences, both ethical and social. Ensuring advances in genomics applied to the health improvement of peoples’ living conditions in developing countries is an important contemporary challenge. The purpose of this project is to give access to worldwide health organizations and local administrations to a real-time embedded and battery powered surveillance solution, not bigger than a smartphone. This solution permits a rapid detection and identification of many diverse infectious disease pathogens by using embedded genomic analysis. To deploy this solution an embedded DNA sequencer should be used for retrieving the genome of each individual at the point of care. A potentially embedded sequencer is the MinION from Oxford Nanopore Technologies. Successively, each genome is analyzed in order to find the presence of known pathogen patterns using proprietary algorithms that have been developed by the Swiss Institute of Bioinformatics (SIB). This step is extremely computationally expensive and nowadays solutions require sending genomic data to remote analysis laboratories through cellular data networks which can be extremely slow and unreliable. The objective of this project is to revolutionize this part by providing an embedded and low-power solution that enables the analyses in-loco without requiring any expensive clinical equipment or other kinds of technologies. For this purpose, a multiprocessor-system-on-chip architecture that contains a reconfigurable logic (MPSoC with FPGA) will be used. This kind of chip provides low-power massive parallelism but with the cost of being difficult to program. The scientific work achieved during the PhD studies of the candidate has demonstrated that MPSoCs can be easily and efficiently programmed exploiting high-level dataflow programming paradigm and models. Finally, his current research work within the Swiss Institute of Bioinformatics (SIB) has already proved how genomic analysis algorithms can be effectively implemented on FPGAs platforms.
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