When are the events scheduled?


Oct 13-14th




How next-generation sequencing can change clinical biology and therapeutics

@Campus Biotech, Geneva,  Oct 13-14, 2016



Metagenomics, based on next-generation sequencing (NGS), has been available for a decade and is now widely used for research purposes. In parallel, clinicians are currently paying a growing interest in how NGS could help in the diagnosis and management of several diseases. In the field of infectious diseases, metagenomics has demonstrated its potential in the identification of pathogens and the inference of the antibiotic susceptibility profiles of bacteria. On a broader perspective, metagenomics of the intestinal microbiota has open several opportunities in various clinical fields such as obesity, autism and cancer.

From all those findings, we believe that at this point a new, exciting discipline is emerging that we propose to refer as clinical metagenomics, located at the interface of clinical biology and bio-informatics.

While many obstacles remain to be overcome before clinical metagenomics could be used as a routine diagnostic tool, namely the costs, turn-around time and the specific skills it requires, now is a relevant time to gather the major players in clinical metagenomics (clinicians, microbiologists, bio-informaticians, sequencers-manufacturing companies) to discuss the new opportunities, perspectives and ways to bring clinical metagenomics from research laboratories to the patient.

Here, we propose to hold the first international conference on clinical metagenomics in Geneva, Switzerland.



To inform a wide audience (students, junior and senior clinicians, biologists, microbiologists, bio-informaticians, private companies) about the new field of clinical metagenomics, from concepts to the possible application for patients.


Scientific Board

F. Aarestrup, S. Antonarakis, D. Ehrlich, G. Greub, D. Hochstrasser, E. Ruppé, J. Schrenzel, D. Trono, G. Weinstock, I. Xenarios



E. Zuffi, E. Ruppé, J. Schrenzel, and K. Tugay


Post Grad CME

Infectious Diseases, Gastro-Enterology, Oncology, Internal Medicine, Microbiology, Lab Medicine

FAMH (4 + 6 hours)

Société suisse d’infectiologie (4 hours)

Société Suisse de Médecine Interne Générale (8 credits for "formation continue essentielle MIG")






13.45 WELCOME ADDRESS: Jacques Schrenzel (Geneva)



14.00 P. Wincker (Evry): Next-generation sequencing

14.30 Nick Loman (Birmingham): What's next in NGS? The Nanopore technology

15.00 Aitana Lebrand (Geneva, Switzerland): Overview of bioinformatics analyses for metagenomics data

15.30 Georges Weinstock (Farmington): Probing the Medical Microbiome




16.30 Marc Eloit (Paris): Clinical metagenomics in immunocompromized patients

17:00 Jerôme Bouquet (San Francisco): Clinical Metagenomics for Diagnosis of Acute Inf. Diseases

17:30 Gilbert Greub (Lausanne): Clinical metagenomics for the discovery of new pathogens







09.00 Derrick Crook (Oxford): Inferring the antibiogram from genomes

09.30 Etienne Ruppé (Geneva): Clinical metagenomics in hospital-acquired pneumonia

09.50 Frank Aarestrup (Lyngby): Clinical metagenomics in urinary-tract infection

10.10 Judith Breuer (London): Detection of Mycobacterium tuberculosis directly from samples




11.00 Dusko Ehrlich (Jouy-en-Josas): The intestinal microbiota and the link with diseases

11:30 Eric Pamer (New York): Microbiota-mediated defense against intestinal infections

12:00 Christopher Ford (Cambridge): Microbiome therapeutics




14.00 Stylianos Antonarakis (Geneva): New diagnostic and research perspectives

in genome/exome sequencing

14.30 Peer Bork (Heidelberg): Diagnostic of colon cancer using metagenomics

15.00 Cynthia Sears (Baltimore): Using Biofilms and Metagenomics to Diagnose Colon Cancer



15.30 Jacques Schrenzel (Geneva): Conclusions and remarks

15.40 End of conference




Frank Aaretrup (Copenhagen, Denmark)

Frank Aaretrup is Professor, Head of Research Group at the Danish Technical Institute (DTU) in Copenhagen, Denmark. His research has primarily targeted the association between use of antimicrobial agents to farm animals and the emergence and spread of antimicrobial resistance including the human health consequences. He has now focused on the genomic and metagenomic fields, especially with respect to the antibiotic resistance typing. He has co-authored more than 400 papers.




Peer Bork (Heidelberg, Germany)

Peer Bork is group leader, senior scientist and joint head of the Structural and Computational Biology unit at EMBL. He works in various areas of computational biology and systems analysis with a focus on function prediction, comparative analysis and data integration. He is a worldwide leader in the field of metagenomics of the intestinal microbiota. He coauthored more than 600 research articles in international, peer-reviewed journals, among them more than 50 in Nature, Science and Cell.




Judith Breuer (London, UK)

Judith Breuer is professor of Virology at the Faculty of Medical Sciences of London. Her research at the MCR-UCL Centre for Molecular Virology has resulted in the successful development of methodologies to recover low copy viral DNA from clinical samples and subsequent generation of template suitable for whole genome sequencing, including the detection

of rare variants. She is currently applying these methods to investigate the genetic association of Varicella zoster (VZV) and Herpes Simplex Virus (HSV) with different disease states. Other research interests include genetic variation of alpha HSV and pathogenesis in skin tissue, and broader molecular diagnostic tools in viral disease.




Patrick Wincker (Evry, France)

Patrick Wincker has been the director of the sequencing technology and eukaryote genomics groups at Genoscope in Evry, France since 1997. He is coordinating the use of sequencing and bioinformatics technologies to assemble and analyse complex genomes and metagenomes. He is since 2009 one of the scientific coordinators of the Tara Oceans program. In this frame, he is developing meta-omics methods to study complex eukaryotic communities in ocean plankton.






George Weinstock (Farmington, CT, US)

GW is one of the leaders of the Human Microbiome Project, an international effort to apply and develop the latest technologies to comprehensively characterize the microbiome and its impact on human health. While not addressing brain diseases, the unprecedented insight on the normal composition of the human GMB is instrumental to study its relationship with neurodegenerative diseases.





Jérôme Bouquet (San Francisco, CA, US)

Dr. Jerome Bouquet is a postdoctoral scholar in Dr. Charles Chiu’s lab at UCSF, San Francisco, USA, specialized in clinical metagenomics and human transcriptomics to develop the next generation of diagnostics for infectious diseases. His work focuses on the identification of known or novel pathogens in idiopathic cases by next generation sequencing, and human biomarker discovery in Lyme disease, Ebola virus and Zika virus infections. He earned his PhD from the University Pierre and Marie Curie, Paris, France, studying genomes and quasispecies of hepatitis E virus to explore its zoonotic potential from swine to human. He is the recipient of the 2014 Emerging leader award from the Bay Area Lyme foundation.




Christopher Ford (Cambridge, MA, USA)

Christopher Ford is a senior scientist who recently joined Seres Therapeutics, Inc. ("Seres"). He previously worked at the Broad Institute where he studied pathogenesis of Candida albicans. He then moved to Harvard School of Public Health where he studied the evolution of drug resistance in Mycobacterium tuberculosis.






Derrick Crook (Oxford, UK)

Derrick Crook is currently Professor of Microbiology in the Nuffield Department of Medicine at Oxford University and is a practicing clinical microbiologist and infectious diseases physician at the Oxford University Hospitals NHS Trust. His work focuses on translating new molecular technologies and advances in informatics into the investigation of microbial transmission, diagnosis of infectious disease and identifying novel outbreaks of communicable disease. The aims and objectives of this research is to translate deep sequencing of pathogens on an epidemiological scale for tracking hospital and locally acquired infections and it is focused on four different major pathogens; Staphylococcus aureus (including MRSA), Clostridium difficile, Norovirus and Mycobacterium tuberculosis.



Aitana Lebrand (Geneva, Switzerland)

Aitana Lebrand is project manager at the Clinical Bioinformatics group of SIB Swiss Institute of Bioinformatics. During her PhD and a couple of postdocs in bioinformatics, she gained experience in systems biology, transcriptomics, immunoinformatics for virus identification and genomics to predict phage-bacteria interactions.

The SIB Clinical Bioinformatics group focuses on the harmonization of clinical bioinformatics analysis pipelines between Swiss university hospitals. In this context, she is co-leading a Swiss-wide working group to define best practices for the NGS-based identification of pathogens and microbiomes in patients care.





Dusko Ehrlich (Jouy-en-Josas, France)

Stanislav Dusko EHRLICH was trained in Organic Chemistry at the University of Zagreb, Croatia and obtained PhD degree in Biochemistry at the University Paris VII, France. He was a research associate of Dr. Joshua Lederberg, Nobel Prize winner, in the Department of Genetics, Stanford University Medical School, California. He founded and directed Microbial

Genetics Research Unit and the Microbiology Department at the National Institute for Agricultural Research (INRA). He also founded a start-up company Enterome, developing microbiome-based biomarkers. He is Research Director Emeritus at INRA, Professor at King’s College London and Chief Scientific Officer of Enterome. His research interests are in

Human Microbiome; he coordinated the EU-funded project MetaHIT and is the PI of the French Government Investissement d’Avenir 19 M€ grant MetaGenopolis.




Marc Eloit (Paris, France)

Marc Eloit is professor of virology and head of the laboratory of pathogen discovery at the Institut Pasteur in Paris, France. He is also the scientific founder of Pathoquest, a pioneer, spin-off company of Institut Pasteur dedicated to clinical metagenomics



Nick Loman (Oxford, UK)

Nick Loman works as an Independent Research Fellow in the Institute for Microbiology and Infection at the University of Birmingham, sponsored by an MRC Fellowship in Biomedical Informatics. His research explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. Nick has so

far used high-throughput sequencing to investigate outbreaks of important pathogens such as Pseudomonas aeruginosa,Acinetobacter baumannii and Shiga-toxin producing Escherichia coli. His current work focuses on the application of novel sequencing technologies such as the Oxford Nanopore for genome diagnosis and epidemiology of important pathogens. A more general aim is to develop bioinformatics tools to aid the interpretation of genome and metagenome-scale data in routine clinical practice in collaboration..



Eric Pamer (New York, NY, US)

Eric G. Pamer received his MD degree from Case Western Reserve  University Medical School and completed clinical training in Internal  Medicine and Infectious Diseases at UCSD Medical Center. He was a  postdoctoral fellow with Charles E. Davis at UCSD, Maggie So at  Scripps Research Institute and Michael Bevan at the University of  Washington and then moved to Yale University. In 2000 he moved  his laboratory to Memorial Sloan-Kettering Cancer Center in New  York where he a Member of the Infectious Diseases Service, Head of  the Division of Medical Subspecialties and Director of the Center for  Microbes, Inflammation and Cancer



Cynthia Sears (Baltimore, MD, USA)

Cynthia L. Sears, M.D. is a Professor of Medicine, Oncology and Molecular Microbiology and Immunology at the Johns Hopkins University School of Medicine and Bloomberg School of Public Health. She is an infectious diseases specialist with expertise in the molecular pathogenesis of enteric infections, in particular, enterotoxigenic Bacteroides fragilis. Dr. Sears’ research focuses on experimental and translational studies to define how the colonic microbiota and/or specific microbiota members induce chronic colonic inflammation and colon cancer.


Stylianos Antonarakis (Geneva, Switzerland)

Stylianos Antonarakis is Professor and Chairman of Genetic Medicine at the University of Geneva Medical School, and director of the iGE3 institute of Genetics and Genomics in Geneva, Switzerland. He is the President of the Human Genome Organization (since 2013), a member of the scientific council of the Swiss National Science Foundation, and chair of the Genetics panel of the European Research Council. Previously he was the President of the European Society of Human Genetics. His research focuses on the relationship between genomic and phenotypic variations, in particular the functional analysis of the genome, effect of human genetic variation to phenotypic variation, the molecular pathogenesis of trisomy 21 and polygenic phenotypes, the functional characterization of the conserved fraction of the genome, diagnostics and prevention of genetic disorders, and the societal implications of genetics and genome research. Antonarakis coauthored more than 620 papers and is listed as one of the highly cited scientists by the Institute for Scientific Information (h-index 94).




Gilbert Greub (Lausanne, Switzerland)

Gilbert Greub(MD, PhD) heads the microbiology laboratory at the Vaud University Hospital and the Institute of Microbiology in Lausanne. His research focuses on the discovery of new pathogens and those for which are unculturable. In this perspective, he has a strong experience in molecular tools, especially genomics and metagenomics.





Etienne Ruppé (Geneva, Switzerland)

Etienne Ruppé (PharmD, PhD) is a clinical microbiologist. After graduation in 2008, he spent 4 years as an assistant in the bacteriology laboratory of the Bichat-Claude Bernard University teaching hospital and obtained his PhD in Infectiology for his work on the epidemiology of carriage of multidrug-resistant bacteria. After a first post-doc focusing on the resistome of the human gut microbiota, he moved as research assistant in the Genomic Research Laboratory in the Geneva University Hospitals where he works on the development of clinical metagenomics .





Jacques Schrenzel (Faculty of Medicine, University of Geneva) JS is co-founder of the Center of Excellence in Bacteriology at the University of Geneva (CEBUG). He is in charge of the bacteriological laboratory and the genomic research laboratory of Geneva University Hospitals (www.genomic.ch). He is recognized for his work on bioinformatics, metagenomics, microarrays and next-generation sequencing in clinical microbiology.


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What you can expect from these events.

Western Switzerland hosts more than 700 companies and 500 research laboratories active in the life sciences sector. Due to this extraordinary ecosystem, Switzerland has recently been designated as the most innovative country in the world.
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The NexTrends Events also address a growing concern of many stakeholders who regard periodical events around life sciences in extenso as an added value to initiate new collaborations and enlarge their perspectives.
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Where are these events.

This event will take place at Campus Biotech

When are the next events.

Next event: Nov 3rd, 2015, 13h30

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Where are these events.

This event will take place at Campus Biotech

When are these events.


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Next event: Oct 13-14th, 2016

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