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Expedition Genomics Lab: the mobile revolution in genetic analysis
Through the integration of a platform that allows on site DNA extraction and amplification and a
new mobile sequencing device with cloud based analyses, DNA can be sequenced for the first
time directly in the field freeing biological exploration from the constraints of large and expensive
research laboratories and allowing real time DNA barcoding.
On May 4, 2015, the MUSE - Science Museum (Trento, Italy) and the University of Verona (IT)
presented Expedition Genomics Lab, a technology innovation project developed in collaboration
with Oxford Nanopore Technologies (Oxford, UK) and Biodiversa (Trento, IT).
Expedition Genomics Lab uses the first system that can perform DNA sequencing outside a
controlled environment, as a laboratory. The DNA Finder by Biodiversa allows DNA extraction,
purification and amplification with a battery-powered device without the need of special lab
equipment like centrifuges and frozen chemicals. The portable DNA sequencer MinIONTM and
cloud based analysis system MetrichorTM from Oxford Nanopore Technologies, allows to sequence
the DNA in any part of the world, as it is powered by the USB3 port that transfers data to a laptop
computer. This portable lab brings molecular analysis directly in the field, revolutionizing
biological exploration.
The first public test of Expedition Genomics Lab was performed during a press conference held in
Trento, by Michele Menegon, researcher of the MUSE, and Massimo Delledonne, Professor at the
University of Verona. A non-invasive biological sample was taken from a frog in Nkuka Forest,
Tanzania (as part of an on-going project under the auspices of the Tanzania Wildlife Research
Institute), which was immediately released back into its environment. Using Expedition Genomics
Lab, they sequenced the DNA of the wild frog species and sent the data via a standard smartphone
to Oxford Nanopore’s cloud based application and to the MUSE of Trento. This allowed the team in
Tanzania to determine in real time the identification of the sampled frog, providing live data to
researchers based in Italy.
The innovative technology of Expedition Genomics Lab opens up a wide range of possible
applications in all contexts where the portability of the system and the speed of the results can make
a difference. It is the hope of the inventors that the low cost of the system and the autonomy from
traditional labs, will enable its use in more regions and fields of biology. Particularly in developing
countries in the tropics where in many cases the lack of infrastructure dedicated to genetic analysis
is a limiting factor for scientific research. Elsewhere, the potential fields of application of
Expedition Genomics Lab extend from personalised medicine to customs controls, analysis of
food security, crop science and environmental applications.
If you are interest in receiving more information and covering this event please contact:
Massimo Bernardi
MUSE – Science Museum Trento
[email protected]
Office: +39 0461270344
Mobile: +39 3404949106
Expedition Genomics Lab - Description
The kit contains optimized versions for use in the field, and at room temperature, of devices and
reagents for extraction, purification, amplification and DNA sequencing. Expedition Genomics Lab
is based on the use of technologies that enable the extraction of DNA without the need for complex
laboratory equipment. It is equipped with a small thermocycler specially designed to operate at 12V
and with a fluorometer for DNA quantification. Expedition Genomics Lab sequences the target
region by means of a third-generation sequencer, the MinIONTM from Oxford Nanopore
Technologies. Analyses are performed in the cloud using the system MetrichorTM from Oxford
Nanopore. The sequence obtained can then be sent worldwide by using standard (3G / 4G) or
satellite network.
Areas of application of Expedition Genomics Lab
Since 1977 DNA sequencing has become possible and information obtained from DNA sequencing
has revolutionized different fields such as medicine, forensic science, and evolutionary biology. But
DNA sequencing is still constrained by the use of expensive infrastructure and processes that are
virtually absent from the large majority of the countries in the tropics, where most of the earth’s
biodiversity is located. Expedition Genomics Lab has been designed primarily to allow DNA
analysis of wild species in these countries. Its portability, low cost, and intuitive use will accelerate
the acquisition of information critical in biodiversity studies and conservation activities. The
initiative takes its first steps at a time, today, where a loss of about 150-200 species every twentyfour hours has been estimated (UNEP) - the so-called "sixth mass extinction".
The assessment of biodiversity based on molecular data is an imperative of every action of
prioritization of important areas for conservation and is therefore an essential tool for scientifically
informed planning. Key areas of application of the kit will be:
1. Conservation of biodiversity
Expedition Genomics Lab will produce real-time data on biological complexity of the sites
investigated by rapid molecular identification of taxa. This allows an identification of cryptic
biodiversity and therefore to distinguish between similar taxa. From a practical point of view the
use of Expedition Genomics Lab would allow cutting down times and logistics costs due to
collection and storage of samples. It will also promote a rapid and effective collaboration between
local researchers and those from abroad in order to quickly define, on a molecular basis, indices of
biological diversity for investigated areas.
2. DNA barcoding and taxonomic implications
Expedition Genomics Lab has been primarily developed to perform DNA barcoding and can
therefore provide an effective contribution to all the research projects based on this method, such as
the Barcode of Life (www.barcodeoflife.org), which aims to create public databases of species
diversity. The kit will however allow fast and efficient comparison between any genomic region,
even among organisms which are evolutionarily very distant. Furthermore, the possibility to obtain
molecular data directly in the field will help limiting the collecting of museum specimens that might
be rare and endangered, while focusing effort on collecting poorly understood species.
3. Forensic investigations on wild species
The ability to sequence, locally and quickly, any suspect sample will make of Expedition Genomics
Lab an effective tool to fight the illegal trade of endangered species. The kit will be of particular
help in contrasting all illegal practices that are based on the impossibility to verify the identity of
the traded species at customs (e.g., exported species 'under' the name of other parts of animals
attributed to non-CITES species).
Potential users of the Expedition Genomic Lab
1. Research Institutes, Museums of Science, University working in the documentation of
biodiversity.
2. Non-governmental organizations working on species and land conservation.
3. Government agencies concerned with land management.
4. Parks, Protected Areas, etc.
5. Institutes dealing with eradication of alien species.
6. Customs, and trade control of illegal wildlife.
7. Any agency/company dealing with quality control (e.g. food).
Partner of the project
Biodiversa SRL. is a start-up founded in 2014 by a multidisciplinary team (physicians, geneticists,
biologists, biotechnologists, chemists and physicists) convinced of the utility of genetic testing to
understand the state of health of humans, animals and plants, to assess possible therapies and to
quantify the amount of biodiversity present in a certain environment. The company has developed a
portable device of great sensitivity and precision which is at the same time inexpensive and easy to
use: it is called the Finder and allows rapid amplification and quantification of DNA. Within the
Expedition Genomics Lab, the Finder plays a vital role in providing the genetic material necessary
to phase sequencing.
http://www.biodiversa.it
Oxford Nanopore Technologies established in 2005 is a company dedicated to the development of
new methods of molecular analysis, based on the development of nanopores technologies with
potential applications in scientific research, personalized medicine, crop science and security /
defense. Born from the idea Hagan Bayley, from Oxford University, the company is a leading
developer of technologies boasting several collaborations with prestigious international research
institutions such as Harvard, University of California at Santa Cruz and Boston University.
https://www.nanoporetech.com
Funding
Fondazione Cassa di Risparmio di Trento e Rovereto provided financial support to the project.
The Expedition Genomic Lab team
Massimo Delledonne: designer and scientific director of the project Expedition Genomics Lab.
He is professor of genetics at the University of Verona, where he coordinates an extensive program
of research characterized by an interdisciplinary approach that connects genetics, molecular biology
and genomics. He collaborates with various international research institutions for the development
of projects in the fields of bioinformatics, microbiology, plant genomics, and medicine.
He is co-founder (2007) of the Center for Functional Genomics dedicated to the development of
new technologies in genomics and co-founder and scientific director of Personal Genomics Ltd, a
spin-off of the University of Verona founded in 2011, which operates in human genomics and
personalized medicine.
Michele Menegon: designer and general coordinator of the project Expedition Genomics Lab.
He is a researcher at the MUSE - Science Museum of Trento, where for over 15 years he has been
working on research and conservation of the herpetofauna of the mountain forests of Eastern Africa.
His numerous explorations led to the discovery and description of more than 60 vertebrate species
new to science, and the definition of the biological value of many areas of high biodiversity. He
collaborates with several scientific institutions and with some of the most important international
agencies for the conservation of biodiversity, including the Wildlife Conservation Society and
Conservation International and is a member of the Species Survival Commission of IUCN. He has
published many scientific papers, educational texts and books on biodiversity.
Ana Rodriguez Prieto collaborates with the Section of Tropical Biodiversity of MUSE - Science
Museum of Trento, within a project on morphological and phylogenetic analysis of various species
of Amphibians and Reptiles of East Africa. She graduated in Biology and Biochemistry, continuing
his studies with a Master of Biodiversity and Conservation Biology and a PhD at the Institute of
Evolutionary Biology (IBE, CSIC-UPF, Barcelona). In the context of the project Expedition
Genomics Lab she was responsible for implementing the protocols for the use in the field of the
sequencing kit and has collaborated on the overall project.
Chiara Cantaloni works at Personal Genomics SRL, a spin-off of the University of Verona. She
graduated in Industrial Biotechnology and worked at the Department of Environmental
Engineering, University of Trento for the development of protocols for the detection of pathogens
in surface waters. From 2008 to 2013 she was the head of the tissue bank of the "Trentino
Biobank", Hospital of Trento. She earned a second degree in Biology and Health working on the
development of protocols for the detecting the biological markers in lung and prostate cancer, using
sequencing techniques. In the context of the project Expedition Genomics Lab she was
responsible for implementing and tuning the protocols required for use in the field of the
sequencing kit and has collaborated on the overall project.
Massimo Bernardi is a paleontologist at the MUSE - Science Museum of Trento. His research
activities focus on the evolutionary history of reptiles and amphibians. He is the author of about 50
scientific publications dealing with tetrapod ecology, biomechanics and phylogenetics. He is also
author of outreach texts and curator of numerous exhibition projects. In the context of the
Expedition Genomics Lab he was responsible for the development of the project and for the
identification of the cultural and social implications of the scientific innovation; he also
collaborated on the overall project.
Cesare Centomo is a bioinformatician working at the Center for Functional Genomics, University
of Verona, directed by prof. Massimo Delledonne. In 2014 he obtained a degree in Bioinformatics
and Medical Biotechnology working on the identification of genetic variants in the resequencing of
the human genome. In the context of Expedition Genomics Lab he was responsible for the
development and finalization of the bioinformatics tools necessary for the analysis of the
sequenced data.
Simon P. Loader and Elena Tonelli (University of Basel and MUSE) have collaborated on the
development of the project and provided expertise on amphibian genetics.
This work was carried out under the Tanzania Wildlife Research Institute and the Tanzania
Commission for Science and Technology permit No 2014-338-ER-2008-157