Difference between revisions of "Open-Food-DNA"
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The informatics pipeline will be in a public repository on GitHub.
The informatics pipeline will be in a public repository on GitHub.
This is the summary of the sequencing run from the second workshop: [[
This is the summary of the sequencing run from the second workshop: [[191102report.pdf]]
Revision as of 16:39, 13 December 2019
The Open Food Repo - DNA is a project that stems from the interest of Hackuarium members and the Digital Epidemiology lab at EPFL in food, genes and openness. The project is coming to life in a multi-partner collaboration coordinated by the EPFL Digital Epidemiology Lab and including the food safety company founded by a Hackuarium member: SwissDecode. The project is funded by the Jebsen foundation, an independent foundation that supports innovation in nutrition and citizen science. It is hosted in the Open Food Repo, Switzerland's first independent and participatory repository (=database) on barcoded food products.
The project BeerDeCoded was Hackuarium’s first project using new-generation-sequencing for a food product - in fact it was published in F1000Research in 2017, an open publishing platform for scientists: https://f1000research.com/articles/6-1676/v2
You can visit the project website here: http://www.foodrepo.org/dna.
Applying DNA sequencing to food
Citizens are increasingly faced with issues related to interpretation of scientific results. Here we are assessing sampling of food sources for DNA data acquisition. Following a steep decrease in costs, the sequencing of DNA is now almost a routine procedure. Whole genome sequencing and genotyping are typically used in genomic studies, microbiome analyses, diagnostics, drug development, environmental monitoring or forensics. Alongside public health initiatives and academic research projects, for-profit companies such as 23andMe or uBiome sell personal kits, collect genetic data from their customers and provide personal information in return. However, there is little awareness about how this data is generated and for what it is subsequently used. Private companies collect genetic information from customers. Recent food scandals have been shaking citizens' trust. This confusion leads to some absurdities. For instance, 80% Americans support “mandatory labels on foods containing DNA” (source: okstate.edu), as if containing DNA means it has been genetically modified. To improve the global impact of DNA technologies, it is crucial that citizens understand them better. Health-related data is a sensitive topic, and preventing abuse requires citizen literacy. Our project aims to open the dialog on issues related to genetic testing using food as an example. Using DNA from food as an example, our project aims to provide unbiased information about DNA sequencing technologies to the general public. Our initiative includes data collection, processing, interpretation and dissemination. With food, we avoid the many pitfalls related to health data, such as privacy and regulatory issues and at the same time, do some detective work on what we eat as consumers To foster participation of the public, anyone can suggest foods to be sequenced, here: http://tinyurl.com/y6gra27d and register for the FoodRepo newsletter which will update you when sequencing results are available http://eepurl.com/diBIfP. In turn, everyone will be rewarded with access to the data and knowledge generated in its entirety, without restriction. Open Food DNA is a project by EPFL Digital Epidemiology Lab, SwissDecode and members of the Do-It-Yourself biology (DIYbio) community Hackuarium. All stakeholders willing to increase public understanding of technologies related to DNA sequencing are invited to join - send an email to firstname.lastname@example.org. All data and processes developed as part of the initiative will be free to access.
- Pave the way for food DNA analysis to be affordable, easy and accessible
- Demystify and explain genetic data
- Produce an open access knowledge database.
Why citizen science?
Switzerland is amongst the world’s most productive countries in terms of research and innovation. Citizens have a direct impact on the future role of genetic technologies in our economy and society. Our project demystifies DNA science and stimulates public interest for topics usually confined to R&D departments. We want to let people engage in science and make more informed decisions.
The project initially turned to food as a tool to explain genetic technology while avoiding the many pitfalls related to health data, such as privacy and regulatory issues. However, this has since taken on a life of its own as food transparency is a crucial issue in today’s industrialized and globalized food chains. Food concerns everybody. Some people have health, religious or ethical reasons for avoiding certain types of food. Others just want to choose healthy, natural, or local ingredients. But how can we know? As previous studies and whistleblowers have shown, the food industry is a complex black box of sorts - where additives and relabelling often lead consumers to eat something they would otherwise have stayed away from. We have limited knowledge about what exactly composes our diet. Today's information comes from the suppliers who themselves rely on their suppliers. Does a dish really contain what is written on the label? Where do the ingredients really come from? Does the food contain allergens, pesticides, GM crops, etc.?
How much more complex is it than what the label says?
We cook and eat animals (meat, fishes), plants (vegetables, spices) and fungi (mushrooms, yeast). These are all life forms, so they all contain DNA - thus our food is full of DNA. With DNA, it could be possible to identify, classify and count all the species present in a food serving. In a portion of lasagna, ground beef and horse meat may look similar, but their but that contain small differences between each species. This sequence can be used like a barcode to identify different species, and infact these sequences are referred to as DNA barcodes. The consortium barcodeoflife.org has made a list of unique DNA identifiers for 300,000 species collected around the world. We have access to this data and to the technology to examine thousands of different DNA species in a complex sample.
Why Open Data?
By making all the data generated by the project open, we want to explore and promote an alternative to proprietary initiatives. Open data supports literacy and fosters innovation by both citizens and scholars.
What are the specific challenges of the project and has anyone done this before?
The technique of DNA barcoding has mainly been used to identify species in the wild. Imagine a biologist in the Amazon jungle who comes across a plant he has never seen before - he can use this technique to check if this plant’s DNA matches another plant or if he has discovered a new species! A big difference and difficulty we are encountering in applying this to food is that when food is transformed, unlike a species in the wild, it sometimes undergoes processes that damage the DNA, such as sterilization, high-temperature cooking etc. With smaller fragments of DNA it is harder to extract it and compare it to a reference. Another challenge with processed food is the frequent use of additives, some of which it appears interfere with the enzymes used in the lab to extract and analyse the DNA. There are tests available that use genetic sequencing to identify presence or absence of a particular ingredient - for example, salmon or corn. However, what we have the ambition to do is to answer a different question: rather than “Does this food contain x”, we ask “what does this food contain”? A few companies have announced that they have a way of ascertaining this - all different species in a food sample. However, these are commercial entities so the processes are proprietary (we don’t know how they do it) and rely on a relatively big infrastructure and means. Public health authorities in Switzerland do not have any equivalent tool and use a combination of biochemical tests to identify presence or absence of specific ingredients in a food.
With the contribution of the general public and the biohacking community, Hackuarium, EPFL Digital Epidemiology lab and SwissDecode hope to find a way to crack this question - and provide open, affordable and relatively simple protocols for this to be replicated around the world.
The first protocol developed by SwissDeCode was applied to 370 products, generating DNA datasets for > 200 products. This protocol was also piloted in a community setting during a workshop in spring 2019. An open bioinformatics pipeline (WIMF) was set up to analyse this data. While some showed clear ingredient identification, there remained a lot of ambiguity with closely related species. To try and solve this challenge, a second protocol was designed with different primers. This was tested for the first time in a second workshop in autumn 2019, and is being tested in a professional lab at SwissDeCode to provide a large enough dataset to examine in detail. In parallel, the bioinformatics pipeline is being expanded to accommodate the new markers. Workshop participants have been biohackers, scientists, soupmakers, teachers, high school students and open science and consumer rights advocates. We believe everyone can take an interest in and take action on food transparency! Results will be posted here shortly - if you are impatient you can write to email@example.com! The informatics pipeline will be in a public repository on GitHub.
This is the summary of the sequencing run from the second workshop: 191102report.pdf
- Metagenomic pizza: an outreach project by the Swiss Institute of Bioinformatics to introduce the concept of DNA barcoding http://education.expasy.org/bioinformatique/PizzaMetagenomic.html
- GMO Detective: https://gmodetective.com
DNA learning center does workshops on DNA barcodes (not food specifically): https://www.dnabarcoding101.org/programs/
If you know of something we’ve omitted, please let us know! We’d be happy to learn and update this page.
Paulina Martinez (Field Application Scientist at SwissDeCode, PhD biochemistry) and Pietro Cattaneo (Product Development Scientist at SwissDeCode, PhD molecular plant biology) joined forces to use their expertise to develop the first protocols for genetic sequencing of complex food samples and produce a large dataset of food DNA, under the helm of Gianpaolo Rando. They also guided participants through both versions of the protocol when they were piloted in a community setting (v1: Pietro, v2: Paulina).
Gianpaolo Rando (Founder and CEO at SwissDeCode) is one of the initial instigators of the project to sequence food using NGS with an open science approach and was part of the ancestor project: BeerDeCoded. Gianpaolo holds a Ph.D in biotechnology and has 10 years of experience at the interface between genomics and nutrition. He is a proud member of Hackuarium and has a passion for food and drinks.
Luc Henry (co-founder of Hackuarium) holds a DPhil in chemical biology and has a strong interest in the impact of new technologies on society, in particular in the fields of biotechnology and health. He is scientific advisor to the presidency at EPFL and wants to promote an open approach to science and innovation. Luc is also one of the first to have conceived the project and was part of BeerDeCoded.
Rachel Aronoff (president of Hackuarium) is biosafety officer and project manager at Hackuarium, in which she has been involved since 2015. Rachel is a passionate biologist who has worked on a wide range of projects since her PhD in microbiology, including founding the non-profit, AGiR! Action for Genomic integrity through Research!, focussing upon dynamic cellular processes and making wiser choices to improve public health. She has provided a lot of support to the project including hosting the workshops.
Olivier Emery is an expert bioinformatician who has been active at Hackuarium for several years, especially for his project BeeMos which was connected to his PhD on bee gut microbiota. Olivier took part in the first Food DNA workshop and then took on an active role as the project's bioinformatician and Hackuarium, coordinator for the second stage of the project.
Marcel Salathé (head of Digital Epidemiology lab, EPFL) works at the interface of biology, computational and social sciences. Driven by open science and innovation, Marcel has been committed to making this project happen from the get-go, providing a home for it in his lab within the FoodRepo project and championing it to funders, partners and the media.
Talia Salzmann (Project Manager at Digital Epidemiology Lab, EPFL) trained in Life Sciences and in Public Health. She coordinates the project and is enthusiastic to see it develop. Besides being excited by the scientific progress involved, she believes it can improve health through food transparency and awareness as well as bring together a vibrant community around Hackuarium with an interest in food.
Partners - You?
Each step of the Open Food Data can accommodate external partners who are eager to support the project and increase its impact - do get in touch at firstname.lastname@example.org.