GetGenome is our newly formed charitable organisation that provides equitable access to genomics technology for early career researchers all over the world. GetGenome also provides training in the use and publication of genomics data using open science principles.
Cite as: Canham, J. and Kamoun, S. (2022). Introducing GetGenome — Genomics for all! Zenodo https://doi.org/10.5281/zenodo.7186205
It’s genomics for all but it started with just one student
During the COVID-19 pandemic, one of us (Sophien Kamoun) was invited to attend the online thesis defense (viva) of a Tunisian PhD student. The student’s project focused on characterizing bacterial strains they had isolated from diseased plants. One aspect of the project involved polymerase chain amplification (PCR) of regions of interest that were hypothesized to occur in the genomes. The relatively tedious experiments didn’t always yield conclusive results. This prompted Sophien to offer to sequence the genomes of the bacterial strains. Once the genome data was acquired, it became evident why some of the regions were challenging to amplify, they were simply absent in the studied strains. In one stroke, the genome sequences saved months of unfruitful work and helped generate new hypotheses. And it all cost just a few dozen pounds to do it.
This experience led us (James Canham and Sophien) to formulate GetGenome as a vehicle to empower biologists all over the world to access genomics technology. We believe that genomics technology and genomics-related education should be available to all and we have developed GetGenome as a bottom-up concept to empower individuals to access genomics. This is how it works,
You chose the organism(s), GetGenome does the genome sequencing at no cost to you and assists you with the analysis and publication of the genome data. GetGenome enables biologists to leapfrog the challenge of genome sequencing and propels them into the post-genomics era.
Genomics is an information science — let’s focus on the information
Genomics has become an integral component of life science research. The dramatic decrease in the cost of DNA sequencing — beating even the famed Moore’s Law of the computer industry — means that the technology is becoming increasingly accessible. It’s now estimated that the cost of sequencing a human genome can be as low as $200, down from millions of dollars just 20 years ago. However, the genome sequence isn’t an end in itself — it’s the end of the beginning. The important and impactful work starts after the genome sequence is acquired. GetGenome propels biologists into the post-genomics era, enabling them to focus on genome analysis rather than get bogged down in the technical aspects of genome sequencing.
Genomics is an information science. Once the genome sequence is available, the next analytical steps are in silico, taking the research away from the wet lab to the computer. Computational analyses of genomics data (bioinformatics) have proven over and over to be a powerful way to generate hypotheses about the sequenced organisms that, in turn, help guide wet lab research. GetGenome assists and trains scientists to make the most out of their genome data to advance their research.
The challenge — inequitable access
Even though genomics has become integral to life science research, inequitable access to genomics technology remains prevalent resulting in reduced scientific and commercial output. GetGenome addresses this unequal access to genomics across the globe. Many life science research communities across the world cannot access genomics technology. The issues include inefficient sequencing at host institutions, limited research funds and restricted access to hard currencies that prevent sub-contracting to DNA sequencing providers. GetGenome addresses these challenges by covering the cost and logistics of sequencing the genomes of the scientists organisms of interest. GetGenome primarily targets regions of the world that can gain the most from improved access to genome sequencing and bioinformatics training.
What does GetGenome do?
GetGenome is a non-profit organisation that empowers early career scientists by providing equitable access to genomics technology and related education. We enable early career researchers (ECRs) to….
DEPOSIT samples of your favourite organisms for genome sequencing.
ACCESS and learn to analyse the genomics data of your favourite organisms.
SHARE and publish the data using open science principles.
NETWORK with other biologists to make the most out of the data.
How can I receive support from GetGenome?
GetGenome is genomics for all. We operate primarily through Call for Projects (CFPs) within geographical regions or research communities. A local committee is established and tasked with assessing applications for support. Following the selection process, GetGenome will generate the genomic sequences of the applicants organism(s) of interest and will support a cohort of beneficiaries through workshops aimed at acquiring the necessary skills to interrogate the data.
Follow us on social media to hear about open CFPs. If your project is in-scope, then you can submit it using the application form.
GetGenome embraces open science principles
An important principle of GetGenome is open science. GetGenome is a strong advocate of open science publication because we believe scientific research should be made available to the public without charge. Equally, we believe that scientists should be able to publish their data for the benefit of everyone, including themselves, without cost.
GetGenome will assist its partners to publish the data acquired via the initiative on free-to-publish and free-to-access platforms, such as Zenodo. This not only fulfils GetGenome’s public benefit requirement but gives GetGenome beneficiaries the opportunity to showcase their research and elevate its impact.
Open science doesn’t mean sharing your research without any credit. Quite the opposite. Publishing your work as “mini-papers” on platforms like Zenodo allows you to produce a citable permanent scholarly output associated with a doi (digital object identifier).
“Mini-papers” are the underrated scholarly outputs of academia. For many Early Career Researchers (ECRs), publishing a full fledged research article is a daunting task. So, why not break down this task into smaller, less intimidating units and publish them as datasets or method papers? We will help you do this. And it will cost you nothing to publish your work.
Check the current GetGenome sponsored publications of our Zenodo Community page.
#GGTunisia2022 — Our first CFP
The future of GetGenome is an exciting one and its success will be underpinned by our boundless ambition and purposeful intention. We recently kicked off our first CFP in Tunisia — an incredibly exciting milestone for the initiative. #GGTunisia2022 focuses on non-pathogenic, culturable bacteria. The call has already been met with a positive response from the Tunisian research community and the first applications are already in. We are grateful to Professor Naceur Djebali, Centre of Biotechnology of Borj Cedria (CBBC), for Chairing the Selection Comittee. We have already conducted a pilot with Naceur and his team that has resulted in multiple bacterial genomes and mini-papers.
Stay tuned, we have big plans
GetGenome was born on April 4th, 2022, when James Canham became fully employed by the organisation. We are honored to count as our Founding Board of Trustees Professors Appolinaire Dijkeng, Saskia Hogenhout, and Nick Talbot (Chair) in addition to Sophien Kamoun. We will formally launch the organisation as soon as we receive approval for UK charitable status from the Charity Commission (application submitted in July 2022).
One key reason why we can launch GetGenome is that James has committed to lead the project. James is a biologist who recently completed his PhD at the John Innes Centre working with Saskia Hogenhout. During his PhD, James was motivated to further understand how UK scientists and institutes could support research in East Africa. This led him to undertake a placement in Kenya to establish collaborative partnerships between UK and Kenyan institutes. His work was recognized with a 2021 Student Engagement Award.
James has kept really busy since April. He’s been formulating the project, putting together the documents necessary for the Charity Commission filing, designing the logo and website, coordinating with the international network, and finally launching the first CFP. His next steps will be to identify more regions and researchers with the ambition to match our own. He is also conducting a pilot with Nigerian student Olaide Ogunsanya to sequence fungal genomes.
We have big plans for the first year. Stay tuned.
Acknowledgements
We thank Hsuan Pai, Mia Cerfonteyn, Joe Win and members of Board of Trustees for helping articulate the GetGenome vision. Pai led the design of the logo with input from many others, including Chiraz Khrouf and Khadija Kamoun. We are particularly grateful to Sabrine Dhaouadi, Manel Chaouachi, Amani Ben Alaya, Bilel Khiari, Takwa Marzouk, Imen Ben Slimene, Naceur Djebali for their ideas and contributions to the pilot projects.
Funding
Funancial support for launching GetGenome was obtained from The Gatsby Charitable Foundation, UKRI-BBSRC Norwich Research Park Biosciences Doctoral Training Partnership, Doctoral Career Development Fund and private donations.
