Project ACCESSIBLE GENOMICS Reusable Statements with Support
A. Late June Project Update
Video: https://www.loom.com/share/80ed60ffd81f4c8e965105fe02bb8ef8
Twitter thread: https://twitter.com/kcorazo/status/1275703757112819713
Usable statements
A.1 We are creating an open playbook for deploying low-cost genomic pathogen surveillance in the global south.
A.2 “Studies already show that outbreaks tend to be shorter and smaller when genomics is used to help contact tracing.”
A.3 Viral genomics is like 23andMe for pathogens.
A.4 When vaccines arrive, genomics would tell governments which locations and possibly which reservoir species should be prioritized for vaccination.
A.5 Genomics could also also tell researchers the root cause of vaccine failures: is it due limited cross protection due to high genetic divergence from vaccine or reversion to virulence? This will help in improving vaccines.
A.6 Currently, genomic pathogen surveillance is only available in high-income countries.
A.7 The numbers show how concentrated genomics is to high-income countries today. For instance, the UK has produced almost half of SARS-CoV-2 genomes uploaded in GISAID. The United States has produced a third of the rest.
A.8 There are 17 countries with less than 10 SARS-CoV-2 genomes uploaded in GISAID and their populations total to almost 1 billion people.
A.9 The next epidemics will most likely come from the global south, where contact between humans and wild animals is most prevalent.
A.10 Access to genomics might follow the history of mobile phone penetration. At the start, only developed countries had a significant percentage of their population with mobile phones. Now, the developing world has the most phones in the world.
A.11 A sequencer used to cost more than a brand new car. Now, you can get the Oxford Nanopore MinION at less than the cost of an iPhone.
A.12 Multiple scientists have demostrated and documented the feasibility of a low-cost and mobile laboratory with usage in developing countries.
A.13 Project pitch:
A.13.1 What is the missing piece to brining genomic pathogen surveillance to the developing world?
A.13.2 One piece is a deployment playbook. In order to create one, we would need to overcome the following challenges:
A.13.2.1 Get funding
A.13.2.2 Logistics of bringing in equipment and reagents
A.13.2.3 Train local lab workers, bioinformaticians, and decision makers in epidemic management
A.13.2.4 Get SARS-CoV-2 samples
A.13.2.5 Add a genomics layer to a partner lab or equipping a lab from scratch
A.13.2.6 Ensure biosafety
A.13.2.7 Do the actual sequencing and genome assembly
A.13.2.8 Create the playbook and the training to use the playbook
A.13.2.9 Outreach to other developing countries
A.13.2.10 Help these other countries deploy genomic pathogen surveillance
A.13.3 The scientists and technologists have done their part. These are project management challenges. What is needed is a project team with the right capabilities.
A.13.4 We have built a project team with the right mix of project management, genomics and experience in operating in the developing world.
B. Application template of JOGL
1.0 Introduction
1.1 Problem and Background
1.2 Solution summary in simple terms
1.3 Solution summary in technical terms
1.4 State of advancement of the project
1.5 Project Timeline
2.0 Project Implementation
2.1 Solution
2.3 Methodology
2.4 Results/Expected results
3.0 Safety, quality assurance and regulation
3.1 What steps have you taken to ensure your solution’s safety? How advanced are you in this process?
3.2 Have you planned the conduct of your manufacturing process that ensures quality, what are the steps you have taken? How advanced are you in this (if applicable)?
3.3 Will you need assistance with the regulation system? If not, which regulatory system do you plan on using to distribute the product? Please elaborate (please see: Regulatory-Strategies) (if applicable)
3.4 Have you talked to medical staff about the feasibility of your project? What did they say?
3.5 Have you planned the testing, verification and validation of your solution? How advanced are you? (if applicable)
4.0 Impact, issues and risks
4.1 What impact do you feel your project could have?
4.2 What do you think would make your project a success?
4.3 Please list the known issues, potential risks, grey-areas, etc in your project
5.0 Originality
5.1 What other projects on JOGL are like yours? Search for them and Link them!
5.2 Is this an innovative project? What makes this project different if it’s unique on JOGL?
5.3 Is there already an open source version of this project?
6.0 Team experience
7.0 Funding and Costs
7.2 How is your project being funded so far?
7.3 How much funding do you need and how do you plan to use that funding?
C. Judging criteria of JOGL
C1 Project Timeline: How achievable is this project within 3 months?
C2 What is the quality of the project budgeting?
C3 (Optional) How could the project cost be improved/reduced? Please provide any details of contacts if applicable.
C4 Is the project's current team composition sufficient to achieve the projects goal?
C5 Does the project have access to the materials/ facilities required to complete the project?
C6 How clear is the project proposal?
C7 Project design: What is the project design quality? Are there flaws?
C8 Which category would you say the project falls under?
C9 Clarity and relevance of the project timeline and it's needs for future (major tasks, milestones)
C10 If this project is biological in nature, do they address the biosafety and regulations requirements to address? (if applicable)
C11 If it is a data driven project how feasible is the data collection for this project ? (Really Hard / The data exists already) (Data analytics projects only)
C12 What is the project's state of progress?
C13 Is this project a product or data analysis/model
C14 Fit between the project's approach/methodology and the problem they have stated to resolve
C15 How relevant is the project to the COVID-19 crisis and alleviation of suffering?
C16 The scalability of the project in the long term, taking manufacturing into consideration
C17 How well has the project addressed concerns such as quality testing?
C18 The project's dissemination strategy (quality of documentation for goals, results, methods and needs; open access model, outreach) is this/will this project be easily reproducible?
C25 How accessible will the result of the project be to the general public?
C26 How accessible will the result of the project be to policy makers?
C19 Project Originality
C20 Project practicality: Although the design quality may be high, there may be more suitable alternatives. Is this the case?
C21 Fit between the project's approach/methodology and the problem they have stated to resolve
C22 How relevant will the result of this project be for policy makers?
C23 How relevant will the result of this project be for the public?
D. Questions
What is genomic pathogen surveillance?
Why is genomic pathogen surveillance important?
When vaccines arrive, genomics would tell governments which locations and possibly which reservoir species should be prioritized for vaccination.
Genomics could also also tell researchers the root cause of vaccine failures: is it due limited cross protection due to high genetic divergence from vaccine or reversion to virulence? This will help in improving vaccines.
What is the difference between RT-PCR, antibody tests and viral genetic sequencing?
Why are you the right project team for this?