Who developed GPAS?
The GPAS tool was built by a long-established world leading pathogen genomics team at the University of Oxford and supported by the cloud computing scale and security provided by Oracle. Originally focused on tuberculosis, when the COVID-19 pandemic began the team at the University of Oxford repurposed their technology to analyse the spread and mutation of the SARS-CoV-2 virus.
GPAS Ltd was created as an English registered not-for-profit organisation, in order to make this applied research available globally. In this we are supported by the University of Oxford, and enabled by Oracle.
What are the benefits of using GPAS?
GPAS provides a rapid, standardised and easy-to-use method of analysing and comparing genomic sequences. Results can be downloaded or viewed in dashboards to understand trends and inform public health decisions. If organisations choose, data can be shared, and GPAS’s standardised genome assembly process allows for direct comparison of data between laboratories or across borders.
Speed – Many labs around the world currently wait days or even weeks for their Covid-19 sequencing results, with decisions made on out-of-date information. GPAS works in near real time, delivering a critical early warning system, and bringing swift clear data to aid effective decision making. A single sequence can be completed in 20 minutes on average, concurrently assembling and analysing up to 100,000 genomes per day. This rapid analysis allows disease outbreaks and subsequent mutations to be tracked and acted on effectively.
Efficiency – The platform lowers the global barrier to entry. Currently genomic data can only be assembled by highly trained experts. GPAS automates this assembly service, allowing a wider range of scientists and public health experts to interpret and analyse the data, and expert bioinformaticians to concentrate on in-depth analysis of results, rather than spending time on routine operations.
Scale – GPAS allows simultaneous processing, analysis and comparison of thousands of sequences, allowing multiple countries to track variants globally, spot outbreaks, and take appropriate action. Countries who wish to do so can share data and compare side-by-side across borders at the touch of a button.
Standardisation – The platform removes variation. Currently organisations assemble their genomes in many different ways (often in response to local resource constraints). GPAS works with a range of sequencing technologies, allowing organisations to share data, compare sequences and precisely track pathogen spread and mutation as scientific understanding evolves.
Security – Each user has full control over the data uploaded to GPAS with sharing and privacy options available. The platform automatically removes personally identifiable information (PII) before upload, and the cloud infrastructure is protected by industry-leading security measures designed by Oracle.
Breadth – GPAS aims to be ‘platform agnostic’ working with a range of sequencing platforms. Currently available for SARS-CoV-2, the platform will rapidly expand to TB, foodborne illnesses, influenza, and other pathogens.
What is the cost associated with the GPAS service?
As a not-for-profit entity, GPAS Ltd makes the SARS-CoV-2 toolset available free at the point of service for academic and research laboratories, and public health bodies, in low and middle income countries. GPAS Ltd is able to do this through a philanthropic donation from Lawrence J. Ellison.
GPAS users are responsible for the costs of their local sequencing hardware, consumables and internet bandwidth. We are actively seeking partnerships with organisations which may be able to meet these additional costs for GPAS Ltd customers, and would welcome discussions which will help further reduce the costs of genomic sequencing and analysis for low and middle income countries.
High income countries (as defined by the World Bank) will be expected to meet the costs associated with GPAS through tender/procurement and contracting processes.
Is GPAS a sequence database or repository? How does this differ from existing repositories?
GPAS is not a sequence database or repository. Unlike pathogen repositories, GPAS standardises the data into a comparable format, including information on date and sample collection location and displays it in near real-time dashboards which can be used to support public health decision making. Outputs from GPAS can be submitted to pathogen repositories by users who wish to do so.
Who can access data uploaded to GPAS?
GPAS is built on the principle of data sovereignty. Each organisation has full control over what data is uploaded to GPAS, and whether that data is shared with the community of “sharing” organisations. By granting full control over data sharing to each organisation, (on a sample-by-sample basis) GPAS respects the autonomy of each organisation to decide what to do with its data.
Uploaded data will not be shared with or sold to private sector companies. GPAS Ltd, the University of Oxford and Oracle Inc do not have access to an organisation’s uploaded data, unless an organisation chooses to join the “sharing” community.
As we develop future versions of GPAS with input from users, we will create additional sharing functionality to facilitate research partnerships and public health response to outbreaks. GPAS Ltd will facilitate relationships between users, for those who wish to collaborate on analysis or publications, but neither University of Oxford nor Oracle expects to be included in any such activities by default.
How does GPAS collect and process personal data through your use of the Portal?
Is GPAS only for SARS-CoV-2?
Considering the pressing global health emergency of the Covid-19 pandemic, GPAS was initially offered for analysis of SARS-CoV-2. However GPAS can be adapted to support the processing, analysis and interpretation of data related to a range of pathogens. In late 2022 we plan to launch a product for TB, followed by products to identify and classify foodborne illnesses, influenza, and other pathogens.
What is genomic surveillance?
Pathogens are organisms that cause disease to their host. They may be viruses, bacteria, fungi or parasites and they all contain genetic code, such as DNA or RNA. It is now possible to sequence the DNA/RNA of a pathogen rapidly and cost-effectively and use this information about the pathogen’s genetic make-up to inform patient care and public health decision making.
The greatest benefits from sequencing pathogens DNA/RNA are seen when it is done on a global scale, in order to track the spread and possible mutation of disease.
What are the challenges of genomic surveillance?
To date, there has not been a universal approach to genomic pathogen sequencing, making rapid sharing of information and comparison of results challenging.
There is also inequity in the spread of sequencing resources, resulting in a wide variation in the amount of sequencing countries can conduct.
Consequently, it is not possible to get a true understanding of the scale, spread and mutation of pathogens, making informed decision making challenging.
What are the benefits of genomic surveillance?
Whilst vaccines have mostly allowed a return to normal life, SARS-CoV-2 is here to stay, and continues to change and mutate. It is critical that close monitoring is maintained to provide rapid information pertaining to Covid-19, e.g. if the virus is mutating into something which can evade vaccines, or make people really unwell.
EARLY WARNING SIGNALS
Covid-19 taught us how quickly a new disease can emerge, and that it is best to be prepared. Similar to global earthquake warning systems, GPAS has the technology to help look out for new diseases, or new versions of existing diseases. This information helps public health decision makers to make decisions for their countries and communities.
Covid-19 research increased global knowledge about how diseases mutate and change. The world has sequenced and shared nearly 10 million Covid-19 samples since 2020. If we start doing this for other infectious diseases, such as TB or Influenza, this would help the world to understand these diseases better, and support the development of treatments or vaccines.
How long does it take to process a genomic sequence on GPAS?
Processing a single sequence on GPAS takes 15-20 minutes. Multiple samples are processed in parallel. Uploading, processing and downloading a batch of 100-300 samples should take 2-4 hours with moderate internet network connectivity.
What data is being uploaded to the cloud? Is any personally identifiable information (PII) being uploaded?
GPAS does not collect clinical PII. GPAS Ltd does not have access to any PII held on the local computer.
The upload client creates a lookup table, stored on the user’s computer, to enable users to link anonymised GPAS results back to their local records. The GPAS upload client removes human genetic reads, then sends the pathogen genomic sequence to the cloud, along with relevant metadata (to capture provenance of the data: date the sample was collected, method of sample collection, fuzzy location from which the sample was collected, organisation that uploaded etc).
What sequencing technology do I need to use GPAS? What other infrastructure?
GPAS is already proven with data collected from Oxford Nanopore Technology (ONT) and Illumina sequencing platforms. We will support other sequencing platforms in future releases.
To send data to GPAS, users install the upload client, and use the client to upload the data to the cloud. Users can choose a command-line interface, or a user-friendly graphical interface. The graphical interface is designed to be intuitive and not require specialist training and will work with common operating systems (Linux, Mac and Windows). Uploading data to the cloud requires an active internet connection. Once data has been uploaded and processed, users may view their results in a web browser, using our online dashboard, or download their results for local analysis.
What technical support is available for using GPAS?
GPAS Ltd, the University of Oxford and Oracle work together to provide high quality seamless user support.
Which primer sets does GPAS support?
GPAS already supports Artic-V3, Artic-V4, Arctic-V4.1 AmpliSeq and Midnight. We continue to monitor available primer sets and update our system accordingly.
How does GPAS handle human read removal?
The GPAS upload client removes human genetic reads from users’ samples, prior to uploading them to the cloud, to ensure patient Personally-Identifiable Information (PII) is not sent to the GPAS cloud.
How does GPAS handle re-classification of lineages over time?
SARS-CoV-2 samples can be named in different ways. https://covariants.org/ is a helpful resource to understand the relationships between nomenclatures.
GPAS currently provides automatic lineage calls for all samples, following:
- PANGOLin (e.g. B.1.1.7)
- WHO Variants of Concern list (e.g. alpha, beta, delta)
- UKHSA Variants of Concern list (e.g. VOC-20DEC-01)
GPAS uses NextClade to perform viral genome alignment, mutation calling and quality checks, but does not retain NextClade lineage calls (e.g. 20I/501Y.V1).
Lineage is a complex topic and these lineage definitions are frequently updated by their respective organisations. GPAS Ltd updates all of these components to the latest version once a week, to apply the latest definitions.
Currently, samples are assigned lineage names at the point of initial processing. GPAS Ltd updates all samples to the latest lineage definitions: the process is continually improved in consultation with GPAS users to ensure that local lab workflows are supported.
Partnerships and Legal Arrangements
Are there opportunities for collaboration and partnership
Yes! There are opportunities for collaboration in areas such as academic research, publications, capacity building for genomic sequencing facilities and providing input to improve future iterations of GPAS. If you are interested in partnering, please contact us: firstname.lastname@example.org
We would like to know more about GPAS. Will you come and speak at our event or conference?
We are always keen to share the work we are doing at GPAS Ltd. Please drop us a line at email@example.com with details of your event, and we will get back to you.
What is the legal status of GPAS Ltd?
The Global Pathogen Analysis Service Ltd (GPAS Ltd) was created as a private English company limited by guarantee that is run on a not-for-profit basis, in order to make this applied research available globally. GPAS Ltd is funded by a philanthropic donation from Lawrence J. Ellison. We are supported by the University of Oxford and enabled by Oracle.
We also have a US subsidiary, GPAS USA, Institute, which is applying for charitable status, and will develop a global presence.
How does my organisation become a GPAS user?
If you would like to learn more about GPAS or have a demonstration of the system, please email us at firstname.lastname@example.org and our team would be delighted to arrange a meeting.
Can I become an individual GPAS user?
Since GPAS handles data which is collected and controlled by organisations, there must be an access agreement in place at the organisation level to ensure data is handled properly. Individuals can only use GPAS if they have been nominated to do so by their organisation.
What legal arrangements are required to use GPAS?
Use of GPAS is subject to terms and conditions and completion of a specific document which allows organisations to choose their data sharing preferences.