Blog

By Judy Siegel-Itzkovich

Over three days in late May, iReceptor Plus researchers led a team in Hackseq RNA’s peer-led hackathon of open-science, interdisciplinary collaborations to help fight the COVID-19 pandemic.

iReceptor Plus team members Brian Corrie, Laura Gutierrez Funderburk and Felix Breden from Simon Fraser University in Canada led the hackathon team, working on a project called the AIRR Adaptive Adapter.

Microsoft and Adaptive Biotechnologies, who are collecting anonymous blood samples from people diagnosed with COVID-19, are seeking to understand how the human immune system responds to the virus and why some patients become critically ill from the infectious disease while others are asymptomatic. The research findings will be shared through an open-access dataset so others can use it to maximum advantage for the development of better treatments for COVID-19. 

The goal of the AIRR Adaptive Adapter RNAseq hackathon project is to develop tools to transform the data from the Adaptive/Microsoft project into  standard AIRR-seq data formats as created by the AIRR (Adaptive Immune Receptor Repertoire) Community.

The AIRR Community is organizing and coordinating stakeholders in the use of next-generation sequencing technologies to study antibody/B-cell and T-cell receptor repertoires. It comprises a multidisciplinary group of several hundred stakeholders who are dedicated to the development of methods and standards for the generation, analysis and sharing of AIRR-seq data. 

Defeating the coronavirus pandemic will require unprecedented cooperation from the research community and the AIRR Community has recently made a call  upon its members and the wider research community to share experiences, resources, samples and data as openly and freely as possible, and to work within their respective systems to break down barriers to achieve this goal, subject to the guiding principles of respect, privacy, and protection for patients and all people.

The goal of AIRR Adaptive Adapter hackathon project is to develop a tool (or set of tools) to query the Adaptive ImmunoSeq repository, download data, and convert it to the standard AIRR Community data formats. Once a converter has been developed, it will be possible to load the COVID-19 data produced by the Microsoft/Adaptive project and place that data in an AIRR Compliant repository.

The iReceptor Plus team is working closely with the AIRR Community to curate COVID-19 AIRR-seq data, with two AIRR-seq COVID-19 datasets currently available in the AIRR Data Commons and searchable through the iReceptor Gateway. Once data from the Adaptive/Microsoft project is available, the tools developed through the AIRR Adaptive Adapter hackathon project will be used to transform that data so that it can be uploaded into the AIRR Data Commons.

Defeating the coronavirus pandemic will require unprecedented cooperation from the research community. This is especially true for the AIRR Community, given the paramount importance of antibodies and T cells for vaccines, diagnostics and therapeutics in viral infection.