MIODx: A Breakthrough Leader in the precisionFDA COVID-19 Precision Immunology App-a-thon

MIODx Precision Immunology

The results are in for precisionFDA’s COVID-19 Precision Immunology App-a-thon, and we are thrilled to announce our partner, MIODx, demonstrated strong leadership in their field by taking home medals in multiple categories!  

Motivation Behind the COVID-19 Precision Immunology App-a-thon 

Despite the accelerated scientific pace of COVID-19 research, treatments, and vaccine development, critical questions remain unanswered, including the role of genetic variability of an individual’s immune system on their response to SARS-COV2 infection. To effectively combat the widespread transmission of COVID-19 infection and save lives, better understanding of its pathophysiology is needed to help enable effective diagnosis, prognosis, and treatment strategies. 

Through the precisionFDA COVID-19 Precision Immunology App-a-thon, the Food and Drug Administration (FDA) called upon the scientific community to develop innovative and user-friendly tools to explore the relationship between personalized immune repertoires and COVID-19 disease outcomes. Participants were evaluated by judges in six categories (Table 1), and MIODx took home awards in 5 out of the 6 categories for their ClonoMapTM Immune Profiler and ImmuneInsight tools. 

ClonoMapTM Immune Profiler Evaluation Categories
Table 1. Evaluation Categories

The ClonoMapTM Immune Profiler and Immune Insight tools were featured due to their high-quality visualizations, excellent documentation, ability to be an out-of-the-box solution for exploratory analysis, and potential impact to the field of precision immunology. See all the results of the app-a-thon here

MIODx’ Impact on COVID-19 Biomarker Discovery and Disease Severity Prediction 

Excelling in the eyes of the judges was just one highlight for the MIODx team. Their analytics and visualization tools, ClonoMapTM Immune Profiler and Immune Insight, were used to generate hypotheses and find preliminary evidence of T Cell receptor (TCR) repertoire genes as biomarkers of significance for COVID-19 clinical outcomes.

ClonoMapTM Immune Profiler is an automated TCR repertoire analysis pipeline that utilizes FASTQ files for downstream analyses and was used in the app-a-thon to investigate whether there are biomarkers in the TCR repertoire data that are predictive of disease severity.

Among the key findings, Immune Profiler highlighted specific T Cell Receptor Beta Variable (TRBV) genes and CDR3 clonotypes at different frequencies in healthy individuals compared to COVID-19 recovered patients. These results provide candidate TCRs for further investigation with respect to COVID-19 disease severity.

One particularly interesting TRBV (TRBV19) was found at high frequency in all samples (healthy and COVID-19). Using their Immune Insight literature search tool, the MIODx team determined that this TCR is specific to influenza virus antigens. MIODx is now investigating the link between this public clonotype and COVID-19 disease progression.

Overcoming TCR Analysis Computational Challenges 

Despite the enormous potential of TCR analysis in precision medicine, big data and computational challenges remain to effectively sequence and analyze T-cells at scale. To that end, MIODx has launched ClonoMap™ Immune Profiler on DNAnexus Titan™, which provides a cloud environment, enabling seamless sharing of projects, data, and pipelines to team members who have approved access. Researchers can upload their data, integrate new data sources, conduct analyses with the ClonoMap™ pipeline, visualize, and share results with collaborators – all within an intuitive user interface. 

The DNAnexus Titan™ Platform allows MIODx to maintain multiple versions of their pipeline. They can give customers access to the production version, while also testing updates and making changes to the pipeline’s research version. DNAnexus enables MIODx’s customers to securely bring their own data online within their shared project and immediately apply the MIODx ClonoMap™ pipeline to generate results.

See ClonoMap Immune Profiler in Action 

Ankita Das, Head of Product, at MIODx will be joining us for a precision immunology webinar, where she will present the clinical relevance of sequencing the TCR repertoire, methodologies for analyzing and interpreting TCR data, and an in-depth look into how their tools generated preliminary evidence of biomarkers in the TCR repertoire that are predictive of COVID-19 disease severity. 

Save your seat here. 

Date: May 27th, 10am PT / 1pm ET

Responding to the Evolving World of COVID-19 Through Global Collaboration

COVID-19 Research Global Collaboration

Will the next wave of COVID-19 surveillance come via wastewater? What challenges lay ahead as we try to detect variants in a constantly evolving viral population, and adjust our therapeutics accordingly? How could bioinformatics help?

These were some of the questions raised during a recent roundtable of genomics experts brought together by DNAnexus to explore ways in which enhanced scientific collaboration tools could contribute to pathogen surveillance and global pandemic response. 

The right tool from the toolbox

The public has become all too familiar with the term ‘variants’ thanks to evolving versions of the SARS-CoV-2 virus that is plaguing the world. But identifying low frequency variants in genomes has always been a challenge. From PCR testing to short- and long-read whole genome and transcriptome sequencing, different detection methods have different benefits, from speed and cost, to accuracy and depth of coverage. 

As scientists set their sights on monitoring urban wastewater supplies to track pathogens in the population, they will have to grapple with samples that contain a ‘grab bag’ of microbes, viruses, bacteria, and lots of other fun stuff, said Todd Treangen. 

Treangen, Assistant Professor of Computer Science of Rice University, warned that environmental metagenomics presents many challenges. Distinguishing between actual low prevalence genetic variants and sequencing errors is high among them. Reassembling viral genomes from the limited information you’re likely to recover is also extremely difficult, he said.

Fritz Sedlazeck, Assistant Professor of Bioinformatics & Data Analysis at Baylor College of Medicine, said quick, easy and affordable tests to detect variants of clinical interest would be required in order for such surveillance to be practically implemented. DNAnexus’s Ben Busby suggested that the creation of simple pipelines for metagenomic assembly might help the effort.

Richard Copin, a senior staff scientist at Regeneron, said deep sequencing still has a role, especially in the development of new therapeutics. It is important to be able to estimate the reservoir of diversity of variants in the virus among different pockets of the population, in case minor variants become dominant, he said.

“What is the selective pressure that would lead to these minor variants taking over the entire virus population, so that our vaccines or treatments would be totally useless?” Copin asked.

Sharing from the start

Another big challenge during the current pandemic has been data access, Copin noted. 

“Sharing sequencing data among scientists, which sounds like something that’s obvious, has been a big challenge, especially in the U.S.,” he said. “It’s something I’ve been shocked about.”

Treangen said coordinated response may have been a bit late out of the gate, but initiatives like the open-science research consortium COV-IRT (the COVID-19 International Research Team) have helped facilitate collaboration to accelerate research and drug development. The group of nearly 200 scientists from 11 countries and 75 institutions recently marked its one-year anniversary with a scientific symposium. Treangen, a founding member, said he is optimistic that such collaboration will help ensure the global response to future pandemics will be timely, well-coordinated and hopefully, proactive. 

DNAnexus has been a partner in that effort, providing IT infrastructure as well as assistance accessing and analyzing data. 

Copin said DNAnexus’s data sharing platforms and tools like the UK Biobank Cohort Browser will be critical for the success of global team science efforts.

Busby, who has helped with several COVID-related hackathons, said he was keen to continue contributing to pathogen surveillance by developing virus detection toolkits and enhanced phenotype/genotype management systems, and he welcomed collaboration with other scientists.

Seqera Labs and DNAnexus Announce Availability of Nextflow App on DNAnexus

Nextflow App now Available on DNAnexus

If Linux is the lingua franca of data science, then Seqera Lab’s open-source workflow orchestrator, Nextflow, is the ideal tool to simplify writing and deploying of data-intensive pipelines. And we are excited to now be able to offer beta availability of Nextflow as a third-party app on the DNAnexus Platform. 

Nextflow is a popular workflow engine supporting a wide range of batch schedulers and public cloud providers. Many Nextflow users wanted the ability to deploy their pipelines on DNAnexus, and leverage our state-of-the-art data management and collaboration capabilities in a secure, compliant environment. So we teamed up with Seqera Labs to make it happen.

This new solution enables DNAnexus users to leverage any new or existing Nextflow pipeline to deploy and manage their data analyses collaboratively, in a computationally efficient way, all within their familiar DNAnexus environment. 

While DNAnexus customers can run Nextflow through a Cloud Workstation or JupyterLab terminal, this integration extends the Nextflow runtime by providing enterprise-level application for scalability and performance on the DNAnexus Platform.

Customers already using Nextflow do not need to change code in their pipelines, and it gives them access to the thousands of publicly available Nextflow pipelines from the community. It also ensures that DNAnexus users can leverage the full orchestration of native Nextflow with the guarantee that any changes to the Nextflow syntax or runtime are fully conformant with the DNAnexus Platform.

For more information and to trial the beta release of the Nextflow app for DNAnexus, please visit www.seqera.io/dnanexus

You can learn more about the release in a May 20 webinar (8 a.m. PT). Sign up now to save your seat.