Visit us at Bio-IT World 2021!

We’re excited to see you back in you person at Bio-IT World in Boston! We’ll be there, masked up, and ready to join fellow life sciences, clinical, healthcare, pharma, and IT professionals to discuss recent advancements in the field, and the future of precision medicine. Come to our talks and visit us in booth 204 to learn about the latest enhancements to our biomedical data platform. Can’t make it to any of our events? Email us at marketing@dnanexus.com to schedule a meeting with one of our scientists.

DNAnexus Talks & Booth 204 Events

Tuesday, September 21 

COVID & IT: SARS-COV-2 Genome Analyses and Computational Tools for Infectious Disease Surveillance

  • 8:40am  
  • Speaker: Ben Busby, Director Research Platforms

The COVID-19 pandemic has revealed the criticality of computational approaches for monitoring environmental microbiomes for emerging pathogens. This talk will focus on computational tools that enable rapid and robust global surveillance of infectious disease and will focus on existing computational approaches for SARS-CoV-2 detection and monitoring.

Booth Spotlight: Synthesis Data Harmonization on DNAnexus  

  • 9:30-10am 

As scientists seek to manage and interrogate larger volumes of diverse datasets, data harmonization becomes ever more complex. The Snthesis platform ingests data from a wide range of sources, including LIMS platforms, electronic lab notebooks, structured data extraction from handwritten notes, PDFs, Excel files, EHR data, and data output from lab instrumentation, and harmonizes them in an automated way. Join this booth session to learn more about data harmonization on DNAnexus with Snthesis.

Explainable ML for Adverse Drug Reactions Using DNAnexus

  • 10am – Track 5: AI for Drug Discovery & Development 
  • 12:30-1pm – Booth Spotlight 
  • Speaker: Mike Lelivelt

Pharmacogenomics researchers can leverage UK Biobank to better understand how genes affect a person’s response to drugs. Learn how DNAnexus Apollo efficiently analyzes this massive dataset with explainable machine learning models to gain insight into ADRs.

Booth Spotlight: UK Biobank Research Analysis Platform 

  • 2:30-3pm

UK Biobank contains a trove of genomic and clinical information from 500,000 volunteers, including exome and whole genome sequencing data, blood samples, medical imaging and extensive environmental and lifestyle data.. To address the scale of the dataset, UK Biobank partnered with DNAnexus to build the UK Biobank Research Analysis Platform. Leveraging the power and scalability of the cutting-edge, cloud-native DNAnexus Apollo Platform, the Research Analysis Platform enables researchers easily and quickly to search and analyze the incredibly rich UK Biobank dataset.

Wednesday, September 22 

Data Federation Panel: From Biobank Scale to Individual Patients: Bringing Complex Multi-Omic Data to the Clinic and Clinical Research 

  • 9:55am – Track 2: Data Management 
  • Panel Speakers: Ben Busby, DNAnexus; Ankita Das, MIODx; Rory Kelleher, NVIDIA, Ahmad Khleifat, King’s College London

Multi-omics datasets of different diseases are available to researchers, and for the first time the availability of new analytical tools allow for the incorporation of these datasets in clinical research. However, there are serious challenges involved in realizing the promise of these developments. Developing new methods for multi-omics data will allow for better patient stratification, more targeted treatments, and greater understanding of disease mechanisms.

A Multi-Omics Data Science Platform Powering a Comprehensive Precision Oncology Strategy 

  • 11:25am – Track 3: Software Applications & Services 
  • 1:15-1:45pm – Booth Spotlight 
  • Speaker: David Fenstermacher, VP Precision Medicine & Data Sciences

DNAnexus and City of Hope Comprehensive Cancer Center (COH) embarked on a partnership to develop a scalable cloud-based oncology platform, POSEIDON, to democratize data for COH’s research and clinical programs, accelerating the fulfillment of its Precision Oncology Strategy. POSEIDON leverages DNAnexus bioinformatics technologies to combine multi-omics data in a unified platform that supports advanced analytics and visualizations within a collaboration portal to discover new evidence-based treatments.

Panel: Deconvolution of Massive Scale Datasets from Etiological Lessons: Technical Tips and Tricks, Data Interoperability for Training, and Feature Extraction

  • 4:00pm – Track 2: Data Management 
  • Panel Speakers: Ben Busby, DNAnexus; Emerson Huitt, Snthesis; Vivian Neilley, Google Cloud Healthcare; Sean Davis, University of Colorado Anschutz Medical Campus 

Computational Immunology: Tailoring Tools to Tackle the T-Cell Triad

Whether you’re a seasoned computational scientist or an armchair immunologist, the growing focus on the T-cell triad — MHC, peptide & TCR — in both infectious and chronic diseases is necessitating easy access to complex datasets and analysis tools that can make sense of the human adaptive immune response.

In a recent webinar, DNAnexus research platforms expert Ben Busby joined Ankita Das, Head of Product at immune profiling company MIODx, to discuss ways in which the companies are working together to make it easier to interrogate and interpret TCR (T-cell receptor) data.

As Das explained, T-cell composition and activity are at the center of the immune response and key to tracking immune health. The composition of a person’s T-cell repertoire can vary depending upon factors like age, environment, genetics, infection, and lifestyle. When T-cells sense an infection, they undergo a phenomenon called clonal amplification, wherein a subset of the T-cell repertoire will amplify to orchestrate an immune response, whether that be killing off infected cells or recruiting B cells to generate antibodies. Interpreting clone activity can reveal important clues about immune health and insight that could potentially lead to biomarker and therapeutic discovery.

However, scientists wishing to undertake such research face several challenges. “TCR data is currently very siloed, and the architecture available for hosting and analyzing the immense data sets involved are often not scalable,” Das said. 

The MIODx team set out to overcome these challenges by creating ClonoMap™, a SaaSportal hosted on DNAnexus Titan™, in which TCR repertoire libraries can be stored, managed and analyzed in a secure environment. 

ClonoMapTM subscribers upload raw sequence data from TCR repertoire libraries into the portal and run  the ClonoMap™ Immune Profiler analysis to discover repertoire features. A second tool, ClonoMapTM Immune Insight, searches public datasets to help scientists see the new immune profiles in context and draw translational insights, such as biomarker identification. The MIODx team is now taking it a step further, applying machine learning to create personalized, immune health scores.

The ClonoMapTM suite of tools has already received nods for its innovation during the precisionFDA COVID-19 Precision Immunology App-a-thon. In the webinar, Das shared examples of how it was used to generate data and insights in COVID-19 and rheumatoid arthritis. In the case of COVID-19, for example, the 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, providing TCRs for further investigation with respect to disease severity.

Holy grail of healthcare

Unravelling the immune response is the ‘holy grail of healthcare,’ Busby said. And in what may prove to be the decade of infectious disease research, Busby said he was proud to be able to provide tools to help scientists do so. 

“We want to make this size data accessible to everyone, and the DNAnexus platform really enables scientists and bioinformaticians to be more powerful,” Busby said. 

In addition to ClonoMap™, the iReceptor data discovery platform, curated by the AIRR (Adaptive Immune Receptor Repertoire) community, facilitates the curation, analysis and sharing of antibody/B-cell and T-cell receptor repertoires (AIRR-seq data) from multiple labs and institutions.

JupyterLab is another powerful tool that DNAnexus leverages for multi-omic cohort analysis and data exploration, and Busby recommended it for experts and armchair enthusiasts alike. He also noted that many DNAnexus-created Jupyter Notebooks are available, even to non-DNAnexus users. 

Other open source tools include Bioconductor, Bioconda and Docker. Each can be easily integrated into DNAnexus platforms, and the visualization capabilities of the DNAnexus system make the data obtained by them even more approachable, Busby said.  

You can watch the full webinar below.

How New Practices in Biomedical Research are Changing the Future of Healthcare

Biomedical Research Changing Healthcare

Five years ago, we were ushering in the ‘era of precision medicine,’ with researchers and clinicians alike embracing advances in genomics to help tailor treatments to individual patients, especially in cancer care. 

How has biomedical research and clinical care changed since then, and what does the future hold?

Precision medicine continues to garner attention, with its applications expanding into other areas, such as neuroscience, immunology, women’s health, and rare diseases. 

Patients are not only the focus of targeted therapies; they are also being placed front and center of many aspects of healthcare. 

Researchers are eager to incorporate diverse data from more representative patient populations, and registries from large-scale public sequencing efforts and patient advocacy groups are proving to be valuable resources in these endeavours.   

They are also more willing than ever to work together to accelerate discovery, thanks in part to the recent (and ongoing) global COVID-19 pandemic. 

How prepared are we to not only cope with these changes, but also harness their enormous potential? 

From Real-World Data to Real-World Evidence to Real-World Action

Advancements in technology supporting genomics, proteomics, metabolomics (and all the other ‘omics) have generated great insights into the biology of many diseases — and an enormous amount of information. Managing the vast ocean of data and fishing for answers within it are two of the primary challenges in precision medicine.

City of Hope is tackling the data challenge by creating a system that pools a wide variety of data from multiple sources in a way that can be easily accessed by bioinformaticians and physicians alike. 

Created with the help of DNAnexus, the system integrates DNA sequencing information with other data affiliated with the patient journey, from disease registries to pathologies, molecular characterization of the tumor, medical record data, and clinical trials information.

The POSEIDON platform has become more than just a static repository of data. It’s helped inform City of Hope’s unique in-house drug development. It’s helped place patients into clinical trials. It’s assisted tumor boards, where clinicians, researchers, and technical curators come together to make decisions on tricky cases. And it has led to new research ideas, new methods, and new translational projects. 

As precision medicine expands, so will the hunt for new biomarkers and the use of companion diagnostic tools. Laboratories will need an informatics environment that can flexibly scale to meet the demand for increased test volume. Cloud-based systems enable labs to optimize analysis pipelines for quality, speed, runtime, and cost, in a secure, compliant way.

Myriad Genetics uses the DNAnexus Titan platform to power its computationally intensive AI and machine learning methods. The company uses the technology for biomarker discovery, improvement of its current molecular diagnostic test portfolio, and disease risk prediction. 

The Apollo Platform and its Cohort Browser can also be used in pharmacogenomics to predict an individual’s risk to adverse drug reactions, another area that is likely to be in high demand as precision medicine becomes the norm.

Harnessing Rare Resources 

When researching a rare disease with many subtypes driven by diverse and distinct genetic alterations, data sharing is key. Samples acquired by a single institute, a single research initiative, or even a single nation may lack sufficient statistical power for genomic discovery and clinical correlative analysis.

St. Jude Children’s Research Hospital was an early adopter of cloud-based collaboration,  partnering with DNAnexus and Microsoft in 2018 to create a data-sharing ecosystem that has proved to be a model for harmonized genetic data across the pediatric cancer community. Since then, more than 1.25 petabytes of data have been incorporated into the St. Jude Cloud, and several research studies have been published about scientific discoveries made using the data.

The Muscular Dystrophy Association (MDA) is harnessing its patient registry to improve current and future patient care. Its neuroMuscular ObserVational Research (MOVR) data hub collects longitudinal data in seven neuromuscular disease indications, and a new visualization and analysis platform powered by DNAnexus is enabling 37 MDA Care Centers to easily access and analyze the information.

The MOVR Visualization and Reporting Platform (VRP) allows different levels of analysis, from overviews of disease progression and outcomes across sites, to in-depth dives into clinical parameters across large cohorts of neuromuscular patients. This level of correlative analyses could ultimately stimulate new drug, biologics and gene therapy discoveries. Exploration of deeply curated neuromuscular disease cohorts could also help in clinical trial design, by enabling clinical researchers to rapidly identify populations that meet specific clinical criteria.  

DNAnexus platforms are also being used by the Children’s Tumor Foundation to delve deeply into gene expression and transcriptome data to identify elusive therapeutic options for three forms of neurofibromatosis.

Going Global

Progress in science and medicine accelerates when researchers collaborate around responsibly shared datasets. As the complexity and scale of data increases, collaboration becomes more difficult to manage.

Tools developed on DNAnexus Apollo, such as the cloud-based UK Biobank Research Analysis Platform, have helped harmonize and democratize sequencing data by making it easily accessible to any scientist, from an individual field researcher accessing the database from her laptop, to pharma companies like Biogen, which is using the UKB information to rank candidate compounds in its drug portfolio as well as identify novel gene targets.  

The COVID-19 pandemic has underscored the importance of real-time data sharing, and an emerging focus on global pathogen surveillance will require even more companies to scale up their operations, from vaccine discovery and production, to rapid sample sequencing and diagnostics. 

The DNAnexus Apollo Platform was designed to seamlessly integrate and analyze diverse datasets, including multi-omic & clinical data, driving actionable insights in real time. We’ve compiled some tips for diagnostics businesses looking to scale their operations, as well as pointers for drug discovery companies

As we race towards a more interconnected, interpersonal future in healthcare, we need to ensure the industry is moving at the velocity of technological innovation. At DNAnexus, we’re proud to set the pace and provide solutions that allow all types of users to board the big data train.