Collaborative Genomics: Highlights From 2016

This has been a remarkable year for DNAnexus and the genomics industry at large. As 2016 comes to a close, we celebrate the year’s accomplishments, and everyone who contributed to its successes.

The past 12 months were jam-packed with innovative research, strategic partnerships, platform enhancements, productive meetups, and plenty of conferences. Here are some of our favorite highlights from 2016!

  • In that vein, we are humbled to have contributed to a wide range of efforts with the goal of working together to advance precision medicine. We kicked off the year by powering a collaborative breast cancer study by the National Comprehensive Cancer Network. Researchers from 14 different institutions worked together to identify potential therapies for a patient with metastatic triple-negative breast cancer — an unprecedented level of collaboration as a result of leveraging the DNAnexus Platform.
  • We also celebrated the one-year anniversary of President Obama’s Precision Medicine Initiative (PMI) with the first PMI Summit. This set in motion much of our year to come, particularly our work delivering the precisionFDA platform, an important component of the President’s PMI. PrecisionFDA, a Bio-IT World Best Practices award-winning program, was designed to leverage community participation to advance regulatory science for next-generation sequencing assay evaluation. 

Highlights of precisionFDA’s initiatives this year included three challenges with the goal of engaging and sharing data to improve DNA test results. Community members had the opportunity to test pipelines, discuss best practices, and add software to the precisionFDA platform. These challenges were wildly successful, and garnered a great amount of community involvement.

  • We would be remiss not to mention the powerful insights coming out of the Geisinger and Regeneron collaboration, powered by DNAnexus. De-identified EMR data from Geisinger’s MyCode Community Health Initiative is integrated with whole exome sequencing data from these same patients. The power of this joint approach was apparent in a paper published in the New England Journal of Medicine, revealing a genetic variant that appears to result in reduced levels of triglycerides and a lower risk of coronary artery disease. As the partnership continually adds more patients with associated EHR data and sequenced exomes, the power of these studies will only increase. Learn more about the program in this Mendelspod podcast.
  • To further move the needle on cancer research, Singapore-based POLARIS (Personalized OMIC Lattice for Advancing Research and Improving Stratification) began using DNAnexus to enable a series of genomic tests for cancer. These include gastrointestinal and solid tumor cancer tests, which are part of a systematic effort to develop a framework for omics-based tests within Singapore.
  • M2Gen also adopted the DNAnexus Platform to support data data analysis and collaboration for the Oncology Research Information Exchange Network (ORIEN) Avatar Research Program. This innovative program joins academic cancer centers and pharmaceutical companies in their efforts to study and treat cancer through the development of more precise treatments for patients.
  • In addition to powering POLARIS and ORIEN, DNAnexus reanalyzed The Cancer Genome Atlas (TCGA) dataset. TCGA is a joint effort between the National Cancer Institute and National Human Genome Research Institute, and includes data from 10,487 patients across 33 cancer types. This reanalysis project was a massive undertaking, whereby during a four-week period, approximately 1.8 million core-hours of computational time were used to process 400 TB of data — a testament to the scalability of the DNAnexus Platform.
  • A number of partnerships were announced to further build out DNAnexus as a seamless end-to-end solution for genome analysis. The integration of the DNAnexus Platform with Sapio Science’s Exemplar Next Generation Sequencing Laboratory Information Management System (LIMS) enables laboratory management and informatics solutions in the cloud. We also partnered with SolveBio to provide access to their curated data analysis services, offering a rapid and secure progression from data analysis through interpretation. Finally, Genomics plc entered into a collaborative effort with DNAnexus to break down the barriers for population-scale sequencing analysis.
  • Together with PacBio, we worked to simplify structural variant discovery and decrease barriers to de novo assembly. As PacBio’s cloud bioinformatics partner, we are able to support researchers working with long-read sequencing data. Through this effort, the SMRT Analysis Suite v3.1.1 has been optimized for the cloud environment and is available on the DNAnexus Platform. Other long-read analysis tools, such as PBHoney, PBJelly, and the Parliament are also optimized for use on the platform.

A particularly exciting development in the realm of long-read sequencing was the release of the first public Sequel dataset of NA12878, demonstrating you don’t need expensive high-fold coverage to discover novel structural variants. The Sequel System is faster, half the cost, and provides higher throughput, delivering around 7 times the amount of data as the PacBio RS II. These added benefits will hopefully make long-read sequencing available to a broader audience.

  • Finally, from a corporate perspective, DNAnexus also had some serious wins. Our team  nearly doubled in 2016 to keep up with the ever-increasing activity from our customers, and to keep pace with the burgeoning genomics industry. We couldn’t be more fired up about the growth of our team!

Special thanks to all our customers, partners, and collaborators for contributing to another amazing year filled with exciting milestones. We’re delighted by the developments within the genomics industry, and look forward to 2017 with excitement and inspiration.

What is your favorite memory from 2016? Let us know on Twitter. #Genomics16