Salute! Nexus Negronis On Us at AGBT!

The DNAnexus team is gearing up for the biggest genomics party of the year: AGBT. This annual meeting brings together leaders in the field of genomics to network and share the latest advances in cutting edge sequencing technologies, analytical approaches for genomic studies, and groundbreaking new discoveries.

If you’re headed to Hollywood (Florida), we invite you to visit DNAnexus, any time, in our Hospitality Suite (#218) where you can rub elbows with your colleagues and ask our team about the far-reaching applications and powerful network effect of our secure and collaborative platform. And don’t worry about whetting your whistle, we have you covered.  We’ll be serving our signature Negroni cocktails.

If you find you want to spend even more time with the DNAnexus team, you have many opportunities, including these other great events:

Bites & Insights: Collaborative Genomics at Scale
Tuesday, February 14th, 5:15pm

Join us Tuesday night to share bites and insights with Rady Children’s Hospital and Baylor College of Medicine, two research rock stars performing collaborative genomics at scale. Refreshments will be provided.

  • Scaling the World’s Fastest  Clinical Whole Genome Pipeline for Pediatric Clinical Care
    Narayanan Veeraraghavan, Ph.D., Rady Children’s Hospital
  • eMERGE: Clinical & NIH Data Commons
    Eric Venner, Ph.D., Baylor College of Medicine

Passport Party
Tuesday, February 14th, 9:30pm -11:30pm

Make your way to the DNAnexus suite to get your passport stamped and sample our signature AGBT cocktail: the Nexus Negroni!

Sentieon Coffee Breaks: A Better Alternative to GATK
Tuesday, February 14th, 10:30am-11:00am and
Wednesday, February 15th, 10:20am -10:55am

Learn how Sentieon’s variant discovery pipelines improve upon BWA, GATK, MuTect, and MuTect2 to deliver results 20-50x faster, while reducing costs by 5-7x. Try it license-free for a limited time on DNAnexus.

Can’t make it to one of our events? Email us (info@dnanexus.com) to schedule a 1:1 meeting ahead of time.

We look forward to seeing you in the Sunshine State!

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

Join Us for a Lunchtime Discussion at ASHG

At DNAnexus we always look forward to attending the American Society of Human Genetics (ASHG) annual meeting.  It’s the world’s largest genetics meeting and this year it’s held in the quintessential coastal seaport of Vancouver, BC.  This meeting always delivers by showcasing cutting edge science in the genetics and genomics industry. ashg

Stop by the DNAnexus booth (#100) to demo the latest platform features, hear about new research applications the DNAnexus Platform is supporting, and join our lunchtime discussion to learn how DNAnexus has created the global network for genomics – and what that means for you.

The lunchtime discussion, The Rise of the Genomics Network, will highlight the need for improved approaches to data integration, scalability, and global collaboration within the genomics industry. In clinical genomics, pipelines need to be reliable, assembled quickly, and integrate with existing processes. During this lunch hour, the DNAnexus Team will explore how customers use the DNAnexus Platform to construct and deploy end-to-end solutions for health data networks.  

David Shaywitz, MD, PhD, Chief Medical Officer and Andrew Carroll, PhD, Vice President of Science will discuss real world examples from:

  • Regeneron Genetics Center
  • Geisinger Health System
  • Rady Children’s Hospital,
  • ORIEN – Oncology Research Information Exchange Network
  • Natera
  • Ebola viral sequencing onsite, and more.

Lunchtime Talk Details:

  • Friday, October 21, 2016
  • 1:00pm – 2:30pm
  • Convention Centre Room 18, East Building
  • Lunch and refreshments will be provided for attendees
  • RSVP here

Poster Presentations:

The DNAnexus Platform is leveraged in a variety of research applications. 

WED, OCT 19 — 2:00PM-3:00PM

Poster #655W: GWAS to 30X genomes: Evolution of sequencing in the ARIC cohort to reveal the genetic architecture of complex traits.
Lead Author: Ginger A. Metcalf, Baylor College of Medicine, Human Genome Sequencing Center

Poster #1885W: High-throughput clinical reporting of gene panels with the Neptune Pipeline.
Lead Author: Eric Venner, Baylor College of Medicine, Human Genome Sequencing Center

Poster #1309W: EHR data illuminates patient subtypes in obstructive lung diseases yielding new insights for genetic discovery.
Lead Author: Nilanjana Banerjee, Geisinger-Regeneron DiscovEHR Collaboration

Poster #3247W: Enhanced screening performance of a SNP-based NIPT for five clinically significant microdeletions in a large clinical cohort.
Lead Author: Kim Martin, Natera

Poster #1315W: Disease associations of common and rare calcium sensing receptor variants in the 50K DiscovEHR cohort.
Lead Author: Gerda E. Breitwieser, Geisinger Health System

WED, OCT 19 — 3:00PM-4:00PM

Poster #682W: Exome-wide association analysis of cardiac structural traits in large healthcare provider organization identifies genetic heterogeneity underlying left ventricular structure and overlapping genetic architecture with cardiomyopathy genes.
Lead Author: Jonathan Chung, Regeneron Genetics Center

Poster #2638W: Penetrance in the EHR record of 76 DiscovEHR Cohort participants with two recurrent pathogenic variants.
Lead Author: Kandamurugu Manickam, Geisinger Health System

THUR, OCT 20 — 2:00PM-3:00PM

Poster #1775T: Structural variant calling combining Illumino and low-coverage PacBio.
Lead Author: Andrew Carroll, DNAnexus

Poster #1205T: Exome  sequencing in DiscovEHR identifies rare variants in anion transporter genes that exert large effects on uric acid levels and gout.
Lead Author: Jan Freudenberg, Regeneron Genetics Center

Poster #2099T: The role of the ENCODE Data Coordination Center.
Lead Author: Jean M. Davidson, Department of Genetics, School of Medicine, Stanford University

THUR, OCT 20 — 3:00PM-4:00PM

Poster #1790T: The eMERGE Network: Continuing the legacy of genomic discovery to enrich precision medicine.
Lead Author: Melissa A. Basford, eMERGE Network

Poster #512T: Trajectory of new variants requiring pathogenicity assessment as potential secondary findings across 50,000 exomes in the DiscovEHR cohort.
Lead Author: Uyenlinh T. Mirshahi, Geisinger-Regeneron DiscovEHR Collaboration

Poster #2102T: Integrated metadata-driven access of ENCODE, modENCODE, REMC, GGR and modERN data through a common portal.
Lead Author: Esther T. Chan, Department of Genetics, School of Medicine, Stanford University

FRI, OCT 21 — 2:00PM-3:00PM

Poster #3207F: Rapid, high-throughput clinical sequencing and reporting for personalized medicine
Lead Author: Donna M. Muzny, Baylor College of Medicine, Human Genome Sequencing Center

FRI, OCT 21 — 3:00PM-4:00PM

Poster #1626F: Discovery and replication of rare variant associations using a knowledge-driven PheWas approach in eMERGE and Geisinger Health System.
Lead Author: Anna O. Basile, Pennsylvania State University

Poster #1764F: The ENCODE analysis pipelines: Repeatable and shareable analysis tools for ChIP-seq, RNA-seq, DNase-seq, and whole genome bisulfite experiments.
Lead Author: J.Seth Strattan, Stanford University Medical School

Poster #510F: A phenome-wide gene burden analysis to identify DrugBank genes associated with patient diagnoses.
Lead Author: Sarah Pendergrass, Geisinger Health System