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

DNAnexus Heads to Festival of Genomics

It’s that time again for Festival of Genomics – West Coast edition. The DNAnexus team will be making the journey down to perpetually-sunny San Diego to take part in all the fun. If you’re going to the Festival, visit us at booth #444 to say hi and discuss our latest projects, datasets, and tools.

We’re especially looking forward to joining in the excitement surrounding the precisionFDA App-a-thon that was announced yesterday at the Stanford Medicine X conference. This new feature will allow anyone to organize their own app-a-thon, where they can work together with their peers, collaborators, or friends to add their favorite NGS software to the precisionFDA app library. By contributing apps to precisionFDA, these app-a-thons help promote NGS software and make it easier for the community to discover and run them on the cloud or locally on portable Linux containers. 

If you’re going to the Festival of Genomics, come to the PrecisionFDA App-a-thon Kickoff event, hosted in the DNAnexus booth, to learn how you can contribute to precisionFDA’s platform and advance regulatory science.

Wednesday, September 21st – 3:30pm pFDA
PrecisionFDA App-a-thon Kickoff 
DNAnexus Booth #444

This event will cover:

  • What is the precisionFDA App-a-thon?
  • What is a precisionFDA app?
  • Why organize or participate in an app-a-thon?

The first 10 people that pledge to host a precisionFDA App-a-thon will earn a precisionFDA t-shirt!

We will also be hosting partner hours with Station X and BioNano Genomics in the DNAnexus booth.

Tuesday, September 20th – 1:00pmscreen-shot-2016-09-16-at-12-52-42-pm
DNAnexus Partner Hour: Station X  
DNAnexus Booth #444

Station X’s GenePool® and the DNAnexus Platform provide an end-to-end solution in genome informatics, from raw data to clinically actionable reports. Researchers can now store, manage, analyze, interpret and report on clinical findings with an integrated solution in a secure and collaborative environment. Come see the demo of DNAnexus and Station X to find out how you can accelerate your path to meaningful results.

Wednesday, September 21st – 1:00pm screen-shot-2016-09-16-at-12-54-55-pm
DNAnexus Partner Hour: BioNano Genomics
DNAnexus Booth #444

The hummingbird flies to the cloud! Come explore the genome of a colorful bird that beats its wings at a rate of 80 beats per second. We will be hosting BioNano in our booth, showcasing BioNano’s best-in-class de novo assembly and hybrid scaffolding pipelines and PacBio data with DNAnexus.

Please contact us if you’d like to meet in San Diego, and stop by our booth (#444) to receive a demo. Let the Festival begin!

Cloud Bioinformatics Made Easy: A Workshop with SCGPM

In April, the Stanford Center for Genomics and Personalized Medicine (SCGPM) adopted the DNAnexus portal for its sequencing facility. Researchers across nearly eighty laboratories are now able to use SCGPM’s DNAnexus portal to access, share, and analyze their genomic sequencing data. Last Friday, SCGPM and DNAnexus hosted an interactive workshop with the goal of arming these researchers with the necessary tools to conduct bioinformatics tasks in the cloud, and to maximize the utility of the DNAnexus Platform for hundreds of the university’s researchers.

The workshop began with an introduction of the Platform, and moved into demonstrations teaching attendees how to manage, share, and visualize their genomic data through a Web browser. Participants were also taught how to navigate the Platform and perform the same tasks from the command-line interface (CLI). Although you don’t need to be a CLI expert to use DNAnexus, attendees were able to learn some tips and tricks to run analyses and automate tasks using this feature.

Attendees of the workshop received first-hand experience building custom applets on the DNAnexus Platform. DNAnexus comes pre-loaded with a variety of different apps, but also allows users to build a custom pipeline or port a local pipeline to the cloud easily. For an in-depth tutorial, visit our Developer Portal.

In addition to the hands-on tutorials, attendees heard how genomics experts from Stanford, Natera, and CareDx are using DNAnexus to support their genomic research.

Ramesh Nair, Bioinformatics Manager at Stanford Center of Excellence in Stem Cell Genomics, presented on how he uses DNAnexus to support his RNA-sequencing analysis. He highlighted some best practice pipelines to use for RNA-seq and variant calling and discussed read mapping and transcript quantification strategies. Nair also demonstrated how he conducts his RNA-seq analysis on DNAnexus, giving the researchers a glimpse into wide array of applications of the Platform.

IMG_5192Raheleh Salari, Bioinformatics Manager at Natera, presented how DNAnexus is being used in industry to advance cancer diagnostics. In her talk, titled “Liquid Biopsy: The Next Gold Standard for Diagnosis”, Salari emphasized the benefits of liquid biopsy, including less patient risk, less costly analysis, and the ability to detect cancer at a much earlier stage than traditional tissue biopsies. Furthermore, liquid biopsies have the potential to provide a more complete view of the tumor genetic composition. Natera adopted DNAnexus in January 2015, and has since used the Platform to support data analysis, storage, and sharing of its genetic tests. Natera continues to use DNAnexus as it enters the oncology screening market.

We were also honored to hear from David Ross, Senior Director of Bioinformatics at CareDx, who discussed moving organ transplant diagnostic analysis to the cloud on DNAnexus. Ross presented on AlloSure, CareDx’s next-generation sequencing test for measuring the percentage of donor-derived cell-free DNA (dd-cfDNA) in solid organ transplant recipients. Based on analytical and clinical validity, results demonstrate increased levels of dd-cfDNA in acute kidney rejection using the non-invasive AlloSure assay. Ross also placed a heavy focus on the need for collaboration and data sharing within the transplant community to lead to rapid advancements. The data sharing capabilities of DNAnexus make this kind of collaboration possible.

Through the tutorials and lessons from customer use cases, our hope is that researchers left feeling empowered to use the DNAnexus Platform for their bioinformatics tasks, as well as how DNAnexus can support their broad research initiatives. If you missed the workshop and want to learn for yourself how to get started on the Platform, take a video tour through a collection of videos in our knowledge center.