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.

Countdown to Beantown: DNAnexus at Festival of Genomics

Next week we’ll be at Festival of Genomics in Boston, to join the three-day celebration of all things genomic! The Festival covers a broad range of topics; exploring new research, technology, and groundbreaking advancements in medicine. We’re excited to hear from the stellar lineup of speakers, such as renowned New York Times columnist, Carl Zimmer, providing journalistic perspective from the genome beat, and Diana Bianchi, from Tufts University School of Medicine, discussing prenatal testing in the genomics era. Like all good festivals, we mustn’t forget to take advantage of the full spectrum of attractions, including posters, workshops, exhibitors, technology forums, and more.

We’re particularly excited to showcase how the DNAnexus Platform has been powering precisionFDA. To date, more than 1,500 community members from 600 organizations are using the precisionFDA platform to help shape precision medicine. Members of the precisionFDA team will be at the DNAnexus booth to demo and answer questions about this community platform for NGS assay evaluation and regulatory science exploration.  

The announcement of the winners of precisionFDA’s second challenge, the Truth Challenge, will also be announced at the festival.  Genomic innovators were invited to participate by testing their informatics pipelines on two datasets: the well-characterized Genome in a Bottle’s NA12878 and a new reference sample HG002, of which the results were unknown. Truly a once in a blue moon challenge, the competition was fierce as thirty-five participants from around the world submitted entries. Join us for the announcement and help us congratulate the winners! 

Announcement of the Winners of the precisionFDA’s Truth Challenge
pFDAPresenter: Elizabeth Mansfield, PhD, Deputy Officer Director for Personalized Medicine, OIR/CDRH/FDA
When: Wednesday, June 29th at 9:00am – Main Stage

Additionally, during the Genomic Medicine track, our own Andrew Carroll will speak on the many factors involved when taking genomic data and medical applications global.

Taking Genomic Medicine Worldwide   

Andrew

Presenter: Andrew Carroll, PhD, VP Science, DNAnexus
When: Tuesday, June 28th at 12pm
Where: Genomic Medicine Track

 

 

 

Finally, we have a bevy of activities with DNAnexus and our partners. Check out our full list of booth activities below:


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We hope you join in our excitement as we gear up for the ultimate genomic gathering! Don’t forget to come say hello to the DNAnexus team and receive a demo of the DNAnexus Platform at Booth #240.