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.

The U.S. Cancer Moonshot and a Culture of Collaboration

Yesterday, United States Vice President Joe Biden hosted the National Cancer Moonshot Summit. Scientists, oncologists, donors, and patients convened for a daylong conference intended to pick up the pace of research towards curing cancer. Rather than focusing on one specific type of cancer, the conference broadly discussed more than 100 types of cancer; emphasizing strategies for prevention, early detection, wide access to treatment, and encouraging collaboration among researchers. You can read a first-hand account from our CMO, David Shaywitz, here.

As part of the Moonshot effort, DNAnexus, in partnership with PatientCrossroads, has committed to develop the Integrated Data Engagement Analytics (IDEA) platform to facilitate the collection, analysis, and sharing of genetic, proteomic, and EMR/phenotypic data to accelerate disease research. PatientCrossroads and DNAnexus are currently engaging in a pioneering effort to help patients obtain the raw genetic files and medical records and then integrate these data along with patient reported outcomes data obtained by PatientCrossroads on a secure and compliant platform that allows authorized researcher access to this information and use it to develop novel insights — the IDEA platform. You can review the complete list of public and private sector Cancer Moonshot commitments announced in the White House press release.

Here at DNAnexus, we are particularly devoted to reducing the technical barriers to accessing and working with research datasets.  We believe that a culture of openness in genomic research will lead to greater medical breakthroughs. Most data sharing in cancer genomics research has been centralized through rich, yet controlled-access databases like The Cancer Genome Atlas (TCGA) or International Cancer Genome Consortium (ICGC) — both of which properly approved researchers can easily access on the DNAnexus Platform. Read more about some of the genomic community collaborative initiatives DNAnexus is a part of: precisionFDA, open access cancer genomics pilot, and ICGC.