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:


TuesFlyer

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.

Frost & Sullivan Recognizes DNAnexus as the Enabling Technology Leader in the Global Genomics Industry

F&SAt DNAnexus, we’re honored to be recognized by Frost & Sullivan as one of the most significant enabling technologies driving industry-changing innovation within the genomics community globally. Frost & Sullivan research involves extensive primary and secondary research across the entire value chain of specific products. Against the backdrop of this research, Frost & Sullivan evaluated DNAnexus on two key factors — Technology Leverage and Customer Impact — and compared DNAnexus to other industry players.  DNAnexus’ overall rating was significantly higher than the other industry players, resulting in the Best Practice recognition.

Quadrant

Solve for Scale

As next-generation sequencing (NGS) projects take off with the goal of sequencing tens or hundreds of thousands of genomes, there is a crucial need for a solution that can handle this tremendous amount of data being produced.

As DNAnexus’ own VP of Science, Andrew Carroll puts it, “Life science companies are missing a management system for dealing with petabytes of data and billions of objects. There are challenges of operating at scale – it’s not that difficult to do something that will work once or a hundred times, but when it comes to have the same system work hundreds of thousands or millions of times, there are a lot of random errors and other lower-level problems that turn out to be a big deal.” You can read more on why life sciences and genomics markets are finding cloud approaches more appealing here.

These companies are in need of an efficient way to upload, store, share, and analyze the increasingly massive amounts of data being generated. At DNAnexus, we’re harnessing the power of the cloud to do just that. We are committed to innovation in this area, powering industry and academia as they continually aim to take on more genomic data.

Secure Solutions

Because it’s uniquely tied to an individual, genomic data can be regarded as some of the most sensitive data collected. As organizations seek to make advancements in this field, they need to ensure the sensitivity of genomic information is preserved.

DNAnexus offers layers of platform features and accreditation to support an exceptionally strong security and compliance profile. DNAnexus is continually audited and certified by an independent 3rd party for compliance with ISO 27001, an internationally recognized Information Security Management System and accompanying controls, enabling DNAnexus to address a broad range of global compliance regimes. . These include HIPAA, CAP/CLIA, GCP/GLP, dbGaP, FedRAMP, and European Data privacy laws.  

Collaborative Community

Frost & Sullivan acknowledges the collaborative nature of our platform as one of its key strengths. A dataset is only as good as is the ability to access it. Additionally, as sequencing projects scale, so can the number of organizations working together to draw conclusions.

DNAnexus provides a network of collaborators in the genomics community the ability to share, transfer, access, integrate, and analyze this data – all securely and compliantly within the cloud.  DNAnexus is the Platform of choice for leading academic core labs and consortia, including the Stanford Center for Genomics and Personalized Medicine, ENCODE, 3000 Rice Genomes Project, precisionFDA and more.

Poised for Success

Frost & Sullivan recognizes our commitment to solve some of the biggest challenges facing the field of genomics. DNAnexus, and its broad network of partners, provides pharmaceutical and biotech companies, global diagnostic test providers, genome centers, and sequencing service providers secure and compliant infrastructure and scientific support to solve today’s genomic challenges faster and more effectively than ever before. The company is the platform supporting some of the largest genomic sequencing projects in the world, such as Regeneron Genetics Center, and the underlying platform for precisionFDA, the FDA’s forward-thinking initiative to evaluate the accuracy and reproducibility of next-generation sequencing bioinformatics pipelines.

We’ve been at the forefront of employing the cloud as the ideal platform for genomics and scientific computing and we’re excited to continue our work to create the global network for genomics. You can read the full Frost & Sullivan report here.

Curious to see how our Platform works? Request a demo