DNAnexus Celebrates Rare Disease Day

The moment a baby is born is often described as the happiest day of a parent’s life. But imagine the fear in discovering that your newborn baby is presenting with unexplainable, yet rapidly progressive seizures. Early Infantile Epileptic Encephalopathy 12 (EIEE12) is a rare neurological disorder that causes newborns to develop frequent epileptic seizures and occurs when a child inherits two mutations in the PLCB1 gene. EIEE12 is difficult to diagnose and is associated with high rates of infant mortality. Learning this would be a terrifying reality as a parent, yet EIEE 12 is only one example of a rare disease that is difficult to diagnose and deliver timely treatment.

Despite the nomenclature, there are actually many rare diseases, and an estimated 300 million people around the world live with one of these diseases. A rare disease is defined as a disease that affects fewer than 200,000 people. Today, DNAnexus joins others in raising awareness for those diagnosed, and undiagnosed, with a rare disease by celebrating Rare Disease Day

Select rare diseases, including some cancers, autoimmune diseases, and infections are not inherited; however, 72% of all rare diseases are genetic. Further, an estimated 4% of newborns in North America have a genetic disorder, making rare diseases the leading cause of death for infants. Because of the lack of scientific knowledge of many of these diseases, they can be extremely difficult to diagnose, impeding the ability to deliver timely and precise treatment. For newborns presenting with unexplainable medical conditions, this delay in treatment can sometimes mean the difference between life or death. And for those who survive early childhood, it can feel like a never-ending road of symptoms and misdiagnoses.

Medical professionals seeking to find a treatment for these patients are searching for that needle in a haystack. Genetic diagnostics has become an increasingly common way to diagnose patients presenting with unexplainable symptoms, since DNA sequencing is the most efficient way to define and subtype hereditary diseases and determine the most effective, individualized treatment plan.

Rady Children’s Institute for Genomic Medicine (RCGIM) at Rady Children’s Hospital has the inspiring vision to ensure that genome-powered diagnosis is available to every child who needs it and is carving the path to deliver life-changing diagnoses for children with rare diseases. Rady Children’s, with its network of technology and data-science partners, is forging the way by expanding access to genomic medicine and significantly reducing turnaround time for results, saving childrens’ lives.

Other industry leaders like Blueprint Genetics, a genetic testing company providing diagnostics and clinical interpretation for rare inherited diseases in 14 medical specialties, is working to scale efficiencies to make diagnosis less challenging for physicians. By partnering with DNAnexus, Blueprint was able to scale in velocity and volume by moving its bioinformatics pipelines to the cloud and removing the sequencing and bioinformatics bottleneck from the equation.

Organizations like Rady Children’s Hospital and Blueprint Genetics are just two examples of the myriad of organizations paving the way to better understand the underlying mechanisms of rare inherited diseases and discover treatments. In celebration of Rare Disease Day, we tip our hats to innovative companies like these and others that are leading the genetics revolution to rapidly diagnose rare diseases, and develop treatments for those in need.

Want to participate in Rare Disease Day? Get involved and share your thoughts on Twitter with the hashtag #RareDiseaseDay.

Hackathon-ing into DNAnexus

Ben Busby Hackathon

If you’re a fan of biocomputational hackathons, you’re probably already familiar with Ben Busby (aka @DCGenomics on Twitter and Github). Well, we’re proud to announce he has joined the DNAnexus family, as principal scientist in our xVantage Group. We were able to sit down recently with the former NCBI genomics outreach coordinator to learn what drew him to DNAnexus, and what he plans to accomplish in his new role.

What brought you to DNAnexus?

I am primarily interested in making the bioinformatics world a better place. This not only means improving underlying processes — such as better .bam / .vcf generation and parsing .gff files — but also applying bioinformatics at a large scale so that the world can see the contribution it makes. In other words — pushing translational bioinformatics forward. DNAnexus works with a host of large companies, academic, and governmental institutions to get this done in the healthcare, agriculture, and general scientific research arenas.

What will you be doing in your new role?

I will be working on creating solution architecture for particularly large and difficult bioinformatics challenges, as well as advocacy for external tool, pipeline, and algorithm developers within the organization. My past experience organizing national hackathons, doing outreach for the NCBI, and consulting for companies like Deloitte, Ariel Precision Medicine, and a variant annotation project OpenCravat from Johns Hopkins will also come in handy as I participate in scientific outreach and help DNAnexus forge additional inter-institutional collaborations in the bioinformatics community. 

What are you most excited about?

On the technical side, I like how DNAnexus has no “platform-lock”, and provides easy access for secure computing with some nice pipelining and visualization features thrown in. Specifically, when one builds WDL-based — stay tuned for other workflow languages! — apps or applets on the DNAnexus Platform (try the app building wizard too!), the markdown can be easily ported to GitHub to be shared openly. 

I also love the company culture and its commitment to the success of the entire bioinformatics community. For example, after building a software portal on behalf of St. Jude Children’s Research Hospital, DNAnexus handed over the entire software stack. DNAnexus is willing to work with other entities — even perceived competitors — in bioinformatics to allow practitioners to conduct interoperable data science, unlike some other industry companies, academic labs, and even a few government agencies. 

Anything else we should know about?

I’ve been involved in running more than 40 hackathons over the years, and have made a great many friends doing so. I plan to continue, with the next one taking place in April, hosted by Baylor College of Medicine’s Human Genome Sequencing Center, Everything is Bigger in Texas: Pan-Structural Variation Hackathon in the Cloud. People can follow our progress and keep track of other upcoming hackathons on this Github site.

What Does the Sunsetting of Python 2.7 Mean for You?

Sunsetting Python 2.x

As stated on python.org, the Python core development team sunset Python 2.x on January 1, 2020 and moving forward, will support only Python 3.x. This announcement means that the Python organization will no longer provide security updates, bug fixes, or other improvements going forward. Read on for information about what this means for you as a user of the DNAnexus Platform.

The Fine Print

As mentioned above, any new security vulnerabilities discovered in Python 2 after January 1, 2020, will remain unpatched. The DNAnexus execution environment isolates the execution of apps in a secure Linux container, and mitigates the impact of potential Python 2 security vulnerabilities. Given the lack of support after Python 2 goes End-of-Life (EOL), significant security vulnerabilities may cause the DNAnexus Platform to disable execution of Python 2 or have you assume full liability for execution of your Python 2 code.

As of December 2019, we provide an Ubuntu 16.04 app execution environment, “Python 2 AEE,” which includes the following:

  • The dx-toolkit package (including the “dx” command-line client and the “dxpy” python module), configured in a way that requires Python 2.
  • The stock Ubuntu python2.7 interpreter, available at /usr/bin/python.
  • The stock Ubuntu python3.5.2 interpreter, available at /usr/bin/python3.

To facilitate the migration to Python 3, we plan to provide a new Ubuntu 16.04 AEE in the first quarter of 2020. This new “Python 3 AEE” will include the dx-toolkit package configured in a way that makes “dxpy” compatible with both Python 2 and Python 3. The “dx” command-line client will use Python 3.

Furthermore, we will introduce a new configuration option to dxapp.json so that you can select between “Python 2 AEE” and the new “Python 3 AEE.” In addition, we will introduce a new “python3” value for the “interpreter” dxapp.json configuration option.

In summary, while it’s  possible to use both Python 2.x or Python 3, to prevent any security issues, we strongly encourage you to review your code for Python 2.7 dependencies and consider migrating to Python 3.0. 

For More Information

To help with your planning and to further explain what this means, we’ve put together an FAQ.