DNA Day: Celebrating the Decades-long Unraveling of DNA

DNA day 2014

April 25th marks DNA Day. It’s on the calendar today to commemorate the 1953 publication of the structure of DNA by Francis Crick, James Watson, and others — but really, it’s a time to think about this special molecule and its role in what we do.

Just a decade after the completion of the Human Genome Project, it is truly amazing that it’s possible not only to sequence a human genome or exome, but to do so thousands of times and compare the results for a better understanding of human genetic variation. Studies comparing a few thousand exomes are becoming routine, and we are even seeing studies with 10,000-plus exomes. (Check out our Baylor CHARGE project as an example.)

These massive research and clinical efforts will be necessary to truly parse the meaning of our DNA. We are proud to be part of the community working on this challenge by providing cloud-based computational resources that let scientists run enormous analyses without crushing their local infrastructure. We also host great tools in our platform, so researchers have the option of porting in their own favorite pipelines or using our tools to create plug-and-play workflows in the cloud. And our insistence on enterprise-grade security means that you don’t have to worry about keeping your data safe; we take care of that for you. That’s cause for everyone to be optimistic about the future of these studies on DNA Day.

In case you were wondering, our data consumption isn’t just limited to As, Cs, Ts, and Gs. This week our team had fun looking back at the impressive results of writing contests associated with past DNA Days. Check out last year’s winners of the essay contest sponsored by the American Society of Human Genetics or by the European Society of Human Genetics (both groups are expected to announce this year’s winners today). And if you only have a coffee break to do some link-surfing, don’t miss these winning haikus from previous DNA Day poetry contests. Here’s our favorite:

A spiral staircase
Each step makes you what you are
But not who you are
dpasquantonio

AGBT Posters Featuring DNAnexus

DNAnexus was featured in a couple of posters at AGBT this year. DNAnexus scientist, Andrew Carroll, was in the poster hall, sharing data from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium genomic analysis project. In addition, Narayanan Veeraraghavan, Lead Programmer Scientist at Baylor’s Human Genome Sequencing Center, presented a poster focused their own variant-calling pipeline, Mercury that was built on the cloud via the DNAnexus platform.

If you missed the conference, or you didn’t get a chance to chat with Andrew or Narayanan, here’s your chance to check out their posters:

Andrew presented never seen before data that was generated by Baylor’s Human Genome Sequencing Center using DNAnexus to run Mercury, its own exome and genome analysis pipeline. Interestingly, it was found as exome numbers increase, so do new variants found. Here’s a graph demonstrating that each new exome analyzed yielded novel genetic variation, rather than reaching a plateau after some critical mass of exomes:

variants sites vs exomes sequenced

 

For Andrew’s perspective on the poster, check out this short video:

The heart of Narayanan’s poster centered around Mercury on the Cloud Analytics (MOCA), an automated NGS pipeline HGSC developed, which upon being ported to DNAnexus was used successfully for novel gene discovery in two large-scale projects: CHARGE and Baylor-Hopkins Center for Mendelian Genomics (BHCMG). Some of the key features in this production pipeline cited in the poster include: zero setup, on-demand scale-up, version control, reproducibility, compliance with CAP/CLIA/HIPAA, and ISO 27001 data handling and security and compliance.

We look forward to seeing alternate workflows being built on DNAnexus by CHARGE commons to benchmark studies without the need to install or configure analysis tools.

Feb 28: Celebrating Rare Disease Day

feb 28 rare disease dayA person with Alport Syndrome might have to look far and wide to find somebody else who can truly understand his symptoms. Just 1 in 50,000 newborns is born with this debilitating genetic disease, which shuts down kidney function and causes hearing and vision loss. Though the syndrome has been understood, at least at a rudimentary level, for decades, it can still take years for affected individuals to get a correct diagnosis.

There are thousands of rare diseases with stories just like Alport Syndrome; while individually they struggle to get widespread attention, today is a day to remember all of them. Since 2008, February 28 has marked Rare Disease Day — a time to recognize people around the world suffering from these hard-to-diagnose, primarily genetic, often incurable diseases. Rare Disease Day is celebrated in countries around the world; more than 70 participated last year, and it is expected that even more will take part in 2014.

Indeed, while so much public and private funding goes toward common diseases such as cancer, it is worth noting that in aggregate, the burden of rare disease is also high: it is likely that hundreds of millions of people around the world have a rare disease. While one rare disease may affect only a handful of patients, others may affect thousands – in the EU alone, as many as 30 million people may be affected by any one of over 6,000 known rare diseases.

Teasing out the genetic basis of these diseases requires exome or whole genome sequencing studies — and while clinics are now using the technology to help severely affected individuals already, where underlying genetic variation is especially complex, some of those studies will need thousands of people to have enough statistical power for finding causal mutations. These efforts could get a much-needed boost as scientists compile high-quality sequence data across thousands of subjects and then share it with other groups for additional data mining, use as healthy controls, and more. The spirit of collaboration that has been so strong in genomics will be of tremendous benefit to the scientists and clinicians seeking to understand and ultimately prevent or cure rare diseases.

Efforts like that of the Global Alliance, which aims to develop technology standards around securely sharing genomic and clinical data, will go a long way toward filling in the puzzle. Here at DNAnexus, we support any endeavor to improve health outcomes for people with rare diseases by streamlining access to genomic data, analytical tools, and computational resources. We hope that our platform will be helpful in moving some of these scientific and clinical efforts forward.

In addition to honoring those people struggling with rare diseases, today we celebrate the scientists, clinicians, and medical geneticists around the world who are working hard to alleviate these conditions. Our best wishes to all of you from everyone here at DNAnexus!

Click here to find out more about Rare Disease Day and add your support.