100% Cloud-based Genome Center Integrating Large Healthcare Data Flows

photo: The Cancer Genome Atlas
photo: The Cancer Genome Atlas

In a previous post, our new CMO, David Shaywitz, talked about his vision for DNAnexus and its role in helping fulfill the promise of genomic medicine:

“DNAnexus represents a natural home for these aspirations, offering a compelling, secure, cloud-based data management platform, an enabling tool for any healthcare organization – academic medical center, healthcare system, biopharma company, payor – who recognizes that getting a handle on large healthcare data flows is rapidly becoming table stakes, and that figuring out how to manage and leverage genomic data is a wise place to start.”

Fast-forward two months…  This week, we announced exciting progress in our efforts to accelerate genomic medicine.  The DNAnexus cloud-based genome informatics and data management platform is powering a number of collaborations between Regeneron Genetics Center (RGC) and its leading healthcare provider partners.

In a RGC press release, they announced these new collaborators, which include the Geisinger Health System, Columbia University Medical Center, Clinic for Special Children, and Baylor College of Medicine. The RGC will be using the DNAnexus platform to integrate sequencing data with de-identified clinical records from patient volunteers. To date, the RGC has sequenced samples from more than 10,000 individuals and is currently sequencing more than 50,000 samples per year.

The Geisinger collaboration, which has been described as the largest clinical sequencing project in the U.S., is on track to sequence more than 100,000 patient volunteer samples. This DNAnexus-powered initiative has resulted in the first 100% cloud-based biopharma genome center, and is now operating at scale.

Next-generation sequencing technologies, like Illumina’s HiSeq 2500 or X Ten platform, have reduced the cost and increased the speed of DNA sequencing outpacing Moore’s Law to the point where the new bottleneck is genome informatics. To address this issue, companies like Regeneron are adopting cloud-based solutions to handle the massive volume of sequencing data.

DNAnexus provides the technology backbone that enables the sharing and management of data and tools around large volumes of sequencing data between the RGC and its healthcare collaborators. Currently the RGC is processing more than 1,000 exomes per week and sharing the data easily and safely with their collaborators.

In order to improve patient care and ultimately human health, the integration of genomic and phenotypic data needs to happen on a massive scale (something David has recently discussed from the perspective of phenotype here and here). Combining large cohorts of deeply-phenotyped individuals with their genomic data offers a wide range of medical applications, the most obvious being a more personalized approach to medical interventions such as which therapy might work best for a given individual. These data can also be used to aid in the development of new companion diagnostics and clinical trial participant selection. As an article in GigaOM put it this week: Cloud Computing is Coming for Your DNA, and it Will Lead to Better Drugs and Health Care.

These collaborations are powerful examples of how the DNAnexus platform is enabling an integrated approach between biopharmaceutical companies and their partners to accelerate the research and discovery process. As David said, healthcare industry leaders who prioritize the management of large healthcare data flows will emerge as the pioneers who help us realize the full vision of precision medicine –delivery of the optimal therapy to the right patients at the right time – ideally before they are sick.

DNAnexus Introduces Faster Cloud Options

Spring has arrived at DNAnexus, ushering in important updates! Starting May 1, 2014, we are excited to announce your analyses on DNAnexus will be faster, thanks to new instance types .

What does that really mean? Here’s an example before we dive into all the details…  A specific exome pipeline (e.g., BWA-MEM, GATK-Lite) now runs in less than 4 hours! Previously, the run would have taken nearly 6 hours.

New instance types

We believe, and hope you do too, that DNAnexus is the best choice for expanding your genomic analysis infrastructure. Because, unlike local equipment, which from day one starts collecting dust in your server room while technological advances pile up, the cloud is always on the forefront of computing technology as newer, faster hardware is made available.

These new hardware options are in the form of new instance types (virtual computer configurations) on which your cloud analyses can run. And thanks to the flexibility and reproducibility aspects of the DNAnexus platform, you can start using these new instance types right away—simply launch your existing analyses on one of those new instance types (e.g., using the “–instance-type <…>” option of our “dx run” command-line tool) and enjoy a completely effortless hardware upgrade!

The new instance types are built on high-frequency Intel® processors of the Sandy Bridge and Ivy Bridge microarchitectures, support the Intel® Advanced Vector Extensions (Intel® AVX), and have solid-state drive (SSD) local storage technology for fast I/O performance.

The following table summarizes these new instance types. For a given column (which represents a certain number of cores and local storage capacity), there are up to three different instance types to choose from (with different amounts of memory). Overall these new instance types span a large spectrum, starting at 2 cores, 32 GB SSD, and 3.8 GB RAM, all the way to 32 cores, 640 GB SSD, and 244 GB RAM:

summary new instance types
In an effort to be more informative and transparent, we have also come up with a new, easy to remember, and consistent naming scheme:

  • The prefix (mem1, mem2, or mem3) denotes the memory capacity per core;
  • the infix (ssd1) denotes that these instances have solid-state drive technology;
  • the suffix (x2 through x32) denotes the number of cores.

New names for existing instance types

We liked the convenient new naming scheme so much that we have applied it to existing instance types as well, as shown in the following table.

Compared to the new instance types mentioned earlier, the existing instance types are distinguished by a different storage infix (hdd2), given their regular hard disk drive technology. More information is available on our wiki page, which explains the new naming conventions and includes a detailed list of all instance types.

new instance names
To ease the transition, existing instances can currently be called by either their original name or the new name; the DNAnexus system understands both. However, we encourage you to adopt the new names in a timely manner to avoid any future interruption.

We are very excited to announce these important updates, and we cannot wait to hear your success stories out of them. Drop us a note at support@dnanexus.com if you’d like to get in touch with us.

2014: The Year of the Cloud

 

The Chinese New Year is almost upon us — and the Year of the Horse has us thinking about what 2014 will bring to the world of DNA sequencing. We believe that this will turn out to be the year of cloud computing. Here are a Chinese New Yearfew of the trends that we’re watching:

Availability of large-scale genome studies. At one point, the 1000 Genomes Project was operating on a scale all its own. Today, many organizations are participating in large-scale sequencing projects to study thousands or even millions of people. As that data makes its way into the public realm, the demand for computational resources will soar. Accessing, querying, and manipulating these data sets will present a real challenge to IT teams with bursty episodes of unusually high demand mixed with the regular stream they normally see. That’s precisely the kind of environment where cloud computing makes the most sense: having unlimited on-demand compute resources allows IT teams to meet any infrastructure needs without having to spend the money on scaling up internal resources.

The new human reference genome. The Genome Reference Consortium has released build 38 of the human genome (known as GRCh38). This is a major improvement over the last build. Once the reference has been fully annotated, scientists around the world will want to dust off their existing human data sets and realign them to the updated reference to see if there are any new insights to be had. That will mean a short-term, high-intensity spike in demand for computational resources as these massive alignments are processed — in other words, the perfect occasion to try out cloud computing. It’s the cheapest possible way to add extensive computational resources without the long-term commitment to on-premises infrastructure.

Sequencing costs keep falling. The massive genomic studies underway have all been enabled by the rapidly falling cost of DNA sequencing — a trend that promises to continue, thanks to Illumina’s recent announcement and efforts from startups still working to commercialize innovative new methods for sequencing. As sequencing a genome gets ever more affordable, demand for the resources to process and analyze that data will grow at a faster and faster pace. Trying to keep up with this demand will be an uphill battle for IT teams focused only on internal infrastructure, so we see this leading to interest in how cloud computing can help relieve the pressure from those teams to add boxes and storage components.

Growing number of analysis apps. The ecosystem of available tools for performing specific steps or types of DNA analysis is expanding rapidly. As scientists and bioinformaticians find a growing need to build pipelines utilizing a number of these tools, the ease of doing so in a cloud environment will make this option even more appealing.

Here at DNAnexus, we’re eager for what’s to come in 2014. We have a number of collaborations underway with academic and commercial R&D organizations, and we look forward to sharing details about them with our blog readers in the months ahead. Here’s to the Year of the Cloud and a great and productive year for the biomedical community!