DNAnexus Made Ridiculously Simple

In medical school, perhaps the most indispensable texts were the “Ridiculously Simple” series – Clinical Anatomy Made Ridiculously Simple, Acid-Base Made Ridiculously Simple, etc. While you probably wouldn’t want to operate or dialyze based only on the knowledge in these short books, they nevertheless offered accessible overviews to complex and often intimidating topics.

In this spirit – and in response to questions from friends and family who regularly ask, “What does DNAnexus do” – I thought I might offer this short post.

What Is DNAnexus?
dnanexus genomics
DNAnexus is a platform – basically, a sophisticated software program – that makes it easier for users to do three things, each in a secure and compliant fashion:

  • Analyze large amounts of raw genetic data
  • Share and collaborate around large amounts of data (including but not limited to genetics)
  • Integrate genetic data with other types of data, such as data from electronic medical records or imaging data, to advance science and to improve clinical care

Let’s take these one at a time.

(1) Analysis Of Raw Sequencing Data
The basic idea here is that the machines that are used to read DNA sequence are incredibly powerful, but don’t generate a book of information that starts at the beginning of the first chromosome and concludes at the end of the last one. Rather, most sequencing machines spit out phrases of about 100 letters, phrases randomly located anywhere in the 3 billion letter book that is the human genome. A computer must figure out where each individual phrase fits in the book, and must also determine whether there are any typos. This can be a computationally intensive task, but DNAnexus provides a way to do this efficiently, by dividing the task into multiple parallel streams each of which can be tackled by a powerful computer.

The computers DNAnexus tends to use are run by Amazon (more precisely, by Amazon Web Services, or AWS), and our use of them is an example of what’s known as “cloud computing” because the computers operate from a massive, dedicated central facility, rather than from a user’s own institution. One advantage of using cloud computing is it’s very much “on demand” – i.e. you have essentially unlimited access to as many computers as you need, and you only pay for the computers that you actually use, and only when you are actually using them.

(2) Distributed Collaboration
Progress in both science and medicine can be accelerated when data can be easily shared. When there are large volumes of data, as is increasingly the case in research and clinical realms, this can be a real problem. Remarkably, the most common method of large-scale data sharing today is probably FedEx’ing hard drives between institutions. What DNAnexus enables is for a distributed team of researchers or clinicians to all have access to the same data at the same time; by bringing together the data, the experts, and the tools for analysis, DNAnexus facilitates collaboration and accelerates knowledge turns.

DNAnexus is ideally suited to power consortia, whether NIH investigators (as in the case with our work with CHARGE in the area of cardiovascular disease or our work with ENCODE in the area of genetic annotation), diagnostic companies (our work on precisionFDA), translational research partnerships (our work with Regeneron and Geisinger Health system), or a public/private partnership of cancer researchers (our work with ITOMIC led by University of Washington’s Tony Blau).

The ability to support distributed innovation also enables DNAnexus to provide global support for companies like Natera that send kits to sequencing labs worldwide, but collect and analyze the data centrally using DNAnexus.

(3) Integration With Other Data Types
The insights that may be available in genetic data are often revealed only when the information is considered and analyzed in the context of other data types, such as data from electronic health records (EHR) or imaging data (such as radiology images or pathology images). Integrating genetic and EHR data is fundamental to the drug discovery work of Regeneron, for example. In the same way our partners can easily access and efficiently utilize the fundamental tools of genetic analysis on our platform, so too can they access and utilize the tools required for integrating genetic data with other data types. DNAnexus is adding tools constantly, based on the needs expressed by our partners.

Looking Ahead
Guided by the visionary partners with whom we are privileged to work, DNAnexus continues to enhance our tools around each of these three areas: DNA analysis, distributed collaboration, and integration with other data types. We are constantly seeking opportunities to leverage the technology we’ve developed, as well as innovative leaders looking to bring the power of our platform to bear in original and impactful ways.

DNAnexus Heads to Orlando for AGBT 2016

AGBT_logo_350Each February, droves of scientists descend upon Florida for the annual Advances in Genome Biology and Technology (AGBT) conference. The conference is a mix of long days filled with presentations, and lively nights consisting of cocktail parties and networking. This February 10-13th , the conference takes place in Orlando, considered by some to be the “happiest place on earth,” where global researchers, leaders, and innovators will meet to share new discoveries and cutting edge breakthroughs.

If you’re headed to AGBT, please join us in Marbella 2 to discuss our latest projects, datasets, and tools. It’s been one heck of a rocket ship ride in 2015; already 2016 promises even more opportunities for fruitful collaborations.

Learn how DNAnexus is transforming the PacBio de novo assembly experience by providing industry-leading reference-quality genome assembly services. We’ve updated the most popular PacBio SMRT Analysis 3.0 tools and structural variant callers (e.g. Parliament) on the DNAnexus Platform.

DNAnexus Events at AGBT
Software Demo
DNAnexus, The Global Network for Genomics
From structural variant analysis to ENCODE pipelines & more, just ask Singer how DNAnexus might help your genomics research project.
Singer Ma, Scientist, DNAnexus
Thursday, February 11th, 5:00pm – 7:00pm
Coquina North & South

Party Under the Stars
Friday, February 12th, 9:30pm
Fairways Lawn
Join us for libations and lively discussions under the stars.
Co-hosted with Pacific Biosciences, BioNano Genomics, New England BioLabs, Sage Science, and DNAnexus.

DNAnexus Supported Science
We’re proud to support the truly innovative research of our customers who push the envelope in advancing genomic science and medicine. Be sure to check out these posters at AGBT!

Poster #609:  Challenges in Large-Scale Human Whole Genome Sequencing with HiSeq X Ten: Towards Clinical Applications 
Yi Han, Baylor College of Medicine

Poster #704:  Rapid Capture Methods for Comprehensive Carrier Screening
Donna Muzny, Baylor College of Medicine

Poster #705:  Transplanted Organ Surveillance by Genomic Analysis of Donor-derived cfDNA 
Marica Grskovic, CareDx, Inc.

Poster #1210:  Rapid and scalable typing of structural variants with assembly-based indexing 
Will Salerno, Baylor College of Medicine

Poster #1906:  Analytical Validation of a Clinical Grade NGS dd-cfDNA Assay: Lessons from cloud computation Infrastructures and methods-based proficiency using NIST–GIAB Resources 
Yue Sarah Wang, CareDX Inc.

For more details on this year’s meeting, and to see the complete agenda check it out here.

See you in Orlando!

DNAnexus in Real Life: Tackling Precision Medicine Through Real-Time, Multi-Institution Cancer Collaboration

tony blau
C. Anthony Blau, M.D.

Today, the National Comprehensive Cancer Network (NCCN) announced an unprecedented collaborative breast cancer study in the Journal of National Comprehensive Cancer Network. On the DNAnexus Platform, C. Anthony Blau, MD, Director of the Center for Cancer Innovation and Professor of Medicine at University of Washington in Seattle implemented an innovative approach to clinical research and brought 32 researchers from 14 different institutions together to identify potential therapies for a patient with metastatic triple-negative breast cancer (TNBC).

Approximately one in five breast cancers are triple-negative. TNBC tend to be more aggressive, grow and spread more rapidly and are also less likely to respond to standard treatments.

The method used to study the TNBC patient, Intensive Trial of OMics in Cancer (ITOMIC), inversely differs from retrospective examinations of “exceptional responders” from conventional trials. Rather than evaluate a single intervention across hundreds of patients, ITOMIC aims to distribute the analysis of an individual cancer patient, predict drug susceptibilities, allow treatment in accordance to these predictions, monitor response and repeat…again and again. This creates a feedback loop to continuously learn and hopefully lead to the use of targeted therapies for complex patients in the future.

This study covers a single TNBC metastatic to bone patient, where tumor samples were monitored 48 times over a nine-month period. A team of researchers, led by Dr. Blau, performed exome sequencing, RNA-sequencing, and deep sequencing of a targeted gene panel. Data from these samples were shared on the cloud-based DNAnexus Platform. By providing a secure and centralized location 32 researchers located in disparate parts of the country were able to easily access and collaborate on the clinical data and provide medical predictions to what treatments might be effective against this specific type of cancer.

Quoted from the press release:
“On a molecular level, every cancer is unique,” said Dr. Blau, a UW Medicine researcher. “By breaking down institutional barriers, this collaborative study brings a ‘no-holds-barred’ effort to trying to help an individual cancer patient using tools that virtually unite experts from around the world.”

Added Dr. Blau:
“I’m not sure how much time this level of cooperation would have required had we not been able to utilize the DNAnexus Platform.  Without it, 32 researchers would have been FedEx-ing hard drives back and forth cross-country.  DNAnexus let everyone work from the same playbook; decreasing the time that we can complete our research and potentially save some lives.”

The ITOMIC method allows scientists to study rare tumor-associated variants of unknown significance, like ROS1 in this patient’s case. In more standard clinical trials researchers typically try to identify variants of known significance. By deep evaluation of a cancer patient over a distributed network of experts, multiple treatments/therapies can be used and observed, rather than in a standard clinical trial where only one treatment/therapy would be.

At DNAnexus we are proud to be the supporting this, and many other collaboration networks for groundbreaking research. We believe that accelerating the use of genomics information to advance cancer research requires novel approaches and are humbled to enable the work of researchers at the forefront of of precision medicine.