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Overcoming the Exabyte-Sized Obstacles to Precision Medicine

Wolfgang Mertz

CTO of Healthcare, Life Sciences and High performance Computing

As we make strides towards a future that includes autonomous cars and grocery stores sans checkout lines, concepts that once seemed reserved only for utopian fiction, it seems there’s no limit to what science and technology can accomplish. It’s an especially exciting time for those in the life sciences and healthcare fields, with 2016 seeing breakthroughs such as a potential “universal” flu vaccine and CRISPR, a promising gene editing technology that may help treat cancer.

Several of Dell EMC’s customers are also making significant advances in precision medicine, the medical model that focuses on using an individual’s specific genetic makeup to customize and prescribe treatments.

Currently, physicians and scientists are in the research phase of a myriad of applications for precision medicine, including oncology, diabetes and cardiology. Before we are able to realize the vision President Obama shared of “the right treatments at the right time, every time, to the right person” from his 2015 Precision Medicine Initiative, there are significant challenges to overcome.

Accessibility

In order for precision medicine to become available to the masses, this will require researchers and doctors to not only have the technical infrastructure to support genomic sequencing, but the storage capacity and resources to access, view and share additional relevant data as well. They will need to have visibility into patients’ electronic health records (EHR), along with information on environmental conditions and lifestyle behaviors and biological samples. While increased data sharing may sound simple enough, the reality is there is still much work to be done on the storage infrastructure side to make this possible. Much of this data is typically siloed, which impedes healthcare providers’ ability to collaborate and review critical information that could impact a patient’s diagnosis and treatment. To fully take advantage of the potential life-saving insights available from precision medicine, organizations must implement a storage solution that enables high-speed access anytime, anywhere.

Volume

Another issue to confront is the storage capacity needed to house and preserve the petabytes of genomic data, medical imaging, EHR and other data. Thanks to decreased costs of genomic sequencing and more genomes being analyzed, the sheer volume of genomic data alone being generated is quickly eclipsing the storage available in most legacy systems. According to a scientific report by Stephens et. al published in PLOS Biology, between 100 million and two billion human genomes may be sequenced by 2025. This may lead to storage demands of up to 2-40 exabytes since storage requirements must take into consideration the accuracy of the data collected. The paper states that, “For every 3 billion bases of human genome sequence, 30-fold more data (~100 gigabases) must be collected because of errors in sequencing, base calling and genome alignment.” With this exponential projected growth, scale-out storage that can simultaneously manage multiple current and future workflows is necessary now more than ever.

Early Stages 

Finally, while it’s easy to get caught up in the excitement of the advances made thus far in precision medicine, we have to remember this remains a young discipline. At the IT level, there’s still much to be done around network and storage infrastructure and workflows in order to develop the solutions that will make this ground-breaking research readily available to the public, the physician community and healthcare professionals. Third-generation platform applications need to be built to make this more mainstream. Fortunately, major healthcare technology players such as GE and Philips have undertaken initiatives to attract independent software vendor (ISV) applications. With high-profile companies willing to devote time and resources to supporting ISV applications, the more likely it is scientists will have access to more sophisticated tools sooner.

More cohort analysis such as Genomic England’s 100,000 Genomic Project must be put in place to ensure researchers have sufficient data to develop new forms of screening and treatment and these efforts will also necessitate additional storage capabilities.

Conclusion

Despite these barriers, the future remains promising for precision medicine. With the proper infrastructure in place to provide reliable shared access and massive scalability, clinicians and researchers will have the freedom to focus on discovering the breakthroughs of tomorrow.

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Big Data Analysis for the Greater Good: Dell EMC & the 100,000 Genome Project

Wolfgang Mertz

CTO of Healthcare, Life Sciences and High performance Computing

It might seem far-reaching to say that big data analysis can fundamentally impact patient outcomes around cancer and other illnesses, and that it has the power to ultimately transform health services and indeed society at large, but that’s the precise goal behind the 100,000 Genome Project from Genomics England.

DNA backgroundFor background, Genomics England is a wholly-owned company of the Department of Health, set up to deliver the 100,000 Genomes Project. This exciting endeavor will sequence and collect 100,000 whole genomes from 70,000 NHS patients and their families (with their full consent), focusing on patients with rare diseases as well as those with common cancers.

The program is designed to create a lasting legacy for patients as well as the NHS and the broader UK economy, while encouraging innovation in the UK’s bioscience sector. The genetic sequences will be anonymized and shared with approved academic researchers to help develop new treatments and diagnostic testing methods targeted at the genetic characteristics of individual patients.

Dell EMC provides the platform for large-scale analytics in a hybrid cloud model for Genomics England, which leverages our VCE vScale, with EMC Isilon and EMC XtremIO solutions. The Project has been using EMC storage for its genomic sequence library, and now it will be leveraging an Isilon data lake to securely store data during the sequencing process. Backup services are provided by EMC’s Data Domain and EMC Networker.

The Genomics England IT environment uses both on-prem servers and IaaS provided by cloud service providers on G-Cloud. According to an article from Government Computing, “one of Genomics England’s key legacies is expected to be an ecosystem of cloud service providers providing low cost, elastic compute on demand through G-Cloud, bringing the benefits of scale to smaller research groups.”

There are two main considerations from an IT perspective around genome and DNA sequencing projects such as those being done by Genomics England and others: data management and speed. Vast amounts of research data have to be stored and retrieved, and this large-scale biologic data has to be processed quickly in order to gain meaningful insights.

Scale is another key factor. Sequencing and storing genomic information digitally is a data-intensive endeavor, to say the least. Just sequencing a single genome creates hundreds of gigabytes and the Project has sequenced over 13,000 genomes to date, which is expected to generate ten times more data over the next two years. The data lake being used by Genomics England allows 17 petabytes of data to be stored and made available for multi-protocol analytics (including Hadoop).

For perspective, 1 PB is a quadrillion bytes – think of that as 20 million four-drawer filing cabinets filled with text. Or, considering the Milky Way has roughly two hundred billion stars in its galaxy, if you count each single star as a single byte – it would take 5,000 Milky Way galaxies to reach 1PB of data. It’s staggering.

The potential of being able to contribute to eradicating disease and identify exciting new treatments is truly awe inspiring.  And considering the immense scale of the data involved – 5,000 galaxies! – provides new context around reaching for the stars.

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