ACCELERATING COLLABORATION IN LIFE SCIENCE WITH DDN STORAGE

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1 WHITEPAPER ACCELERATING COLLABORATION IN LIFE SCIENCE WITH DDN STORAGE INTRODUCTION Imagine a world where the genome of each and every citizen is sequenced at birth and several more times throughout their life. Now imagine as a CIO having to define, source and implement a datacenter infrastructure to host, share and archive that data, compliant to HIPAA and CLIA for up to 20+ years. These are just some of the big data issues and challenges that healthcare, pharmaceutical, analytics and SEQuencing as a Service (SEQaaS) companies will need to address in the very near future. With the rapid decline in the cost of sequencing and time to results approaching $1,000/Exome 1 in less than a week, sequencing a patient s DNA will be as common-place as an CAT scan or MRI. Today, the art of sequencing a full human genome is still in its infancy, compared to what is just on the horizon. The most advanced second generation sequencing instruments available today (NGS2), like the Life Technologies Post-Light Ion Semiconductor Sequencing platform Proton and Illumina s HiSeq2200, will soon be surpassed by the emerging and highly anticipated third generation (NGS3) single molecule, PCR free, micro-fluid Nanopore solutions. These pending advancements, combined with emerging improvements in data analytics, will soon enable physicians to access a fully aligned, map-reduced genome in less than 24 hours. In short, the data deluge we have been hearing so much about is just about to start. In this paper, we will examine how a state-of-the-art facility like Baylor or Yale Medical Center processes a human genome with analysis and diagnosis. We will then contrast that against what an outsourcing paradigm might look like with its benefits. The outsourcing of high-value tasks is a natural evolution in business. It virtually guarantees that a product or service will persist and evolve to their highest level of value. For sequencing, we see this evolution being led by companies like PerkinElmer, Illumina, and Beckman Coulter. In parallel, we also see genome interpretation for profit emerge from providers who specialize in analytics. The focus of the outsourcing discussion will be around the massive amounts of data which have to pass between the various points of the process. We will then show how a well thought out private cloud solution from DataDirect Networks can provide a fast, flexible, secure and cost-effective means for automating the movement of big data while improving quality of service. 1 Exome efficient way to selectively sequence the coding regions of the genome of one individual

2 TABLE OF CONTENTS INTRODUCTION...1 TABLE OF CONTENTS...2 CLINICAL GENETIC SEQUENCING...3 Sequencing Today... 3 Sequencing... 4 Outsourcing Services... 4 HOUSTON WE HAVE A PROBLEM...5 WEB OBJECT SCALER (WOS)...6 HOW WOS CAN ACCELERATE THE DISCOVERY PROCESS...7 A CASE STUDY...8 CONCLUSION...10

3 Figure 1 - NGS2 vs. pending NGS3 Nanopore Technology CLINICAL GENETIC SEQUENCING GENETIC TESTS ARE NOT ALWAYS DEFINITIVE--THEY ARE JUST ONE TOOL USED IN THE ART OF DIAGNOSIS. As it stands today, none of the sequence manufactures are FDA approved. So, technically you can t use a commercial sequencer from Life Technologies, Illumina, Roche 454 or others for full chromosome or exome sequencing and/or diagnosis. So, how are FDA approved geneticscreenings done today? It turns out that only very specific genetic tests are FDA approved. A well known example of this is the BRCA1 (BReast CAncer gene one) and BRCA2 (BReast CAncer gene two), where targeted tests via arrays or kits are used. By today s standards, a full genetic screening for BRACA1/BRACA2, or the hundreds of other known genetic disorders is possible, but not sanctioned by the FDA. SEQUENCING TODAY For our discussion, let s assume there is an FDA approved sequencer that is accurate enough for human diagnosis (both of these assumptions will come true in the next 12 to 18 months). How would a research hospital like Yale or Baylor perform these genetic screenings to make an early and informed diagnosis? And do so for the vast number of genetic disorders that carry through the population? There are two possible paths, one is preemptive and the other is reactive. Preemptive screening implies sequencing a child s exomes in vivo or shortly after birth and looking for genetic code variations that could lead to future disorders. The second is to sequence when an undiagnosed genetic symptom is encountered. In either case, the process would look something like this (which is performed for each requested sequence): The physician would take a sample (blood or cheek swab), from the patient and send it off to the sequencing center (via mail, internal mail or courier). Both Baylor and Yale have well staffed centers local to the hospital. The sample is queued, scheduled then prepared, sequenced and aligned. The resulting aligned genome or exome files (it s just data now) are sent to a bioinformaticians who runs a number of searches against known genetic disorders. The bioinformatics center sends their results to a geneticist who creates a report for the requesting physician. The results are sent back to the physician who may consult with a geneticist before meeting with the patient. The genetic data is then archived per HIPAA and CLIA for up to 20 years. It should be noted that, as of today, genetic tests are not always definitive; they are just one tool used in the art of diagnosis. 3

4 AUTOMATED ANALYTICS TOOLS ARE VERY SOPHISTICATED AND ARE CONSTANTLY EVOLVING AND BEING UPDATED WITH NEW BIO- MARKERS WEEKLY IF NOT DAILY. SEQUENCING What we are seeing today is the refinement and subsequent consolidation of SEQaaS market to four or five players who will ultimately service 80% of the market. These companies focus on the art of human reference sequencing for early stage diagnosis, cancer research, drug efficacy, full de novo sequencing and even Combined DNA Index System (CODIS) for law enforcement. These sequencing as a service (SEQaaS) providers are highly efficient. They are evolving their business models to address the unique and varying needs of clinical and research (Pharma) community i.e.: CLIA and HIPAA compliant facilities, law enforcement and long term archiving. There are even centers today that provide cloud compute and storage services, allowing Pharma and clinicians to run their own alignment programs within a private, secure cloud environment. How are SEQaaS providers any different from the centers at Yale or Baylor? The answer is twofold, the first being the collective combination of cost, quality and time to results; the second is flexibility or their willingness to modify and adopt their process flow, to meet the regulatory and business needs of their customers. OUTSOURCING SERVICES Beyond price, there are several other metrics that customer of SEQaaS providers look for. Attributes like reputation, brand awareness, quality or accuracy of the results (signified by a metric call coverage), these are all very important. For clinical customers, their primary concerns are around accuracy, down to one error in four billion (the number of base-pairs in one of the two human genomes we carry in our cells). This level of accuracy (higher than what is achieved in mitoses) is necessary because just a single letter error in just the right location can indicate a false positive for a number of genetic based disorders. And then there s time to results. Today, a full human genome takes about two to four weeks to sequence, align and analyze. That time will further drop with the introduction of single molecule sequencers (nano-pore), along with other data centric advancements discussed in this paper. SEQaaS Providers are Flexible As noted earlier, a SEQaaS business is financially motivated to listen, quickly respond and adapt their business model to meet customer needs. This behavior positively impacts both their legacy and future customers, while accelerating the discovery process a win-win for all. Internal sequencing centers, associated with large clinical institutions like Yale, are focused primarily on research. Doing ad hock clinical runs is timely, expensive and disrupt lab flow and efficiency. If they were to finance, staff and equip a clinical sequencing center, they would quickly discover that SEQaaS providers can deliver the needed results faster, more accurately and at a price point they could never match, all due to achieving economies of scale. Analytics is an Emerging Market The second emerging trend is the birth of bio analytic companies. These are for profit businesses that have developed a suite of innovative data-mining services to address the needs of the clinical, research and the law enforcement community. There are companies who provide: Human genome interpretation for disease Looking for anomalies such as SNP calls, deletions, insertion, extensions, palindromes, etc. and correlating the results to known genetic disorders as well as noting the relationship to other known genes. Full genome interpretation for drugs efficacy Pharmacogenetics or Chemotherapy. Genome interpretation for law enforcement Creating high-level profiles of perpetrators based on genetic markers; gender, ethnicity, color of eyes, hair, blood type, even age. These analytics firms have a suite of automated software tools that are very sophisticated and can generate detailed target identification reports in minutes. These custom compute intensive programs are constantly evolving and being updated with new bio-markers weekly if not daily. Their workflow involves ingesting terabytes of genetic data from the SEQaaS 4

5 IF YOU ATTEMPT TO PUSH THAT MUCH DATA INTO A PUBLIC CLOUD, IT MIGHT TAKE DAYS. companies and delivering their results to physicians, geneticists, researchers and law enforcement agencies. The deliverable is in an easily understandable, natural language report that summarizes any and all relevant genetic data. For the research and Pharma community, the reports map where anomalies are, their genetic impact, along with their relationship to related-markets. For clinical customers, they can even deliver the results in electronic medical records (EMR) format. As new bio-markers are discovered, archived data can be rescreen, supplement reports generated and forwarded, based on class of services. Future Data Intensive Services As advancement in genetics research and development progress, you can be assured that the research and clinical community will continue to expand and include new institutions who will further strain the process of collaborative research. These include institutions who: Provide Gene Synthesis services for genetically engineered organisms or gene therapy i.e., DNA2.0, IDT, GenScript, etc.; Breed mice or primates with transgenic and gene knockout for drug or genetic marker research i.e., Jackson Labs, DeltaOne, PolyGene, etc.; And in the not so distant future Xenotransplantation firms who grow genetically modified animals i.e., pigs or primates, who are designed (from inception), to grow human organs which are harvested and delivering to surgeons for transplant. HOUSTON WE HAVE A PROBLEM As we have stated, the outsourcing of sequencing, analytics, gene synthesis, transgenic & gene knock and the promise of xenotransplantation, all involve the movement of gigabytes of information between multiple researchers and clinicians. So the question becomes, how do you efficiently move this data around between multiple users, quickly, securely and cost effectively? Today most genetic data is moved via a cloud service or via data programs like Dropbox or sftp. For very large data sets 2, hard disk drives are shipped back and forth between the end customers, the SEQaaS provider and the data-analytics company. If the genetic data is non-clinical (research), then you can use public clouds which are costly and slow. At 10Mb/sec. (that s a very high rate); it takes ~15 minutes to move a single Gigabyte of data into the cloud and then something less than 15 minutes to download. Again, if you re staging base-calls, then your datasets are large (in the order of 100GB). If you attempt to push that much data into a public cloud, via Dropbox or sftp to multiple end points, it might take days. In addition to the size/time constraints, there are other issues: Security i.e., access rights, credentials, encryption and so forth. HIPAA, CLIA and CODIS compliance; Archiving and protecting data, in some cases for >20 years; The logistics of sharing data between multiple sites behind a firewall and How to manage the storage pool and allocate the bandwidth for these moves. 2 Such large data sets are typically associated with base-calls the interpretation of single-strand DNA sequence data 5

6 The answer as it turns out is technology (no surprise here). Over the years, we have all benefited from advancements in Internet bandwidth, the increased density & speed of storage platforms and the migration of computer driven intelligence into every facet of our lives. When these advancements are applied to the above problem, what emerges is an eloquent and very cost effective storage appliance from DataDirect Networks called Web Object Scaler or WOS. To the casual observer, WOS looks like a NAS server, and in some ways it is. However, we will show how a WOS-based private cloud, can fundamentally change how information is shared, managed and processed securely all while lowering the cost of research and accelerating time to discovery. WEB OBJECT SCALER (WOS) A WOS-BASED PRIVATE CLOUD FUNDAMENTALLY CHANGES HOW INFORMATION IS SHARED, MANAGED AND PROCESSED SECURELY. With the rapid adoption of outsourcing, physician, pharmaceutical companies and researchers will all have access to a competing group of service providers who are highly motivated, efficient and customer focused. However, this new emerging paradigm will need a feature rich infrastructure for moving gigabytes data between multiple end points. This is where a private cloud can not only address the stated needs, but significantly improve the rate of discovery, all while lowering cost. The WOS private cloud solution is a highly optimal approach for addressing the growing and complex needs of a global Life Science research community. WOS is a revolutionary object-based, federated storage system for the global distribution of immutable objects. It addresses a collaboration paradigm by providing users a unique name space within their network (directory or drive name-space), where they can read and/or write files which automatically appear in a directory structure somewhere else in the world. The destination is nothing more than a collection of IP addresses associated with the WOS hardware. Data is stored as a WOS object. You can think of an object as a file, or a single tar. gz object or a zip file, etc. Each WOS object has associated with it a unique object ID and a metadata header or preamble. The object ID is created upon placement of the object within the WOS environment (PUT command). The header has a user-defined 65KB metadata preamble which can be filled with either text or binary. This metadata can be used as an object identifier i.e., file name, date, size, etc., patient information, an Electronic Record image, LIMS data, summary of analysis, or any combination thereof. WOS objects also contain a check sum, a signature (used in the creation of the Object ID), and the object s policies which determine: Where to PUT an object (destination as many as 64 unique nodes); Who can GET or access a given object, Who can DELETE the object; DDN WOS is very simple file depository that supports various industry standard interfaces such as native RESTful, S3, NFS, Figure 2 - A Global Collaboration Platform for Pharma DDN.COM

7 and CIFS to name a few. From the user perspective, it behaves like Dropbox with half the latency (peer to peer transaction), and safely located behind the firewall. In figure 4, we see an example of a WOS object containing a 2GB BAM file payload. If we assume a 10 Mb/ sec upload bandwidth, the metadata would appear on the server almost instantly and the BAM payload would be locally accessible in just under 30 minutes just copy the object and WOS does the rest. At its core, WOS is an intelligent software stack that allows a massively scalable content delivery platform to be created out of small building blocks, enabling the system to start small, and easily grow to a multi-petabyte scale (see figure 3). WOS is a fully distributed system, meaning there are absolutely no single points of failure or bottlenecks. This allows the system to scale with each new cloud building block (called nodes) linearly adding to the system s performance capabilities and storage capacity. Detailed technical information on WOS can be found at Figure 3 WOS 6000 storage appliance for Global Collaboration 4BM Sub-Object 4BM Sub-Object 4BM Sub-Object 4BM Sub-Object 2GB BAM file Metadata Header 150GB Payloard WOS Object Profile 64KBUser Metadata Check Sum Policy Signature Figure 4 - WOS Object HOW WOS CAN ACCELERATE THE DISCOVERY PROCESS The WOS solution provides to the Pharma researcher or Clinician the ability to share their research data as quickly and simply as an idea. Gone is the day of zipping up files and sftp or Dropbox or the hundred other different ways researchers and IT departments facilitate data sharing. It is all reduced to a simple file copy, followed by a phone call... Did you see what I did? These are unexpected results. 7

8 Patterson Newark Elizabeth Edison Trenton Cherry Hill wood Vineland Millville Atlantic City A CASE STUDY THE ABILITY TO LEVERAGE WOS POLICIES IMPROVES RESEARCHER EFFECTIVENESS AND PROMOTES COLLABORATION. In this scenario, we will study a sequencing/ analysis effort by a large pharmaceutical company that is globally dispersed. The company is doing research to understand the variability among patients for determining drug efficacy and safety for a new smallmolecule drug. It is becoming increasingly expensive and inefficient for the company to build and maintain a sequencing infrastructure which is not directly associated with their core competence. Hence, they have decided to outsource full genome sequencing to a SEQaaS company in the Northeast and data analytics to a company in the EU. This effort involves three different research centers: Japan, California and Switzerland. The analytics company needs to send their results to all three sites with minimal delay and the SEQaaS company needs to deliver aligned SAM files to the analytics company and FASTQ/SAM files to Bio/Pharma firm in California. The SEQaaS firm has to archive all data for 10 years in two separate locations. The map in Figure 5 shows just how complex a global collaboration initiative can be. However, the WOS private cloud solution, provides a secure namespace where files can be shared globally with a high level of flexibility. In fact, WOS is so flexible that it s possible for the analytics company in France to collaborate only with the Basel Switzerland Pharma location and then leverage their GigE leased line to extend the collaboration to California and Japan. And, this is all accomplished with policy-based automation. The ability to leverage WOS policies at an object level is extremely powerful. It greatly simplifies the global distribution of data, improves researcher effectiveness and promotes collaboration. It has been shown that once this level of collaboration begins, it accelerates and evolves; fostering new applications and innovations. In this scenario, the SEQaaS Company in New England has in its datacenter a petabyte of DDN SFA 12K-E storage running DDN GRIDScaler parallel file system (see Figure 7). The storage array interfaces via InfiniBand FDR to a datacenter server farm. Both the Proliant servers and the Illumina HiSeq2200 sequencers, mount via NFS, directly to the DDN WOS array. Ingested data from the HiSeq2200 is RAID protected in-place, based on pre-set WOS policies. The staged data is then copied to the SFA12K-E where it is processed by the datacenter servers and run through the CASAVA pipeline and GATK for SNP calling. The resulting FASTQ files are then gap aligned with BWA and the final aligned BAM file is pushed back to the WOS storage array along Delano Oxnard Yuma, Arizona Pharma sits SEQaaS Analytics Archive GigE Leased Line Internet (WWW) Figure 5 - Collaboration map 8

9 with the unaligned FASTQ files. This particular setup is furthered automated with irods which is running native on the SFA12-E. irods provides a customizable data management architecture that assigns all the appropriate policies to the objects being posted to the WOS storage array. It also automates the movement of data through the network and retires (deletes) HiSeq2200 staged-data after the FASTQ and BAM file are staged back to the WOS array. Once the data is staged, the WOS policies initiate an asynchronous peer-to-peer copy of the data to the backup-site in New Jersey, the Pharma facility in California and the data analytics company in France. Once the data is safely staged, irods can then send off an to a list of recipients informing them that the data is now local and accessible. Illumina HiSeq2200 Sequencers 10 GigE 10Mb/sec. Upload Web Object Scaler France California New Jersey i.r.o.d.s FDR-IB i.r.o.d.s DDN SFA10K-E Figure 6 - Data flow view of SEQaaS provider in New England HISEQ2200 Data ingested to WOS array Each object is RAID protected in place SFA12K-E As data is staged to WOS, it is copied to SFA12K-E Copy performed via irods rules engine COMPUTER SFA12-E staged data is run through CASAVA and GATK for SNP calling At end of run, SAM and FASTQ data is staged back to WOS Original HiSeq2200 data is deleted WOS ARRAY Data staged via irods rules engine; WOS Policies initiate collaboration rules WOS archived data is copied to data analytics firm in France FASTQ/SAM data is also copied to Pharma in CA and WOS data warehouse in NJ, USA ANALYTICS Local data in the WOS array is processed per customers requirements Results are staged back to WOS array and policies send results to Pharma in Basel WOS policies there send analytics data on the CA and Japan Figure 7 - Collaboration data flow view 9

10 CONCLUSION What is so unique and remarkable about the outlined approach is how a very complex collaboration effort is reduced to a simple file read/write command (Linux bash <cp> command or drag & drop in Windows). Data sets from round the world just appear on a local drive, no need to down-load objects from an S3 cloud or tar & sftp or un-box a shipped drive and hope it will works this time. In short, all the underlining complexities of sending data objects up to 256 destinations while ensuring data integrity is accomplished with a set of pre-determined policies. Once those policies are defined for a given directory space, any transaction within that space will flawlessly execute per those policies. The DataDirect Networks WOS platform is a mature, hardened and highly scalable solution for sharing ideas in a global community. Our account managers, applications specialists and engineering teams are dedicated to delivering the highest value and performance for your investment. DDN storage solutions will grow to meet your needs, help consolidate and simplify your data center while accelerating global collaboration. Our high value storage solutions are backed by enterprise class services and support and our subject matter experts will work with your team to ensure best in class performance and value for the life of the platform. ABOUT DDN DataDirect Networks (DDN) is the world s leading big data storage supplier to data-intensive, global organizations. For more than 15 years, DDN has designed, developed, deployed and optimized systems, software and solutions that enable enterprises, service providers, universities and government agencies to generate more value and to accelerate time to insight from their data and information, on premise and in the cloud. Organizations leverage the power of DDN technology and the deep technical expertise of its team to capture, store, process, analyze, collaborate and distribute data, information and content at largest scale in the most efficient, reliable and cost effective manner. DDN customers include many of the world s leading financial services firms and banks, healthcare and life science organizations, manufacturing and energy companies, government and research facilities, and web and cloud service providers. For more information, visit our website or call SALES@DDN.COM DataDirect Networks, Inc. All Rights Reserved. v2 (5/15) 10