The success of the genomics industry has led to generation of huge amounts of sequence data. If put to good use, this information has the potential to revolutionize medicine, but the expense of the high-powered computers needed to achieve this is making full exploitation of the data difficult. Could cloud computing be the answer?
Over the last decade, genomics has become the backbone of drug discovery. It has allowed scientists to develop more targeted therapies, boosting the chances of successful clinical trials. In 2018 alone, over 40% of FDA-approved drugs had the capacity for being personalized to patients, largely based on genomics data. As the percentage has doubled over the past four years, this trend is unlikely to slow down anytime soon.
The ever-increasing use of genomics in the realm of drug discovery and personalized treatments can be traced back to two significant developments over the past decade: plunging sequencing costs and, consequently, an explosion of data.
As sequencing technologies are constantly evolving and being optimized, the cost of sequencing a genome has plummeted. The first sequenced genome, part of the Human Genome Project, cost 2.4B and took around 13 years to complete. Fast forward to today, and you can get your genome sequenced in less than a day for under 900.
According to the Global Alliance for Genomics and Health, more than 100 million genomes will have been sequenced in a healthcare setting by 2025. Most of these genomes will be sequenced as part of large-scale genomic projects stemming from both big pharma and national population genomics initiatives. These efforts are already garnering immense quantities of data that are only likely to increase over time. With the right analysis and interpretation, this information could push precision medicine into a new golden age.
Are we ready to deal with enormous quantities of data?
Genomics is now considered a legitimate big data field just one whole human genome sequence produces approximately 200 gigabytes of raw data. If we manage to sequence 100M genomes by 2025 we will have accumulated over 20B gigabytes of raw data. The massive amount of data can partially be managed through data compression technologies, with companies such as Petagene, but that doesnt solve the whole problem.
Whats more, sequencing is futile unless each genome is thoroughly analyzed to achieve meaningful scientific insights. Genomics data analysis normally generates an additional 100 gigabytes of data per genome for downstream analysis, and requires massive computing power supported by large computer clusters a feat that is economically unfeasible for the majority of companies and institutions.
Researchers working with large genomics datasets have been searching for other solutions, because relying solely on such high-performance computers (HPC) for data analysis is economically out of the question for many. Large servers require exorbitant amounts of capital upfront and incur significant maintenance overheads. Not to mention, specialized and high-level hardware, such as graphics processing units, require constant upgrades to remain performant.
Furthermore, as most HPCs have different configurations, ranging from technical specs to required software, the reproducibility of genomics analyses across different infrastructures is not a trivial feat.
Cloud computing: a data solution for small companies
Cloud computing has emerged as a viable way to analyze large datasets fast without having to worry about maintaining and upgrading servers. Simply put, Cloud computing is a pay-as-you-go model allowing you to rent computational power and storage. and its pervasive across many different sectors.
According to Univa the industrial leader in workload scheduling in the cloud and HPC more than 90% of organizations requiring high performance computing capacity have moved, or are looking into moving to the cloud. Although this is not specific for companies in the life sciences, Gary Tyreman Univas CEO suggests that pharmaceutical companies are ahead of the market in terms of adoption.
The cloud offers flexibility, an alluring characteristic for small life science companies that may not have the capital on-hand to commit to large upfront expenses for IT infrastructure: HPC costs can make or break any company. As a consequence, many opt to test their product in the cloud first, and if numbers look profitable, they can then invest in an in-house HPC solution.
The inherent elasticity of cloud resources enables companies to scale their computational resources in relation to the amount of genomic data that they need to analyze. Unlike with in-house HPCs, this means that there is no risk money will be wasted on idle computational resources.
Elasticity also extends to storage: data can be downloaded directly to the cloud and removed once the analyses are finished, with many protocols and best practices in place to ensure data protection. Cloud resources are allocated in virtualized slices called instances. Each instance hardware and software is pre-configured according to the users demand, ensuring reproducibility.
Will Jones, CTO of Sano Genetics, a startup based in Cambridge, UK, offering consumer genetic tests with support for study recruitment, believes the cloud is the future of drug discovery. The company carries out large data analyses for researchers using its services in the cloud.
In a partnership between Sano Genetics and another Cambridge-based biotech, Joness team used the cloud to complete the study at a tenth of the cost and in a fraction of the time it would have taken with alternative solutions.
Besides economic efficiency, Jones says that moving operations to the cloud has provided Sano Genetics with an additional security layer, as the leading cloud providers have developed best practices and tools to ensure data protection.
Why isnt cloud computing more mainstream in genomics?
Despite all of the positives of cloud computing, we havent seen a global adoption of the cloud in the genomics sector yet.
Medley Genomics a US-based startup using genomics to improve diagnosis and treatment of complex heterogeneous diseases, such as cancer moved all company operations to the cloud in 2019 in a partnership with London-based Lifebit.
Having spent more than 25 years at the interface between genomics and medicine, Patrice Milos, CEO and co-founder of Medley Genomics, recognized that cloud uptake has been slow in the field of drug discovery, as the cloud has several limitations that are preventing its widespread adoption.
For starters, long-term cloud storage is more expensive than the HPC counterpart: cloud solutions charge per month per gigabyte, whereas with HPC, once youve upgraded your storage disk, you have no additional costs. The same goes for computing costs: while the cloud offers elasticity, Univas CEO Tyreman says that the computation cost of a single analysis is five times more expensive compared to an HPC solution in many scenarios. However, as cloud technologies continue to progress and the market becomes increasingly more competitive among providers, the ongoing cloud war will likely bring prices down.
Furthermore, in the world of drug discovery, privacy and data safety are paramount. While cloud providers have developed protocols to ensure the data is safe, some risks still exist, for example, when moving the data. Therefore, large pharmaceutical companies prefer internal solutions to minimize these risks.
According to Milos, privacy remains the main obstacle for pharmaceutical companies to fully embrace the cloud, while the cost to move operations away from HPCs is no longer a barrier. While risks will always exist to a certain extent, Milos highlighted that the cloud allows seamless collaboration and reproducibility, both of which are essential for research and drug discovery.
Current players in the cloud genomics space
Cloud computing is a booming business and 86% of cloud customers rely on three main providers: AWS (Amazon), Azure (Microsoft) and Google Cloud. Although the three giants currently control the market, many other providers exist, offering more specialized commercial and academic services.
Emerging companies are now leveraging the technology offered by cloud providers to offer bioinformatics solutions in the cloud, such as London-based Lifebit, whose technology allows users to run any bioinformatics analyses through any cloud provider with a user-friendly interface effectively democratizing bioinformatics for all researchers, regardless of skill set.
Federation is a concept from computing now used in the field of genomics. It allows separate computers in different networks to work together to perform secure analysis without having to expose private data to others, effectively removing any potential security issues.
The amount of data organizations are now dealing with has become absolutely unmanageable with traditional technologies, and is too big to even think about moving, explained Maria Chatzou Dunford, Lifebits CEO and co-founder.
When data is moved, you increase the chances of having it be intercepted by third-parties, essentially putting it at significant risk. Data federation is the only way around this unnecessary data storage and duplication costs, and painstakingly slow data transfers become a thing of the past.
Getting ready for the genomics revolution
Its no secret that genomics is key to enabling personalized medicine and advancing drug discovery. We are now seeing a genomics revolution where we have an unprecedented amount of data ready to be analyzed.
The challenge now is: are we ready for it? To be analyzed, big data requires massive computation power, effectively becoming an entry barrier for most small organizations. Cloud computing provides an alternative to scale analyses, while at the same time, facilitating reproducibility and collaboration
While the cost and security limitations of cloud computing are preventing companies from fully embracing the cloud, these drawbacks are technical and are expected to be resolved within the next few years.
Many believe that the benefits of the cloud heavily outweigh its limitations. With major tech giants competing to offer the best cloud solutions a market valued at $340 billion by 2024 we might be able to expect a drastic reduction in costs. While some privacy concerns may still exist, leading genomics organizations are developing new tools and technologies to protect genomic data.
Taken as a whole, it is likely that the cloud will be increasingly important in accelerating drug discovery and personalized medicine. According to Univas Tyreman, it will take around 1015 years to see the accelerated transition from HPC to cloud, as large organizations are often conservative in embracing novel approaches.
Distributed big data is the number one overwhelming challenge for life sciences today, the major obstacle impeding progress for precision medicine, Chatzou Dunford concluded.
The cloud and associated technologies are already powering intelligent data-driven insights, accelerating research, discovery and novel therapies. I have no doubt we are on the cusp of a genomics revolution.
Filippo Abbondanza is a PhD candidate in Human Genomics at the University of St Andrews in the UK. While doing his PhD, he is doing an internship at Lifebit and is working as marketing assistant at Global Biotech Revolution, a not-for-profit company growing the next generation of biotech leaders. When not working, he posts news on LinkedIn and Twitter.
Images via E. Resko, Lifebit and Shutterstock
See original here:
Is Cloud Computing the Answer to Genomics Big Data... - Labiotech.eu
- CTERA Networks Partners with SYNNEX Corporation to Drive Market Demand for Hybrid Cloud Storage, Collaboration and ... [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Cloud storage exempt from Ninefold's uptime boost [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Virsto Named Finalist of 2012 Storage Virtualization & Cloud Awards [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Innovative Hybrid Cloud Storage Solutions Now Available From PROMISE Technology [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Box Talks Integration with BlackBerry 10 and Cloud Storage for Business - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- AG112's Weekly Technology Tutorials Ep.7 Cloud Storage - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Cloud Storage - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Google Cloud Storage Office Hours - 9/5/2012 - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- IBM Cloud Storage -- Future Directions - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Working with best FREE Cloud storage solution - MediaFire - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Best Cloud Storage | How Nate Made $450 His First Hour... - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Cloud Storage Services: Comparison - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Top 10 Free Cloud Storage Services of 2012 - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Cloud Storage Wars - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Secure and Comprehensive Cloud Storage for Health IT - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Free Cloud Storage! - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Microsoft SkyDrive Cloud Storage - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Top 16 Android Cloud Storage Apps Quick Breakdown - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Up to 48GB of FREE Cloud Storage, 14GB Guaranteed - Video [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Nasuni's CEO To Speak At Interop On The Secure Use Of Cloud Storage [Last Updated On: October 6th, 2012] [Originally Added On: October 6th, 2012]
- Oracle vs Amazon Cloud Storage: OpenWorld 2012 - Video [Last Updated On: October 6th, 2012] [Originally Added On: October 6th, 2012]
- Apple extends iCloud storage for another year [Last Updated On: October 7th, 2012] [Originally Added On: October 7th, 2012]
- Interush Introduces Convenient Cloud-Based Storage Service with Release of PHYTTER DOCK Application [Last Updated On: October 9th, 2012] [Originally Added On: October 9th, 2012]
- Get a free 15GB cloud-storage account from 4Sync [Last Updated On: October 9th, 2012] [Originally Added On: October 9th, 2012]
- Cloud Solutions Increase Customer Engagement and Retention [Last Updated On: October 9th, 2012] [Originally Added On: October 9th, 2012]
- Pogoplug offering 100GB of cloud storage to UK users for just £19.99 a year [Last Updated On: October 10th, 2012] [Originally Added On: October 10th, 2012]
- New vFoglight Storage 2.0 Provides Integrated Application to Disk Performance Monitoring [Last Updated On: October 10th, 2012] [Originally Added On: October 10th, 2012]
- Lunacloud Deploys Cloudian® To Grow Business, Offer S3 Compatible Cloud Storage [Last Updated On: October 11th, 2012] [Originally Added On: October 11th, 2012]
- New Cloud Storage Company, ZapDrive, Launches Today Offering 100 GB for $19.99/year. [Last Updated On: October 11th, 2012] [Originally Added On: October 11th, 2012]
- Otixo Adds Ubuntu One to Aggregated Cloud Storage Lineup [Last Updated On: October 11th, 2012] [Originally Added On: October 11th, 2012]
- Cloud Storage Reviews Announcement Video - Video [Last Updated On: October 11th, 2012] [Originally Added On: October 11th, 2012]
- Cloud storage outage strikes Macquarie Telecom [Last Updated On: October 11th, 2012] [Originally Added On: October 11th, 2012]
- Online-Storage.com is Now SIO.CO [Last Updated On: October 11th, 2012] [Originally Added On: October 11th, 2012]
- C2C Maximizes eMail Archiving Flexibility and Control With Support for the Hybrid Cloud [Last Updated On: October 11th, 2012] [Originally Added On: October 11th, 2012]
- OwnCloud: Build your own or manage your public cloud storage services [Last Updated On: October 12th, 2012] [Originally Added On: October 12th, 2012]
- Ubuntu's cloud storage service hits Mac in beta, with 5GB free [Last Updated On: October 12th, 2012] [Originally Added On: October 12th, 2012]
- Akitio Cloud Hybrid Review: Convenient NAS and USB Storage in One [Last Updated On: October 13th, 2012] [Originally Added On: October 13th, 2012]
- Symform Hires Senior Sales Executive to Build Global Partnerships as Distributed Cloud Storage Network Surpasses 5.5 ... [Last Updated On: October 15th, 2012] [Originally Added On: October 15th, 2012]
- Get an extra 25GB of storage in the Dropbox Great Space Race [Last Updated On: October 16th, 2012] [Originally Added On: October 16th, 2012]
- Microsoft Acquires StorSimple To Increase Cloud Storage Capabilities [Last Updated On: October 17th, 2012] [Originally Added On: October 17th, 2012]
- Inktank-Metacloud Partnership Enhances Fully Managed Private Cloud Solution With Enterprise-Class Storage [Last Updated On: October 17th, 2012] [Originally Added On: October 17th, 2012]
- Citrix and NetApp Collaborate to Simplify Cloud Storage [Last Updated On: October 17th, 2012] [Originally Added On: October 17th, 2012]
- Microsoft Acquires Leader In Cloud-integrated Storage [Last Updated On: October 17th, 2012] [Originally Added On: October 17th, 2012]
- Microsoft Buys StorSimple for Enterprise Cloud Storage [Last Updated On: October 18th, 2012] [Originally Added On: October 18th, 2012]
- FreedomPACS, Radiology PACS and Cloud Image Storage Provider, Releases Results of County Hospital Case Study ... [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Nirvanix Selects Brocade as Networking Backbone for Global Cloud Expansion [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Pogoplug offers unlimited cloud storage for $5 a month [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- NTT Communications Chooses Cloudian® S3 compatible Object Storage Platform for Multi Petabyte Cloud Storage as a Service [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- TwinStrata and Google to Host "Beyond Disaster Recovery: Integrating Cloud Storage into Your IT Strategy" Seminar [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Cloud Storage Reviews Outlines "How SugarSync Works" In Latest Guide [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Symform Challenges Users to Think Beyond Centralized Data Centers With Its 'Byte Me' Promotion [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Avere to tart up FTX with cloud storage gateway, mutterings foretell [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Deals WD My Book Live Personal Cloud Storage 2 TB Network Attached Best Price 2012 - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Create and Manage Your Own Cloud Storage Free - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Free Cloud Space 100GB - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- DuraCloud Brown Bag Series: How DuraCloud is Different From Amazon - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- PocketCloud Explore - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Free 1TB Cloud storage - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Store your files on WEB for free - Unlimited and better than dropbox - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- CloudBackupNow - Retention Policy (with audio) - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- CloudBackupNow - Retention Policy - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- CloudBackupNow - Primer II - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- ERP Data Capture animation - Video [Last Updated On: November 1st, 2012] [Originally Added On: November 1st, 2012]
- Cash rains DOWN on the Cloud - Nasuni trousers $20m [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- My PC Backup Review The Cloud Storage Service For You - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- Samsung ATIV S Review - Phones 4u - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- Trust Me mv - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- Product Webinar: Collaborating and Exchanging Large Data at Distance with Faspex 3.0 - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- DT Daily: Facebook takes aim at Craigslist, Halo 4 reviews a - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- 2 MCSE Private Cloud Storage Basics - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- Gladinet Cloud Enterprise Quick Start Guide - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- Installing OfficeDrop Mac File Sync - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- OfficeDrop Mac File Sync - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- Secure Cloud Storage - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- Windows Phone 8: Lenese integrates apps in the camera app - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- Graphic Video on Wuala Secure Cloud Storage from Paula Hansen and Chart Magic - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- Hurricane Sandy Cheat Meal Run to Tastee Diner - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- Cloud Zow Review - Cloudzow Review | Marketing Secret Revealed - Video [Last Updated On: November 3rd, 2012] [Originally Added On: November 3rd, 2012]
- What is Cloud Storage? - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Perfume - Chocolate Disco [ hide@BSB Battle In Feb. Remix ] - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]