The concept of precision medicine is beautifully simple: deliver the right treatment, every time, to the right patient. Making that concept a reality is more complex. Precision medicine is, after all, an entirely new approach to clinical medicine that leverages the power of big data and genomics to transform healthcare.
In a new on-demand webinar, Future of Genomics: The Precision Medicine Solution, our expert panel discusses how Aeon Global Health, the fastest growing clinical lab and healthcare services organization in the United States, partnered with QIAGEN to adopt an end-to-end automation solution that sped up their diagnostic output while lowering costs.
In 2013, when Aeon Global Health entered the hereditary cancer screening market, they knew that automation was critical to success. Together, QIAGEN Bioinformatics and Intel created a solution. By combining QIAGEN’s unparalleled expertise in genomics with Intel’s cutting-edge healthcare technology, the two companies enabled Aeon to provide faster, more comprehensive clinical insights than human cognition alone could permit. Today, one clinical geneticist at Aeon can process up to 50 tests per day.
Instead of taking weeks or months to make sense of a patient’s unique genetic profile, Aeon can now extract insights from colossal amounts of data in only a few minutes. And it’s not just the increase in efficiency that deserves attention. By partnering with Intel, QIAGEN has created an end-to-end solution that provides all workflow components, from analysis to interpretation to reporting, without having to hire hundreds of clinical geneticists and molecular pathologists, who would have to read reports and complete literature searches by hand. Clinical diagnostic test results are delivered quickly, accurately, and at a much lower cost.
As the amount of medical and biological data involved in medical diagnostics increases, so will the need for systems that help researchers, doctors and patients make sense of it. There are few medical advances as promising as precision medicine, and QIAGEN’s AI-based diagnostic tools—powered by Intel’s Scalable Solution Framework—are leading the way.
Join speakers Dr. Shawn Desai, Chief Technology Officer of Aeon Global Health, Dr. Ramon Felciano, Chief Technology Officer and Vice President of Strategy of QIAGEN Bioinformatics, and Kristina Kermanshahche, Global Director of Life Sciences at Intel Corporation, as they discuss how Aeon selected this powerful genomics solution and how you can build upon Aeon’s experience and accelerate your own path to success.
Watch Now — to learn how to put precision medicine on the fast track.
How much compute power do you need to analyze 10 gene panels, exomes, or genomes each day? What about 1,000 genomes each week?
Questions about compute infrastructure are among the most common we hear from our customers, and this has been the primary motivator for our collaboration with Intel. Together, we’ve been working to support affordable, massively scalable whole-genome analysis based on Intel’s world-class infrastructure and our industry-leading analysis tools.
Earlier this year we released the reference architecture that came from this collaboration, and you can learn more about it in the webinar below featuring Michael McManus, Senior Health & Life Sciences Solution Architect at Intel, and Mikael Flensborg, Director and Solution Lead for QIAGEN Bioinformatics. The speakers will update you on the new architecture, which combines our Biomedical Genomics Solution with the Intel Scalable System Framework. They’ll also share advice on sizing and building a genomics cluster based on data-generation needs, as well as how to scale the cluster as demand changes.
The solution represents some of the code optimization work that Intel has focused on lately, teaming up with industry leaders such as QIAGEN Bioinformatics to improve algorithms based on the latest multi-core chip architecture. As genome analysis tools become increasingly complex — newer haplotype-aware callers, for instance, are far more computationally intense than older generations of variant callers — there is greater need for scientists to become experts in computational infrastructure. With solutions like the QIAGEN/Intel reference architecture, we alleviate that burden by recommending a scalable, easily managed system that allows users to focus instead on the science.
For example, this system meets the computational and analysis demands of Illumina’s HiSeq X Ten while providing whole-genome analysis for as little as $22 per genome. With Intel’s 32-node cluster, researchers can save as much as $1.3 million in total ownership costs compared to a vendor-recommended BWA+GATK variant calling pipeline run on an 85-node cluster.
Learn more about our High volume sequencing solution
Reference Architectures for the QIAGEN Biomedical Genomics Solution
https://clcbio.23video.com/12438081.ihtml/player.html?token=9c8598703736f4ebfb60db5c2669f27b&source=embed&photo%5fid=14250926
At Bio-IT World we had the pleasure to demonstrate the results of our work with the information technology leaders Intel and BioTeam.
Our collaborations create infrastructure solutions that make population-scale genomic analysis feasible for more researchers. We’ve been working together with Intel to bring world-class infrastructure together with industry-leading genome analysis tools to enable massively scalable whole genome analysis at lower cost. Together with BioTeam we're creating a proof-of-concept high-performance computing (HPC) appliance.
For more details about the partnerships, please read the official press release below.
QIAGEN partners with IT leaders on novel infrastructure for genomics
Demonstrates high-performance computing and genome analysis solutions at Bio-IT World
“By combining our industry-leading genome analysis applications with hardware solutions from leaders like Intel and BioTeam, QIAGEN Bioinformatics is providing world-class infrastructure to help scientists reveal actionable insights from genomic data,” said Dr. Laura Furmanski, Senior Vice President and head of QIAGEN’s Bioinformatics Business Area. “While next-generation sequencing is a momentous advance, society cannot realize the full potential without a corresponding ability to analyze NGS data quickly and accurately. Researchers and clinicians need cost-effective, comprehensive tools for calling and interpreting variants across whole human genomes, and we are providing these novel solutions.”
QIAGEN’s collaboration with Intel developed a reference architecture designed to produce high-volume whole genome data analysis, keeping up with the world’s highest-capacity sequencers, helping NGS scientists keep their sequencing pipelines running smoothly and efficiently. This offering leverages QIAGEN’s CLC Genomics Server software on a compute cluster of 32 Intel® Xeon® processor E5 family based nodes. It provides built-in analysis tools, scalability, fast connection and parallel storage, using Intel Enterprise Edition for Lustre, the world’s largest parallel storage system. In tests, the solution analyzed data quickly and for as little as $22 per genome. It will be described in a conference presentation at Bio-IT World from 3:30-3:50 p.m. on April 6.
“The collaboration with QIAGEN Bioinformatics targets the vexing challenges presented by soaring demand for genome analysis, commonly faced by NGS scientists,” said Ketan Paranjape, GM Life Sciences at Intel. “Optimized solution architectures for these workloads enable researchers to keep pace as sequencers process more genomes than we could have imagined, even a few years ago — all while taking advantage of open systems to save money as well.”
BioTeam and QIAGEN’s proof-of-concept appliance packages CLC Genomics Server with the BioTeam Appliance scientific computing platform to provide a cost-effective, high-performance offering. The flexible, customizable solution delivers a system that maps the computational requirements of the CLC Bio software to an infrastructure that complements its capabilities. The BioTeam Appliance demo at Bio-IT World will be at the QIAGEN Bioinformatics booth (#229) from 1:30-1:45 p.m. on April 6.
“Bioinformatics is an ideal market for high-performance computing, and our simple, end-to-end appliance removes a significant barrier to adoption for many customers,” said Stan Gloss, Founding Partner and Chief Executive Officer at BioTeam. “Our plug-and-play solution enables scientists to focus on research rather than on creating complex IT systems from scratch. We look forward to continuing development of this proof-of-concept model with the QIAGEN Bioinformatics team.”
About BioTeam
BioTeam is a high-performance consulting practice dedicated to delivering objective, technology agnostic solutions to the life science researchers. We leverage the right technologies customized to our client’s unique needs in order to enable them to reach their scientific objectives.
About QIAGEN
QIAGEN N.V., a Netherlands-based holding company, is the leading global provider of Sample to Insight solutions to transform biological materials into valuable molecular insights. QIAGEN sample technologies isolate and process DNA, RNA and proteins from blood, tissue and other materials. Assay technologies make these biomolecules visible and ready for analysis. Bioinformatics software and knowledge bases interpret data to report relevant, actionable insights. Automation solutions tie these together in seamless and cost-effective molecular testing workflows. QIAGEN provides these workflows to more than 500,000 customers around the world in Molecular Diagnostics (human healthcare), Applied Testing (forensics, veterinary testing and food safety), Pharma (pharmaceutical and biotechnology companies) and Academia (life sciences research). As of December 31, 2015, QIAGEN employed approximately 4,600 people in over 35 locations worldwide. Further information can be found at http://www.qiagen.com.
Certain of the statements contained in this news release may be considered forward-looking statements within the meaning of Section 27A of the U.S. Securities Act of 1933, as amended, and Section 21E of the U.S. Securities Exchange Act of 1934, as amended. To the extent that any of the statements contained herein relating to QIAGEN's products, markets, strategy or operating results, including without limitation its expected operating results, are forward-looking, such statements are based on current expectations and assumptions that involve a number of uncertainties and risks. Such uncertainties and risks include, but are not limited to, risks associated with management of growth and international operations (including the effects of currency fluctuations, regulatory processes and dependence on logistics), variability of operating results and allocations between customer classes, the commercial development of markets for our products in applied testing, personalized healthcare, clinical research, proteomics, women's health/HPV testing and nucleic acid-based molecular diagnostics; changing relationships with customers, suppliers and strategic partners; competition; rapid or unexpected changes in technologies; fluctuations in demand for QIAGEN's products (including fluctuations due to general economic conditions, the level and timing of customers' funding, budgets and other factors); our ability to obtain regulatory approval of our products; difficulties in successfully adapting QIAGEN's products to integrated solutions and producing such products; the ability of QIAGEN to identify and develop new products and to differentiate and protect our products from competitors' products; market acceptance of QIAGEN's new products, the consummation of acquisitions, and the integration of acquired technologies and businesses. For further information, please refer to the discussions in reports that QIAGEN has filed with, or furnished to, the U.S. Securities and Exchange Commission (SEC).
Scalable whole genome analysis
As we discussed in a blog post earlier, we’ve been working together with Intel to bring world-class infrastructure together with industry-leading genome analysis tools to enable massively scalable whole genome analysis at lower cost. Now, we have released a new white paper detailing the reference architecture and other technical information for our joint solution.
Designed to help NGS scientists keep their sequencing pipelines running smoothly even at capacity - all while saving money and producing better results - our solution provides whole genome analysis for as little as $22 per genome. It meets the computational and analysis demands of Illumina’s HiSeq X Ten, but Intel’s 32-node offering can save researchers up to $1.3 million in total ownership costs compared to the 85-node cluster recommended by the vendor for a BWA+GATK variant calling pipeline.
Here’s a quick look at what makes our solution different:
For more details, check out the full white paper.
Our tests showed that the 32-node system could process and analyze 48 genomes in 24 hours, on average - enough capacity to handle all the data produced by a HiSeq X Ten. We also tested the system with exome data and successfully analyzed approximately 1,440 human exomes every 24 hours.
Together with Intel we were presenting this joint solution at the Bio-IT World 2016 conference in a presentation addressing the growing demand for population-scale genomics.
If you’d like to learn more but are not able to attend the conference, please feel free to email us.
More information about Bio-IT World
We're committed to enabling our customers to analyze vast amounts of NGS data quickly and at the lowest total cost possible. This year, we made investments designed to enable scalable discovery through the optimization of the speed, accuracy, and cost of our server solution consisting of CLC Genomics Server with the Biomedical Genomics Server extension and Biomedical Genomics Workbench platform. Through extensive benchmark testing, we were able to show that our solution is able to process the maximum throughput from an Illumina HiSeq X Ten, with high accuracy, and at a total cost of ownership (TCO) much lower than alternative solutions.
Data analysis to keep pace with maximum throughput
The maximum throughput of an Illumina HiSeq X Ten has been established at a total of 18,000 whole genome sequences per year. This equates to an average rate of analysis of one whole human genome sequence every 30 minutes. By testing the optimized speed of our solution (including SSE/SIMD code optimizations for Intel x86), we were able to demonstrate that CLC Genomics Server is not only able to keep pace with the data output of an Illumina HiSeq X Ten sequencer running at maximum throughput, but able to do so with less computing nodes than recommended by others. Testing revealed that CLC Genomics Server requires a computer cluster of only 35 nodes, as contrasted to the 85 nodes recommended by Illumina (variant calling based on BWA+GATK in the HiSeq X System Lab Setup and Site Prep Guide (Part #15050093 Rev. H July 2015)). Our comparison benchmark testing was carried out by installing the CLC Genomics Server software on a compute cluster of 35 nodes, each equipped with a 28-core E5-2697 v3 @ 2.60GHz, 128 GB RAM on a shared lustre file system. We used the standard CLC variant calling workflow that comes with the Biomedical Genomics Server solution.
Full analysis of whole human genomes for as little as $22 each
By minimizing the hardware requirements from 85 nodes to just 35, we also minimize the total cost of ownership (TCO) of the solution over a four-year period, which includes everything from software licenses and hardware, to power, cooling, networking, and floor space. Our calculations of the total ownership costs show that with the given specifications, the cost will be as low as $22 per whole human genome analyzed. Given the high throughput enabled by a HiSeq X Ten, the savings can be sizable.
Accurate identification of disease-causing variants
Of course, the total cost of ownership and speed of the overall solution doesn’t mean much unless the results of the analysis are also accurate. To prove accuracy, we chose hereditary disease trio analysis as a test case, and are proud to say that in most cases the Biomedical Genomics Server solution (CLC Genomics Server and Biomedical Genomics Workbench) together with Ingenuity® Variant Analysis™ for interpretation accurately identified the disease-causing variant without calling any false-positive de novo or causal variants.
But this is not the end of the story; we’re just getting started. Our focus on application performance and accuracy of results is essential, so we expect to improve these even more in the future.
Learn more about Biomedical Genomics Server solution
Read the story on the Intel Health & Life Sciences blog
