Study Demonstrates Potential for AI and Whole Genome Sequencing

July 12, 2017

NEW YORK, July 11, 2017 — In a study published today in the July 11, 2017 issue of Neurology Genetics, an official journal of the American Academy of Neurology, researchers at the New York Genome Center (NYGC), The Rockefeller University and other NYGC member institutions, and IBM (NYSE: IBM) have illustrated the potential of IBM Watson for Genomics to analyze complex genomic data from state-of-the-art DNA sequencing of whole genomes. The study compared multiple techniques – or assays – used to analyze genomic data from a glioblastoma patient’s tumor cells and normal healthy cells.

The proof of concept study used a beta version of Watson for Genomics technology to help interpret whole genome sequencing (WGS) data for one patient. In the study, Watsonwas able to provide a report of potential clinically actionable insights within 10 minutes, compared to 160 hours of human analysis and curation required to arrive at similar conclusions for this patient.

The study also showed that WGS identified more clinically actionable mutations than the current standard of examining a limited subset of genes, known as a targeted panel. WGS currently requires significantly more manual analysis, so combining this method with artificial intelligence could help doctors identify potential therapies from WGS for more patients in less time.

Interpretation of genome sequencing data is a significant challenge because of the volume of genomic data to sift through, as well as the large, growing body of research on molecular drivers of cancer and potential targeted therapies. This informatics challenge is often a critical bottleneck when dealing with deadly cancers such as glioblastoma, with a median survival of less than 15 months following diagnosis.

“Our partnership has explored cutting-edge challenges and opportunities in harnessing genomics to help cancer patients. We provide initial insights into two critical issues: what clinical value can be extracted from different commercial and academic cancer genomic platforms, and how to think about scaling access to that value,” noted the study’s Principal Investigator, Robert Darnell, MD, PhD, Robert and Harriet Heilbrunn Professor and Senior Attending Physician at The Rockefeller University and Founding Director of the New York Genome Center.

In the study, NYGC researchers and bioinformatics experts analyzed DNA and RNA from a glioblastoma tumor specimen and DNA from the patient’s normal blood, and compared potentially actionable insights to those derived from a commercial targeted panel that had previously been performed. The whole genome and RNA sequencing data were analyzed by a team of bioinformaticians and oncologists at the NYGC as well as a beta version of IBM Watson for Genomics, an automated system for prioritizing somatic variants and identifying potential therapies.

The beta version of Watson for Genomics processed abstracts and in some cases, full text articles from PubMed, a comprehensive source of more than 27 million citations for biomedical literature. With this information, the NYGC and Watson collaborated to identify gene alterations that can be therapeutically targeted.

“This study documents the strong potential of Watson for Genomics to help clinicians scale precision oncology more broadly,” said Vanessa MicheliniWatson for Genomics Innovation Leader, IBM Watson Health. “Clinical and research leaders in cancer genomics are making tremendous progress towards bringing precision medicine to cancer patients, but genomic data interpretation is a significant obstacle, and that’s where Watson can help.”

The study was part of the NYGC’s and its Institutional Founding Members’ ongoing efforts to advance the use of next-generation sequencing, particularly WGS, in precision medicine. The NYGC and its founding member institutions are conducting additional studies involving Watson to help accelerate the discovery of potentially actionable sequence variants in various types of cancer, including an ongoing study that involves DNA and RNA from a larger cohort of glioblastoma patients, and a study of 200 patients with different types of cancer.

This study, conducted from 2015-2016, utilized a beta version of Watson for Genomics, which is now commercially available for genomic data interpretation through partnerships with Quest Diagnostics, Illumina, or as a cloud-based software for clinicians and researchers. Watson for Genomics is also used in clinical practice at the VA Health System.

About the New York Genome Center
The New York Genome Center is an independent, nonprofit academic research institution at the forefront of transforming biomedical research with the mission of advancing clinical care. A collaboration of premier academic, medical and industry leaders across the globe, the New York Genome Center has as its goal to translate genomic research into the development of new treatments, therapies and therapeutics against human disease. NYGC member organizations and partners are united in this unprecedented collaboration of technology, science and medicine, designed to harness the power of innovation and discoveries to advance genomic services. Their shared objective is the acceleration of medical genomics and precision medicine to benefit patients around the world. For more information, visit our website at http://www.nygenome.org.

Member institutions include: Albert Einstein College of Medicine, American Museum of Natural History, Cold Spring Harbor Laboratory, Columbia University, Hospital for Special Surgery, The Jackson Laboratory, Memorial Sloan Kettering Cancer Center, Icahn School of Medicine at Mount Sinai, NewYork-Presbyterian Hospital, The New York Stem Cell Foundation, New York University, Northwell Health, Princeton UniversityThe Rockefeller University, Roswell Park Cancer Institute, Stony Brook University, Weill Cornell Medicine and IBM.

About IBM Watson Health
Watson is the first commercially available cognitive computing capability representing a new era in computing. The system, delivered through the cloud, analyzes high volumes of data, understands complex questions posed in natural language, and proposes evidence-based answers. Watson continuously learns, gaining in value and knowledge over time, from previous interactions. In April 2015, the company launched IBM Watson Health and the Watson Health Core cloud platform (now Watson Platform for Health). The new unit will help improve the ability of doctors, researchers and insurers to innovate by surfacing insights from the massive amount of personal health data being created and shared daily. The Watson Platform for Health can mask patient identities and allow for information to be shared and combined with a dynamic and constantly growing aggregated view of clinical, research and social health data. For more information on IBM Watson, visit: ibm.com/watson. For more information on IBM Watson Health, visit: ibm.com/watsonhealth.


Source: IBM

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Machine Learning at HPC User Forum: Drilling into Specific Use Cases

September 22, 2017

The 66th HPC User Forum held September 5-7, in Milwaukee, Wisconsin, at the elegant and historic Pfister Hotel, highlighting the 1893 Victorian décor and art of “The Grand Hotel Of The West,” contrasted nicely with Read more…

By Arno Kolster

Google Cloud Makes Good on Promise to Add Nvidia P100 GPUs

September 21, 2017

Google has taken down the notice on its cloud platform website that says Nvidia Tesla P100s are “coming soon.” That's because the search giant has announced the beta launch of the high-end P100 Nvidia Tesla GPUs on t Read more…

By George Leopold

Cray Wins $48M Supercomputer Contract from KISTI

September 21, 2017

It was a good day for Cray which won a $48 million contract from the Korea Institute of Science and Technology Information (KISTI) for a 128-rack CS500 cluster supercomputer. The new system, equipped with Intel Xeon Scal Read more…

By John Russell

HPE Extreme Performance Solutions

HPE Prepares Customers for Success with the HPC Software Portfolio

High performance computing (HPC) software is key to harnessing the full power of HPC environments. Development and management tools enable IT departments to streamline installation and maintenance of their systems as well as create, optimize, and run their HPC applications. Read more…

Adolfy Hoisie to Lead Brookhaven’s Computing for National Security Effort

September 21, 2017

Brookhaven National Laboratory announced today that Adolfy Hoisie will chair its newly formed Computing for National Security department, which is part of Brookhaven’s new Computational Science Initiative (CSI). Read more…

By John Russell

Machine Learning at HPC User Forum: Drilling into Specific Use Cases

September 22, 2017

The 66th HPC User Forum held September 5-7, in Milwaukee, Wisconsin, at the elegant and historic Pfister Hotel, highlighting the 1893 Victorian décor and art o Read more…

By Arno Kolster

Stanford University and UberCloud Achieve Breakthrough in Living Heart Simulations

September 21, 2017

Cardiac arrhythmia can be an undesirable and potentially lethal side effect of drugs. During this condition, the electrical activity of the heart turns chaotic, Read more…

By Wolfgang Gentzsch, UberCloud, and Francisco Sahli, Stanford University

PNNL’s Center for Advanced Tech Evaluation Seeks Wider HPC Community Ties

September 21, 2017

Two years ago the Department of Energy established the Center for Advanced Technology Evaluation (CENATE) at Pacific Northwest National Laboratory (PNNL). CENAT Read more…

By John Russell

Exascale Computing Project Names Doug Kothe as Director

September 20, 2017

The Department of Energy’s Exascale Computing Project (ECP) has named Doug Kothe as its new director effective October 1. He replaces Paul Messina, who is stepping down after two years to return to Argonne National Laboratory. Kothe is a 32-year veteran of DOE’s National Laboratory System. Read more…

Takeaways from the Milwaukee HPC User Forum

September 19, 2017

Milwaukee’s elegant Pfister Hotel hosted approximately 100 attendees for the 66th HPC User Forum (September 5-7, 2017). In the original home city of Pabst Blu Read more…

By Merle Giles

Kathy Yelick Charts the Promise and Progress of Exascale Science

September 15, 2017

On Friday, Sept. 8, Kathy Yelick of Lawrence Berkeley National Laboratory and the University of California, Berkeley, delivered the keynote address on “Breakthrough Science at the Exascale” at the ACM Europe Conference in Barcelona. In conjunction with her presentation, Yelick agreed to a short Q&A discussion with HPCwire. Read more…

By Tiffany Trader

DARPA Pledges Another $300 Million for Post-Moore’s Readiness

September 14, 2017

The Defense Advanced Research Projects Agency (DARPA) launched a giant funding effort to ensure the United States can sustain the pace of electronic innovation vital to both a flourishing economy and a secure military. Under the banner of the Electronics Resurgence Initiative (ERI), some $500-$800 million will be invested in post-Moore’s Law technologies. Read more…

By Tiffany Trader

IBM Breaks Ground for Complex Quantum Chemistry

September 14, 2017

IBM has reported the use of a novel algorithm to simulate BeH2 (beryllium-hydride) on a quantum computer. This is the largest molecule so far simulated on a quantum computer. The technique, which used six qubits of a seven-qubit system, is an important step forward and may suggest an approach to simulating ever larger molecules. Read more…

By John Russell

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

Reinders: “AVX-512 May Be a Hidden Gem” in Intel Xeon Scalable Processors

June 29, 2017

Imagine if we could use vector processing on something other than just floating point problems.  Today, GPUs and CPUs work tirelessly to accelerate algorithms Read more…

By James Reinders

NERSC Scales Scientific Deep Learning to 15 Petaflops

August 28, 2017

A collaborative effort between Intel, NERSC and Stanford has delivered the first 15-petaflops deep learning software running on HPC platforms and is, according Read more…

By Rob Farber

Oracle Layoffs Reportedly Hit SPARC and Solaris Hard

September 7, 2017

Oracle’s latest layoffs have many wondering if this is the end of the line for the SPARC processor and Solaris OS development. As reported by multiple sources Read more…

By John Russell

Six Exascale PathForward Vendors Selected; DoE Providing $258M

June 15, 2017

The much-anticipated PathForward awards for hardware R&D in support of the Exascale Computing Project were announced today with six vendors selected – AMD Read more…

By John Russell

Top500 Results: Latest List Trends and What’s in Store

June 19, 2017

Greetings from Frankfurt and the 2017 International Supercomputing Conference where the latest Top500 list has just been revealed. Although there were no major Read more…

By Tiffany Trader

IBM Clears Path to 5nm with Silicon Nanosheets

June 5, 2017

Two years since announcing the industry’s first 7nm node test chip, IBM and its research alliance partners GlobalFoundries and Samsung have developed a proces Read more…

By Tiffany Trader

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Leading Solution Providers

Graphcore Readies Launch of 16nm Colossus-IPU Chip

July 20, 2017

A second $30 million funding round for U.K. AI chip developer Graphcore sets up the company to go to market with its “intelligent processing unit” (IPU) in Read more…

By Tiffany Trader

Google Releases Deeplearn.js to Further Democratize Machine Learning

August 17, 2017

Spreading the use of machine learning tools is one of the goals of Google’s PAIR (People + AI Research) initiative, which was introduced in early July. Last w Read more…

By John Russell

Russian Researchers Claim First Quantum-Safe Blockchain

May 25, 2017

The Russian Quantum Center today announced it has overcome the threat of quantum cryptography by creating the first quantum-safe blockchain, securing cryptocurrencies like Bitcoin, along with classified government communications and other sensitive digital transfers. Read more…

By Doug Black

Google Debuts TPU v2 and will Add to Google Cloud

May 25, 2017

Not long after stirring attention in the deep learning/AI community by revealing the details of its Tensor Processing Unit (TPU), Google last week announced the Read more…

By John Russell

EU Funds 20 Million Euro ARM+FPGA Exascale Project

September 7, 2017

At the Barcelona Supercomputer Centre on Wednesday (Sept. 6), 16 partners gathered to launch the EuroEXA project, which invests €20 million over three-and-a-half years into exascale-focused research and development. Led by the Horizon 2020 program, EuroEXA picks up the banner of a triad of partner projects — ExaNeSt, EcoScale and ExaNoDe — building on their work... Read more…

By Tiffany Trader

Amazon Debuts New AMD-based GPU Instances for Graphics Acceleration

September 12, 2017

Last week Amazon Web Services (AWS) streaming service, AppStream 2.0, introduced a new GPU instance called Graphics Design intended to accelerate graphics. The Read more…

By John Russell

Cray Moves to Acquire the Seagate ClusterStor Line

July 28, 2017

This week Cray announced that it is picking up Seagate's ClusterStor HPC storage array business for an undisclosed sum. "In short we're effectively transitioning the bulk of the ClusterStor product line to Cray," said CEO Peter Ungaro. Read more…

By Tiffany Trader

GlobalFoundries: 7nm Chips Coming in 2018, EUV in 2019

June 13, 2017

GlobalFoundries has formally announced that its 7nm technology is ready for customer engagement with product tape outs expected for the first half of 2018. The Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Share This