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Primeur weekly 2019-05-06

Exascale supercomputing

Towards flexible Exascale computing - Installation of the first DEEP-EST module by MEGWARE ...

Quantum computing

HKUST physicist contributes to new record of quantum memory efficiency ...

Researchers discover quantum effect in hard disk drive material ...

Focus on Europe

bluechip partners with E4 Computer Engineering, an HPC specialist ...

Hans Meuer Award finalists selected ...

Middleware

Red Hat drives operational simplicity and modern system support with latest version of Red Hat Virtualization ...

Hardware

Supermicro announces expansion of Silicon Valley Corporate Headquarters and groundbreaking for new 800,000-square foot building in Taiwan ...

New Pittsburgh University computer to launch into Space ...

Parallel Distributed Systems Facility had a storied history in serving high-energy physics and nuclear physics experiments ...

Violin doubles capacity of XVS 8 storage platform with performance-tuned standard NVMe SSDs ...

Arm announces appointment of Inder Singh as Chief Financial Officer ...

Promising material could lead to faster, cheaper computer memory ...

Applications

NCSA contributes to LIGO and Virgo neutron star collision detection ...

Collaborative efforts produce clinical workflows for fast, translational genetic analysis ...

Novel software to balance data processing load in supercomputers to be presented ...

Unhackable: New chip stops attacks before they start ...

Grant to provide computational modeling support for hypersonic vehicles ...

Transforming waste heat into clean energy ...

Liqid enables industry-first unified multi-fabric support for composable infrastructure ...

Simulations identify importance of lattice distortions in ion-conducting fuel cell materials ...

Oak Ridge National Laboratory' Summit to perform cosmological and reactor simulations ...

The Cloud

SDSC's Sherlock Cloud expands hybrid Cloud offerings ...

Cornell investigating multi-cloud cost management with RightScale ...

Red Hat helps Public Health England use open source to pursue hybrid Cloud operations ...

Red Hat Upgrades the business developer's toolbox for a Cloud-native world with latest release of Red Hat Process Automation ...

Collaborative efforts produce clinical workflows for fast, translational genetic analysis

3 May 2019 Urbana-Champaign - With individualized medicine - one of the holy grails of modern health care - diagnosis and treatment of patients would rely in part on each individual's specific DNA profile, enabling truly personalized care. But in order for genetic information to contribute meaningfully to patient care, DNA testing has to be affordable and efficient. In 2017, the Mayo Clinic Center for Individualized Medicine (CIM) and the University of Illinois at Urbana-Champaign embarked on a two-year Grand Challenge under the auspices of the Mayo Clinic & Illinois Alliance for Technology-Based Healthcare with the goal of making DNA analysis a possibility for every patient. The first aim of the project focused on finding faster methods for clinical analysis of the whole human genome.

The Grand Challenge project, led by Eric Wieben, Ph.D. at Mayo Clinic and Matthew Hudson, Ph.D. at Illinois, tasked Liudmila Mainzer, Ph.D., Technical Programme Manager of the Genomics group at Illinois' National Center for Supercomputing Applications (NCSA), with speeding up clinical testing. Her group conducted analyses to find the fastest tools for genetic variant calling, which analyzes how a specific DNA sample differs from a standard reference.

Ultimately, Mayo Clinic decided to adopt a new variant calling software that completes analysis 44 times faster than the traditional industry-standard pipeline - requiring just a few hours to process a whole genome, rather than days. But while faster software makes a significant difference, the bulk of the project lay in the next step for Liudmila Mainzer's team: wrapping the newly adopted software tools into a modularized clinical workflow. The resulting "Mayomics" (Mayo + genomics) variant calling workflow will be easy to maintain, update, customize, and run across Mayo Clinic's many labs and numerous specialized procedures.

Nate Mattson, an IT lead analyst for the Department of IT Executive Administration at Mayo Clinic, coordinated with NCSA and with twelve clinical labs at Mayo Clinic to make sure the finished workflow would meet the needs of hundreds of clinical staff members. Nate Mattson noted that the ability to configure and scale the workflow across multiple procedures and inputs, including whole genome data, is a critical design element - as is automation, which "enables 24/7 processing without any human intervention" once samples have been sequenced.

Modularity - separating tasks into self-contained scripts that can be mixed and matched as needed - is essential on multiple levels, Liudmila Mainzer added. "With so many different assays for so many different diseases and conditions, it would be impractical to write, test, and maintain individual workflows for each of them, and keep them in sync and up-to-date as the field evolves. Our design specifically addresses this through modules that can be used in hundreds of workflows, but only need to be updated once when changes occur."

While the completed workflow satisfied the requirements set forth in the Grand Challenge, Mayo Clinic and Illinois decided to extend their collaborative project in order to add more functionality and configure new workflows, such as variant calling for tumor samples. In the meantime, the first Mayomics workflow has completed a process of rigorous testing by Mayo Clinic's Software Quality Assurance (SQA) team and is now undergoing a "verification" phase in Mayo Clinic labs prior to official clinical deployment. Clinical work requires robust code and quality control, noted Liudmila Mainzer, and has to meet exacting external specifications. According to Nate Mattson, "Mayomics will support and exceed all of the auditing requirements set forth by CAP/CLIA and NYS/CLEP", two sets of national standards for laboratory work.

Nate Mattson and a team comprising Mayo Clinic research IT, clinical IT, and SQA staff work closely with NCSA Genomics to define and clarify requirements for each new request, confirm implementation details, and troubleshoot potential snags. The Mayo Clinic team also develops pieces of the workflow that are highly specific to Mayo Clinic internal systems and procedures. The collaboration works well: "There is value in clinical teams focusing on their own clinical process and medical informatics while someone else worries about code organization, workflow development and functionality", stated Liudmila Mainzer. "These are two different mindsets and it helps when different heads are busy with each one." Nate Mattson is happy that the Mayomics workflows will enable more efficient, cost-effective analysis. "A diagnosis can be life-changing", he noted. "Anything we can do to expedite that process without compromising quality is critical."

This work was a product of the Mayo Clinic & Illinois Alliance for Technology-Based Healthcare. Major funding was provided by the Mayo Clinic Center for Individualized Medicine and the Todd and Karen Wanek Programme for Hypoplastic Left Heart Syndrome. The Interdisciplinary Health Sciences Institute, Carl R. Woese Institute for Genomic Biology, and the National Center for Supercomputing Applications also provided support and resources.
Source: National Center for Supercomputing Applications - NCSA

Back to Table of contents

Primeur weekly 2019-05-06

Exascale supercomputing

Towards flexible Exascale computing - Installation of the first DEEP-EST module by MEGWARE ...

Quantum computing

HKUST physicist contributes to new record of quantum memory efficiency ...

Researchers discover quantum effect in hard disk drive material ...

Focus on Europe

bluechip partners with E4 Computer Engineering, an HPC specialist ...

Hans Meuer Award finalists selected ...

Middleware

Red Hat drives operational simplicity and modern system support with latest version of Red Hat Virtualization ...

Hardware

Supermicro announces expansion of Silicon Valley Corporate Headquarters and groundbreaking for new 800,000-square foot building in Taiwan ...

New Pittsburgh University computer to launch into Space ...

Parallel Distributed Systems Facility had a storied history in serving high-energy physics and nuclear physics experiments ...

Violin doubles capacity of XVS 8 storage platform with performance-tuned standard NVMe SSDs ...

Arm announces appointment of Inder Singh as Chief Financial Officer ...

Promising material could lead to faster, cheaper computer memory ...

Applications

NCSA contributes to LIGO and Virgo neutron star collision detection ...

Collaborative efforts produce clinical workflows for fast, translational genetic analysis ...

Novel software to balance data processing load in supercomputers to be presented ...

Unhackable: New chip stops attacks before they start ...

Grant to provide computational modeling support for hypersonic vehicles ...

Transforming waste heat into clean energy ...

Liqid enables industry-first unified multi-fabric support for composable infrastructure ...

Simulations identify importance of lattice distortions in ion-conducting fuel cell materials ...

Oak Ridge National Laboratory' Summit to perform cosmological and reactor simulations ...

The Cloud

SDSC's Sherlock Cloud expands hybrid Cloud offerings ...

Cornell investigating multi-cloud cost management with RightScale ...

Red Hat helps Public Health England use open source to pursue hybrid Cloud operations ...

Red Hat Upgrades the business developer's toolbox for a Cloud-native world with latest release of Red Hat Process Automation ...