When an outbreak hits, Magellan speeds up genetic sequencing

 

Connecting state and local government leaders

When an E. coli outbreak caused a surge in requests for genetic sequencing, scientists at Argonne National Labs found the capacity in the Energy Department's cloud framework.

For several years, scientists at the Argonne National Laboratory have been using an automated, software-based system to sequence the genomes of bacteria and microbes. But when that system recently became overwhelmed by a surge in demand, researchers turned to a cloud-based system that virtualized the process, allowing them to sequence hundreds of genomes within hours. 

Argonne’s Rapid Annotation using Subsystems Technology program was developed in 2007 to automate the laborious process of making sense of an organism’s genome.


Related stories:

DOE explores cloud computing for big science

Magellan explores the cloud as a research tool


RAST matches segments of the genetic code of a new bacterium or protein against a catalog of sequenced genetic material. The system’s final result is an annotated genome with a list of an organism’s probable genes and proteins.

A human scientist must still verify this final part, but the entire process can be completed in hours rather than the months — or even years — it once took, said Ross Overbeek, an Argonne computer scientist who was involved in RAST’s design.

But the system wasn’t made to handle a sudden surge in capacity. Designed to process 60 to 80 genomes a day, in June 2010 it was hit with an enormous spike in requests resulting from an E. coli outbreak in German hospitals that was resistant to many existing treatments.

Use of the RAST system is free and open to any scientist, but the system was suddenly hit by demands of up to 200 genomes an hour as researchers sought to pin down and characterize the exact strain of E. coli.

The RAST team turned to the Magellan framework, a cloud computing project managed by the Energy Department, which was designed to boost research by providing additional servers and virtualization tools for scientific research. RAST was duplicated on Magellan, which greatly increased the power and capability of the system.

There are two versions of RAST. The current version uses the Magellan cloud framework, Overbeek said. RAST’s gene sequencing has increased from 100 to 200 genomes a month to more than 1,000 — with surges as high as 450 a day. However, he added that sequencing demand is elastic and usually falls in the range of 1,000 to 1,500 genomes per month.

But rapid response and processing are essential; otherwise, the entire system backs up. By moving to Magellan, the laboratory can reasonably handle such surges, Overbeek said.

The changes in the technology are allowing researchers to sequence the genomes of almost every known pathogen group. The ability to sequence a genome in a matter of hours is a major change, Overbeek said. “I’m excited by the fact that you can have access to an annotated genome in hours,” he said. “This used to take a year to do back in the 1990s.”

Advances in the technology also allow scientists to process batches of related genomes, a process that Overbeek encourages scientists to pursue. “I would like people to think that sequencing is essentially free,” he said.

For microbial genomes, the technology allows researchers to sequence a disease’s genes almost immediately after an outbreak has occurred and pass the data on to other health care research facilities around the world. “This is something that wouldn’t have happened two or three years ago,” he said.

The technology for automated gene sequencing is advancing so quickly, Overbeek said, that in the not-too-distant future, he foresees hospitals being able to do their own gene sequencing. “The way hospitals deal with outbreaks or even bacteria is going to change over the next few years,” he said.

A second, updated version of the RAST software is now in use, and there is a laptop version that is being beta tested. The beta version of RAST can annotate a genome within 10 minutes and is capable of running on a handheld device such as a smart phone or tablet computer.

 

X
This website uses cookies to enhance user experience and to analyze performance and traffic on our website. We also share information about your use of our site with our social media, advertising and analytics partners. Learn More / Do Not Sell My Personal Information
Accept Cookies
X
Cookie Preferences Cookie List

Do Not Sell My Personal Information

When you visit our website, we store cookies on your browser to collect information. The information collected might relate to you, your preferences or your device, and is mostly used to make the site work as you expect it to and to provide a more personalized web experience. However, you can choose not to allow certain types of cookies, which may impact your experience of the site and the services we are able to offer. Click on the different category headings to find out more and change our default settings according to your preference. You cannot opt-out of our First Party Strictly Necessary Cookies as they are deployed in order to ensure the proper functioning of our website (such as prompting the cookie banner and remembering your settings, to log into your account, to redirect you when you log out, etc.). For more information about the First and Third Party Cookies used please follow this link.

Allow All Cookies

Manage Consent Preferences

Strictly Necessary Cookies - Always Active

We do not allow you to opt-out of our certain cookies, as they are necessary to ensure the proper functioning of our website (such as prompting our cookie banner and remembering your privacy choices) and/or to monitor site performance. These cookies are not used in a way that constitutes a “sale” of your data under the CCPA. You can set your browser to block or alert you about these cookies, but some parts of the site will not work as intended if you do so. You can usually find these settings in the Options or Preferences menu of your browser. Visit www.allaboutcookies.org to learn more.

Sale of Personal Data, Targeting & Social Media Cookies

Under the California Consumer Privacy Act, you have the right to opt-out of the sale of your personal information to third parties. These cookies collect information for analytics and to personalize your experience with targeted ads. You may exercise your right to opt out of the sale of personal information by using this toggle switch. If you opt out we will not be able to offer you personalised ads and will not hand over your personal information to any third parties. Additionally, you may contact our legal department for further clarification about your rights as a California consumer by using this Exercise My Rights link

If you have enabled privacy controls on your browser (such as a plugin), we have to take that as a valid request to opt-out. Therefore we would not be able to track your activity through the web. This may affect our ability to personalize ads according to your preferences.

Targeting cookies may be set through our site by our advertising partners. They may be used by those companies to build a profile of your interests and show you relevant adverts on other sites. They do not store directly personal information, but are based on uniquely identifying your browser and internet device. If you do not allow these cookies, you will experience less targeted advertising.

Social media cookies are set by a range of social media services that we have added to the site to enable you to share our content with your friends and networks. They are capable of tracking your browser across other sites and building up a profile of your interests. This may impact the content and messages you see on other websites you visit. If you do not allow these cookies you may not be able to use or see these sharing tools.

If you want to opt out of all of our lead reports and lists, please submit a privacy request at our Do Not Sell page.

Save Settings
Cookie Preferences Cookie List

Cookie List

A cookie is a small piece of data (text file) that a website – when visited by a user – asks your browser to store on your device in order to remember information about you, such as your language preference or login information. Those cookies are set by us and called first-party cookies. We also use third-party cookies – which are cookies from a domain different than the domain of the website you are visiting – for our advertising and marketing efforts. More specifically, we use cookies and other tracking technologies for the following purposes:

Strictly Necessary Cookies

We do not allow you to opt-out of our certain cookies, as they are necessary to ensure the proper functioning of our website (such as prompting our cookie banner and remembering your privacy choices) and/or to monitor site performance. These cookies are not used in a way that constitutes a “sale” of your data under the CCPA. You can set your browser to block or alert you about these cookies, but some parts of the site will not work as intended if you do so. You can usually find these settings in the Options or Preferences menu of your browser. Visit www.allaboutcookies.org to learn more.

Functional Cookies

We do not allow you to opt-out of our certain cookies, as they are necessary to ensure the proper functioning of our website (such as prompting our cookie banner and remembering your privacy choices) and/or to monitor site performance. These cookies are not used in a way that constitutes a “sale” of your data under the CCPA. You can set your browser to block or alert you about these cookies, but some parts of the site will not work as intended if you do so. You can usually find these settings in the Options or Preferences menu of your browser. Visit www.allaboutcookies.org to learn more.

Performance Cookies

We do not allow you to opt-out of our certain cookies, as they are necessary to ensure the proper functioning of our website (such as prompting our cookie banner and remembering your privacy choices) and/or to monitor site performance. These cookies are not used in a way that constitutes a “sale” of your data under the CCPA. You can set your browser to block or alert you about these cookies, but some parts of the site will not work as intended if you do so. You can usually find these settings in the Options or Preferences menu of your browser. Visit www.allaboutcookies.org to learn more.

Sale of Personal Data

We also use cookies to personalize your experience on our websites, including by determining the most relevant content and advertisements to show you, and to monitor site traffic and performance, so that we may improve our websites and your experience. You may opt out of our use of such cookies (and the associated “sale” of your Personal Information) by using this toggle switch. You will still see some advertising, regardless of your selection. Because we do not track you across different devices, browsers and GEMG properties, your selection will take effect only on this browser, this device and this website.

Social Media Cookies

We also use cookies to personalize your experience on our websites, including by determining the most relevant content and advertisements to show you, and to monitor site traffic and performance, so that we may improve our websites and your experience. You may opt out of our use of such cookies (and the associated “sale” of your Personal Information) by using this toggle switch. You will still see some advertising, regardless of your selection. Because we do not track you across different devices, browsers and GEMG properties, your selection will take effect only on this browser, this device and this website.

Targeting Cookies

We also use cookies to personalize your experience on our websites, including by determining the most relevant content and advertisements to show you, and to monitor site traffic and performance, so that we may improve our websites and your experience. You may opt out of our use of such cookies (and the associated “sale” of your Personal Information) by using this toggle switch. You will still see some advertising, regardless of your selection. Because we do not track you across different devices, browsers and GEMG properties, your selection will take effect only on this browser, this device and this website.