At the Association for Biomolecular Resource Facilities conference in Saint Louis Missouri USA, Mike Lelivelt described the Thermo Fisher TM Cloud analysis capability with not only real-time PCR data but also Sanger Capillary Electrophoresis sequencing data.
Mike Lelivelt (Thermo Fisher Scientific, San Francisco California USA) shared a talk entitled “Integrating the Analysis of Nucleic Acid Data across Multiple Platforms on the Cloud”. We caught up with Mike to discuss his presentation and what the Thermo Fisher TM Cloud has to offer.
Why cloud computing for genetic analysis?
Thermo Fisher TM Cloud is an exciting offering, as it brings our real-time PCR genetic analysis software and CE/Sanger analysis software to a modern web-based platform. As many of our customers know, before these software products were only available on Microsoft Windows® desktop operating systems, and now it will be available from any computer operating system with a compatible web browser. On top of this is the benefit of collaboration, being able to share your data with others without the difficulties normally associated with “sneaker net” data transfer.
What kind of real-time PCR analysis is available?
We are offering our genotyping analysis and gene quantitation analysis (both absolute and relative) for your research. Other modules (such as presence/absence detection and high-resolution melt analysis) are expected to be made available later.
Is it only real-time PCR analysis on the cloud?
Well as you know our next-generation sequencing Ion Torrent™ customers have been using the Ion Reporter™ software on the cloud for some time now, and we announced at ABRF the pending launch of two new Sanger analysis modules coming to the Thermo Fisher™ Cloud.
What’s the benefit of analyzing Sanger data in the cloud?
Many times researchers who use Sanger capillary electrophoresis are doing so to verify the results from a next-generation sequencing experiment. We have a new Applied Biosystems™ analysis module called Next Gen Confirmation that allows co-analysis of NGS and Sanger data together. This tool allows a user to load up a Variant Call File (.vcf file) from any next-generation sequencing platform (as you know the .vcf file format is a standard) and compare side-by-side those variant results with the specific electrophoretic trace for that variant. Before you’d have to have two different applications open on separate analysis computers, and manually navigate to the variant in question.
And what kind of considerations go into this kind of variant comparison?
From the next-generation sequencing, you will want to consider factors such as base coverage, strand bias, quality scores, and reference allele information. The cloud software makes it easy to evaluate all these parameters side-by-side with the Sanger traces.
This sounds very useful. What about increasing sensitivity of Sanger Sequencing?
We presented data to find lower-frequency variants in Sanger sequencing data with an upgraded analysis software, and are now offering early Technology Access for those interested in trying it out. Given that the existing threshold for somatic variant detection with existing software is about 20%, it will be exciting to see how low a level of detection these Technology Access customers will be able to determine. If anyone is interested in participating in this program and they have some “known truth” samples, we encourage them to talk to their local Thermo Fisher Scientific genetic analysis sales representative for more information.
Aren’t there concerns about data security in the cloud?
Naturally security is a concern, which is why we are deployed on Amazon Web Services® (AWS) that is protected by AES 256-bit encryption as well as HTTPS/SSL for in-transit data. On top of data security is data integrity; the data is backed-up and AWS has SSAE 16 certification, which verifies their controls and processes for data backup and retrieval. In terms of backup and reliability, we believe this is a much better solution than shuffling files around manually. More information about the security of our cloud platform is available is available here.
Is there any cost associated with using this new capability?
No, it is free to try out and use and includes 10 GB of data storage. You can find out more and sign up for free here.
Look for our new Applied Biosystems Sanger Analysis Modules to launch around the middle of April. Our Applied Biosystems qPCR Analysis Modules are available today as is a Sanger quality control analysis module. Upload some data today and share it with a collaborator. We anticipate that we will be continuing to grow the content available on Thermo Fisher TM Cloud.