Genomic research and precision medicine hold a great deal of promise but there are some still some challenges that must be overcome before their potential can be fully realized. Exploring solutions for these challenges was a key topic of conversation at Bio-IT World 2018.
We had the opportunity to talk with NetApp’s David LaBrosse and PetaGene’s co-founders Dan Greenfield, and Vaughan Wittorff after Bio-IT World 2018 about these challenges and the way forward for the field. “The field of genomic research has come so far, so quickly,” said LaBrosse “but it’s clear that in addition to meeting regulatory requirements, there are other challenges that need to be addressed in order to move from concept to making precision medicine a viable part of everyday treatment plans.”
The challenges that LaBrosse is referencing are how to manage the time and expense of genomic research and enabling collaboration when dealing with data volumes that defy imagination. PetaGene’s Vaughan Wittorff agreed that “While the cost of genomic sequencing has fallen dramatically in the last decade, the number of applications has also increased — like RNA and single cell sequencing — that can provide greater guidance for medical treatment.”
These changes have resulted in a deluge of highly useful data, but have also further slowed processing and analysis times, which, as Dan Greenfield noted, is not an option for a patient with a life-threatening disease waiting to begin a treatment protocol. “Patients with a cancer diagnosis need to get started on their protocols as quickly as possible,” Greenfield said. “Our mission at PetaGene is to get data into a manageable format so that it can be moved quickly and inexpensively between all the different groups that need access to the data in order to develop therapies and protocols.”
Greenfield, Wittorff, and the PetaGene team do this by compressing data to as much as one tenth its original size. The data is decompressed on-the-fly and presented back to the user with random access in the original format and even with the original file name, making it easy to share data and collaborate while also reducing costs and accelerating speed.
“Traditionally, cloud adoption has presented several big challenges. First, moving data to the cloud has taken a very long time. Secondly, in order to put it to work once there, it has to again be moved from the object storage part of the cloud to the compute part of the cloud. Finally, to get the results back, the whole process happens again in reverse,” Greenfield shared. “Being able to do lossless ‘just in time’ decompression with our non-cloud product already has a big impact. But now with PetaGene’s Cloud Edition a user is able to take a regular pipeline that works on local storage, and within minutes, run that pipeline on the cloud without modification, streaming directly from object storage with highly-compressed data. This addresses one of the biggest challenges the pharmaceutical and medical communities have had.”
Indeed, a global pharmaceutical leader has used PetaGene’s transparent lossless compression solutions to enable their research. Transparent lossless compression is an essential part of the company’s commitment to identifying genetic sequences that are associated with diseases and will provide a pathway to treatment. “Data compression makes storing data in the cloud feasible, which will drive collaboration between researchers, and accelerate outcomes,” Wittorff said.
With that vision and the 2018 Bio-IT World Best in Show award for Storage Infrastructure and Hardware for PetaSuite Cloud Edition in hand, the future looks bright, both for the team at PetaGene and for the solutions that will come from pharmaceutical companies and medical researchers having accessible, affordable tools for genomic research and precision medicine.
Catchup with Dan Greenfield and David LaBrosse on Wednesday June 27th, 2018 at 11am US Eastern as they share how organizations can achieve faster genomic data sharing, paving an accelerated path to improved patient care. Register here.