Unique turnkey cluster appliance offers privacy, security, and file transfer speed
When Knome needed a turnkey hardware platform for its knoSOFT genome interpretation application and kGAP informatics engine, it turned to Seattle-based solutions provider Silicon Mechanics. Knome had been using Amazon Web Services (AWS) for computationally intensive tasks, but needed to provide a locally-installed system with full control for clinically-oriented customers, who are sensitive about security, version control, and file transfer times.
Working closely with Silicon Mechanics, Knome developed the knoSYS100, which is a combination of Knome’s software and a hardware platform configured by Silicon Mechanics. The system is designed to provide labs with an end-to-end solution for the interpretation of human genome, exome, and targeted sequence data.
Seeking in-house solution
Cambridge, MA-based Knome provides human genome interpretation systems and services, working with pharmaceutical companies and medical researchers to understand the genetic basis of disease, tumor growth, and drug response. In its Interpretation Services division, the company has worked with researchers on a wide range of diseases, including Parkinson’s, Alzheimer’s, asthma, and cancer. Typically, the informatics for large interpretation projects, covering hundreds to thousands of genomes, would be processed in the cloud using AWS.
In 2012, as the market began to turn toward clinical applications, Knome recognized the need for labs to have internal interpretation capabilities. Instead of interpreting a large number of genomes in order to understand a specific disease, the requirement is to address the medical needs of one individual or family. In the clinic, processing and comparing large numbers of genomes is not as important as turnaround time, privacy, security, and version control.
To meet the demands of the newly emerging clinical market, Knome decided to develop an end-to-end system that would enable a lab to effectively handle the computational and interpretation requirements of next-generation sequencing-based tests within their own facility.
One of the most basic issues to be tackled is the transfer of files that are often over a terabyte in size. To transfer files this size to the cloud is typically too time consuming to be practical in a commercial environment. Even a relatively small file of 200 gigabytes can take two days to upload to the cloud. In addition, clinics have significant concerns regarding security and privacy; most early adopters want to keep their patients’ genomic data behind their firewall.
“Ultimately, privacy, security, and transfer speed drove us towards an in-house approach, so we began the process of deciding what hardware would be needed to perform all the computational tasks that AWS did for us in the cloud,” said Michael McManus, Senior Vice President of Knome.