Genome Knowledge Platform
“We have responded to the call for a system to manage the volume and complexity of next-generation sequencing analysis,” says Ben Salisbury, Ph.D., vp of clinical genomics at Knome.
“We have built the knoSYS™ 100, an end-to-end software and hardware platform for developing, running, and sharing in silico genetic tests.”
The knoSYS provides a pipeline that includes sequence alignment, variant calling, interpretation, and reporting. Users can set up their own parameters and filters, and add their institutional knowledge to variant annotation. Different regions of the genome may require different querying strategies. As users develop these querying strategies, Knome facilitates the exchange of query panels between users, allowing expertise to be shared.
The company says that it is recruiting customers and other experts to develop panels that will run on the knoSYS. These panels can then be tailored by recipient labs to reflect their own preferences and adjusted to accommodate differences that arise from variation in production processes.
Knome’s software runs on a high-performance computing grid, installed directly at the customer site. “We specifically did not pursue the cloud computing option,” says Dr. Salisbury. “Many institutions are wary of putting their sequence data in the cloud. On-site computing also avoids wasting valuable time transferring enormous raw data files to remote servers.”
The hardware component of the knoSYS is expandable, designed to grow as the lab’s testing volume expands.
“Another critical feature of our system, and any system that will be successful going forward,” said Dr. Salisbury, “is the ability to re-query stored genomic sequence. That includes capturing information updates that alter interpretation of earlier analyses, and the ability to run new panels, new tests, as new concerns arise for an individual.”
Currently, the company is focusing on Mendelian diseases and cancer-related somatic variations. Knome has designed the knoSYS as a modular system that can incorporate new databases and align and call solutions. One module that has already been incorporated is the align and call software developed by business partner Real Time Genomics, which uses clever algorithms to accelerate analysis and incorporates joint calling and pedigree information to increase variant calling accuracy.