Human Genome Informatics Interpretation System Designed to Break the Genomic Logjam

The first plug-and-play, fully integrated hardware and software system has been developed to help researchers in medical and academic institutions translate human whole genomes. The technology was developed to help geneticists study diseases of undetermined cause, identify pertinent genetic variation, and create next generation in silico gene tests.

Knome, Inc. (Cambridge, MA,USA) reported that the knoSYS100 system will begin shipping in the fourth quarter, 2012. In silico superpanels will allow hundreds of disorders to be tested simultaneously and provide the opportunity to develop of a new class of molecular diagnostics for complex, multi-gene disorders, according to company spokespersons.

Starting at USD 125,000, the knoSYS100 is based on Knome’s big data informatics technology. The system will work with next-generation sequence data from leading sequencers, including those marketed by Illumina, Life Technologies, and Complete Genomics.

With a median throughput of one genome per day, the technology eliminates the current informatics bottleneck in whole genome interpretation--similar to the speed of the current fastest sequencers. In addition to providing geneticists with query and visualization applications for conducting in-depth research into sets of whole genomes, the knoSYS100 comes with tools and libraries that allow developers to create in silico gene tests that can be run by just pushing a button.

“The advent of fast and affordable whole genome interpretation will fundamentally change the genetic testing landscape,” said George Church, PhD, professor of genetics at Harvard University (Cambridge, MA, USA), and co-founder of Knome. “The genetic testing lab of the future is a software platform where gene tests are apps. This will shift genetic testing from a fixed, lengthy process to a rapid and highly dynamic one that makes full use of the data contained in the entire genome.”

Developers can employ the libraries and applications included with the knoSYS100 to replicate existing single gene tests in software. They can also go further, creating next generation superpanels that examine thousands of genes, as well as incorporate artificial intelligence algorithms; deep reference data on protein interaction and expression; statistical functions; and the power of kindred, population, and tumor/nontumor comparison.

“In silico superpanels allow hundreds of conditions to be tested simultaneously and open the door to the development of a new class of molecular diagnostics for complex, multigene disorders,” said Dr. Church. “Moving from a world of assays to apps [applications] will expand the definition of what a gene ‘test’ actually is, raising important questions but also presenting tremendous opportunities to help improve human well-being.”

To demonstrate the system’s capability, the technology will include several superpanels for research into cancer, epilepsy, heart disorders, and other conditions.

The knoSYS100 is an integrated hardware and software system constructed around Knome’s core big data informatics technology, used to decode thousands of whole human genomes and exomes for medical, pharmaceutical, and academic research projects. The components of the system include an innovative informatics engine, which is a scalable informatics engine (kGAP) that rapidly converts sequence data generated by different sequencing platforms into standardized, precisely annotated, and easily comparable data sets. kGAP draws on an ever-growing, harmonized knowledge base of reference information from more than a dozen different third-party data sources.

Sophisticated genome interpretation applications include query and data visualization applications that allow users to access kGAP-enhanced genomes to perform in-depth research to locate the variants, genes, gene sets, and pathways that underlie disease, drug response, and tumor growth.

Functionality for developing next generation gene tests are include within the system with tools and scripting libraries that enable medical researchers to create and share next generation, in silico gene panels on whole genomes and exomes processed through kGAP.

The technology is a genomics supercomputer: the knoSYS100 is optimized for the intensive processing and I/O (input/output) requirements of whole genome informatics. Running at over 1.2 teraFLOPS, it includes four 2.4 GHz 8-core/16-thread Intel Xeon E5-2665 processors, and 18 TB to 54 TB of useable disk storage and Gigabit Ethernet--all contained in a secure, soundproofed enclosure that can be placed in a laboratory environment.

Because the knoSYS100 is installed on-site and is maintained behind the client’s firewall, it is suitable for institutions that do not need to send genome data to third parties or the cloud due to privacy, consent, or confidentiality concerns.

“There are close to 2,000 next-gen sequencers in labs around the world generating enormous amounts of data,” said Knome chief executive officer Martin Tolar, MD, PhD. “Every one of those sequencers should have a knoSYS100 right next to it. To further facilitate the application of genomics in patient care, we are investing over USD 50 million in R&D over the next several years. This is where we intend to make a lasting contribution to molecular-based, precision medicine.”

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