Knome Introduces the knoSYS™100

First Plug-and-Play Human Genome Interpretation System

CAMBRIDGE, MA –  September 27, 2012 – Knome Inc. announced today that it is taking orders for the knoSYS™100, the first plug-and-play, fully integrated hardware and software system designed to help researchers in medical and academic institutions interpret human whole genomes. The knoSYS™100 was developed to help geneticists discover relevant genetic variation, investigate diseases of unknown cause, and create next generation in silico gene tests.

Starting at $125,000, the knoSYS™100 is based on Knome’s big data informatics technology. The system will accept next generation sequence data from leading sequencers, including those sold by Illumina, Life Technologies, and Complete Genomics.

Breaking the genome interpretation bottleneck

The difficulty and cost associated with human genome sequencing has largely been addressed, with the cost of sequencing a whole genome expected to decline to under $1,000 in 2013. But it still takes a team of researchers weeks to months to annotate, compare, and interpret genome data. This slow pace and the lack of robust tools have significantly limited the ability of researchers to scale the process of interpreting human genomes.

With an average throughput of one genome per day, the knoSYS™100 eliminates the current informatics bottleneck in whole genome interpretation—matching the speed of today’s fastest sequencers.

“In the first half of this year, we saw the demand for genome interpretation surge as researchers in many of the world’s leading medical institutions started preparing for the broad utilization of whole genome interpretation for patient care,” said Martin Tolar, MD, PhD, Chief Executive Officer of Knome. “All of these institutions face the same issue—how to industrialize genome interpretation so that it is not only accurate, but fast.”

More than a dozen of the world’s top medical institutions have joined an early access program to pilot Knome’s genome interpretation technology, including: ARUP Laboratories, Cedars-Sinai Medical Center, Cincinnati Children’s Hospital, The Hospital for Sick Children (SickKids) in Toronto, Hyundai Cancer Institute at CHOC Children’s, University of Liverpool, and University of Verona.

An in silico genetic testing “lab in a box”

In addition to providing geneticists with query and visualization applications for conducting in-depth research into sets of whole genomes, the knoSYS™100 ships with tools and libraries that allow developers to create in silico gene tests that can be run at the push of 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 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 use the tools and libraries included with the knoSYS™100 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/non-tumor 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, multi-gene disorders,” said Dr. Church. “Moving from a world of assays to apps 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.”

As a demonstration of capability, the knoSYS™100 will include several superpanels for research into cancer, epilepsy, heart disorders, and other conditions.

The system

The knoSYS™100  is an integrated hardware and software system constructed around Knome’s core big data informatics technology, used since 2008 to interpret thousands of whole human genomes and exomes for medical, pharmaceutical, and academic research projects. The components of the knoSYS™ 100 include:

• State-of-the-art informatics engine: a robust and scalable informatics engine (kGAP™) that quickly transforms sequence data produced by different sequencing platforms into standardized, richly annotated, and easily comparable data sets. kGAP draws on an ever-growing, Knome-curated and harmonized knowledge base of reference information from more than a dozen different third-party data sources.
• Advanced genome interpretation applications: query and data visualization applications that allow power users to access kGAP-enhanced genomes in order to conduct in-depth research to find the variants, genes, gene sets, and pathways that underlie disease, drug response and tumor growth.
• Functionality for developing next generation gene tests: 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.
• Genomics supercomputer: the knoSYS™100 is optimized for the intensive processing and I/O requirements of whole genome informatics. At nearly 600 lbs. and running at over 1.2 teraFLOPS, it includes four 2.4GHz 8-core/16 thread Intel^® Xeon^® E5-2665 processors, and 18TB to 54TB of useable disk storage and Gigabit Ethernet—all contained in a secure, sound-proofed enclosure that can be placed in a laboratory environment.

Since the knoSYS™100 is installed on-premises and is maintained behind the client’s firewall, it is well-suited for institutions that do not wish 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 knoSYS™100 right next to it. To further facilitate the application of genomics in patient care, we are investing over $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.”