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Desktop Genetics Nabs Illumina Investment on Heels of Lab Automation Deal with Transcriptic

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NEW YORK (GenomeWeb) – Genome editing software maker Desktop Genetics today announced an investment from Illumina, for an undisclosed amount. The funding comes as Desktop Genetics seeks to automate the genome editing process, from target selection to validation of edited cell lines.

The deal with Illumina follows a £1.4 million ($2.2 million) fundraising round announced in September and a partnership with lab automation company Transcriptic, announced last month.

Illumina did not respond to GenomeWeb's request for further comment on its investment in Desktop Genetics. However, in a statement, Nicholas Naclerio, Illumina's senior VP of corporate and venture development noted that the company has "been impressed by [Desktop Genetics'] proprietary Deskgen platform for CRISPR-based gene editing. CRISPR is becoming increasingly important for NGS applications, and we are pleased to support [Desktop Genetics] in executing their vision to build this market."

London-based Desktop Genetics' Deskgen platform allows scientists to design guide RNAs (gRNAs) for CRISPR/Cas9 genome engineering. The gRNAs are what make CRISPR/Cas9 a programmable, and therefore powerful, technology. The firm said today that it would use the money from Illumina and its fundraising round to develop its platform and refine its CRISPR-related algorithms, which can evaluate a gRNA for both on-target efficiency and specificity.

But Desktop Genetics Chief Business Officer and Co-Founder Edward Perello told GenomeWeb that the investments and its partnership with Transcriptic put the firm on track to do so much more.

"This is a new model of doing biotech," he said. "This is genome editing from your laptop without having to use a lab."

Perello said he wants Desktop Genetics to do for genome editing in biotech what cloud computing has done for computer technology: reduce startup costs and other barriers to entry. "Today if you want to start a biotech company, you have to buy all the equipment, you have to set up a lab, and hire PhDs to do cloning. Its excessively expensive and unnecessary and we want to get rid of that."

The partnership with Transcriptic, which has developed equipment and software to automate routine laboratory procedures, is the first step in automating every step of the CRISPR-based genome editing process.

Desktop Genetics' users, which include both academic and commercial enterprises, will often request a library of gRNAs to edit particular targets. For example, teasing out the roles of a network of genes might require multiple guides to hit multiple targets, in multiple combinations. "Guides are more effective when designed with a specific application in mind," Perello said. "What we do is consider the experimental intent and design guides that are appropriate for that and we'll design a library for the specific cell line, the desired outcome, and make sure we use guide design rules that are state of the art based on latest industry know-how and the academic literature."

The Transcriptic partnership allows Desktop Genetics to deliver synthesized CRISPR gRNA libraries to its customers on a plate and at a low price, Perello said. Under the terms of the agreement, Desktop Genetics will combine its proprietary design algorithms with Transcriptic's automated, high-throughput assembly methods.

Pricing depends on the number and complexity of gRNAs, but partnering with Transcriptic will lower the price-per-construct by up to a factor of ten, compared to other companies that can synthesize gRNAs.

Menlo Park, California-based Transcriptic has developed what it calls "workcells," self-contained boxes that are miniature, automated molecular biology laboratories. Measuring 20 feet long, 10 feet wide, and 10 feet high, Transcriptic's workcells contain a robotic arm and an assortment of off-the shelf biotechnology equipment, such as plate sealers, shakers, thermal cyclers, imaging systems, and even fridges and plate hotels, Tom Driscoll, VP of business development told GenomeWeb.

"What we're trying to do is take the human hands out of the grunt work at the bench and allow scientists to put more mindshare into designing experiments," he said.

Transcriptic launched in 2012 and has been offering commercial services for just over a year. It has three functional workcells and closed a Series A financing in June, Driscoll said.

Perello said he knew about Transcriptic even before he founded Desktop Genetics. "We've been looking for a way to work with a company like this for a long time," he said. While the firms are initially focused on the CRISPR guide library service, automated lab work could be essential to Desktop Genetics as it improves its core business of CRISPR design.

The firm is writing machine learning-based algorithms to determine the underlying rules governing on- and off-target activity for different gRNAs in different CRISPR applications. To do so, it needs standardized data sets to train the algorithms. Perello said that combining data from different labs doesn't work for that purpose, so at some point it will need automated workflows to generate a unified data set.

While it has already signed partnerships with Horizon Discovery and Transcriptic, Perello said Desktop Genetics is looking for more, to help it add functionality to its platform.

At the moment, the firm is exploring partnerships that would allow scientists to seamlessly put their CRISPR libraries into lentiviral vectors, which can be an efficient way to transfect certain types of cells that are otherwise difficult to do CRISPR with.

Also on the firm's wish list is to hook up the Deskgen platform to next-generation sequencing data streams. NGS could bookend the genome editing process, Perello suggested. Sequencing an organism or cell line would allow scientists to design gRNAs against their particular genome of interest, rather than a reference genome. And sequencing after genome editing can verify that the desired intervention actually took place and help determine off-target effects.

Desktop Genetics currently offers to integrate those data into the CRISPR process on the back end and as a service. "Down the line, we would look for the transfer of data to be seamless," Perello said, "so that the advantages of NGS coverage and accuracy can really be paired with the core advantages of CRISPR."

"What we aim to do is to make it plug and play, so that anyone can do it, so we can just walk users through this and unlock gene editing for any scientist or commercial lab," he said.

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