Knome Expands Sequence Service to Research Community



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By Kevin Davies

November 18, 2009 | Knome, the first company to offer complete personal genome sequencing to the (high-end) consumer market, is expanding its offerings to biomedical researchers and clinical investigators with KnomeDISCOVERY. Knome calls it the first “platform agnostic human genome sequencing and analysis service for researchers.”

According to CEO Jorge Conde, Knome is expanding its DISCOVERY Platform offering to researchers interested in the sequencing and analysis of either partial or whole genomes. Pricing will start at less than $12,000 for targeted sequence or exome analysis to about $70,000 for whole genome studies. “We’d essentially take samples, sequence them, do the analysis we’d do for the consumer, and deliver to the researcher and have them take the next step.”

As sequencing costs tumble, Conde says, “The problem is, what do you do with the data? There will be an interpretation bottleneck. We’ll take anything -- that’s the pain point we’re trying to address. We’re giving researchers an opportunity to tap into something we’ve already built.”

Knome has slashed the cost of its personal genome sequencing operation from $350,000 in 2007 to $99,000. As it did so, Conde says that Knome saw a shift in the interests of its personal genome clients. “When we started, most of the folks we were working with were technophiles,” says Conde. By contrast, “a lot of the folks we’re looking at now are trying to get a specific question answered.”

Earlier this year, Knome auctioned a personal genome sequence on eBay, the winning bid coming from an anonymous European for $68,000. Knome quietly pegged its genome price at that level ever since, even beginning to do some small family studies for “people who had something that ran in their family and weren’t sure what it was.” Conde says they were using this as “a hypothesis-generating machine.”

As Knome gained experience of hunting for candidates to answer specific questions, it started to hear from researchers who, in Conde’s words, said: “I’ve got a bunch of samples, but we don’t have the infrastructure to do all of the ‘data crunching.’” Conde thought: “We’re already treating each client as a research project… Why don’t we partner up with researchers with domain expertise and act as, for want of a better term, a discovery support service?”

Knome’s Genome Analysis Platform (kGAP) has automated a lot of the sequence analysis. “kGAP enables us to upload a genome into the environment and it will map it against various indexed data sources,” Conde explains. The resulting information on sequence variants then flows into Knome’s browsing software.

Conde insists that Knome’s operation is more complementary than competitive with Illumina’s $48,000 personal genome sequencing service, launched last summer, or Complete Genomics. “Nothing would make us happier than have somebody who has worked with Complete Genomics come to us and say, ‘I have all this data, what do I do with it?’” says Conde. “It’s not trivial. From our experience, you get handed over a genome, its 700 Gigabytes to 1 Terabyte of data. Some researchers at certain institutions might be able to handle that, but clinical investigators won’t.”

Knome currently outsources its clients’ sequencing to the Beijing Genomics Institute, Shenzhen, China, and SeqWright in Houston. “We’ll also work with Illumina, if and when they’ll have us,” says Conde. “We’re obviously not a sequencing company. As more platforms become available -- especially if the combination of Knome with that [sequencing] provider can offer something unique -- we’re obviously happy to work with those folks. We’re going to make kGAP flexible in terms of what data it can receive. We don’t want the [sequencing] platform of origin to be an issue.”

Knome’s new offering will inevitably attract comparisons with Complete Genomics, which charges $5,000-20,000 for whole genome sequencing (depending on volume). Complete published the results of three human genome sequencing projects in Science earlier this month. But Knome’s proprietary analysis software, honed over two years of offering personal genomic sequencing, is likely to be as sophisticated as anything currently available.

Knome sees its new offering appealing particularly to two constituencies: first, researchers with expertise in medical genomics who want to streamline data management and preliminary analysis in mass sequencing projects. Knome can handle rapid-turnaround sequencing and “background” genome analysis, freeing researchers to focus on specific question-driven hypothesis testing that can yield novel discoveries in genetic medicine. The other target group would be clinically trained specialists in various disease areas lacking expertise in genome sequencing and analysis. Knome says it can help these researchers pinpoint disease-causing mutations.

Harvard's George Church, Knome co-founder, commented: “We are excited to bring the scientific research community the type of genome sequencing and data analysis services that have previously only been available to a small number of individuals at large institutions.”

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