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With Stanford's Expertise, Personalis Plans to Focus on Clinical Interpretation of Human Genomes


By Julia Karow

Founded by a team of researchers
from Stanford University with expertise in genome analysis and sequencing technology, Personalis will focus on the medical interpretation of human genomes for research and, eventually, clinical applications.

The startup, based in Palo Alto, Calif., began operations last month and plans to add an R&D and customer support site in Cambridge, UK, in the near future.

Among the Stanford founders are Russ Altman, chair of the bioengineering department; Euan Ashley, director of the Stanford Center for Inherited Cardiovascular Disease; Atul Butte, chief of the division of systems medicine at the department of pediatrics; and Michael Snyder, chair of the genetics department and director of the Stanford Center for Genomics and Personalized Medicine.

John West, the former CEO of Solexa, which was acquired by Illumina in 2007, is the new firm's CEO.

The founding team has proven expertise in interpreting human genomes with an eye toward medical and pharmacogenomic information. Altman, Ashley, and Butte were the lead and senior authors of the first published clinical interpretation of a human genome, that of Stanford colleague Steve Quake, which appeared in the Lancet last year (IS 5/4/2010).

The company resulted from a collaboration between West, Altman, Ashley, Butte, Snyder, and others on the interpretation of West's genome and those of his wife and two children, which led to a publication in PLoS Genetics earlier this month (CSN 9/20/2011).

Following that project, the team realized that as genomes of hundreds of families are sequenced for research studies, their interpretation will no longer be feasible in an academic setting, so it would make sense to form a company.

Personalis has licensed intellectual property from Stanford, including patent applications and databases that are "generally in the area of interpretation of human genomes," West said.

The company is not yet providing specifics on its IP, but Altman spearheaded the development of PharmGKB, a database that provides information on genetic variants linked to drug response, and Butte is the principal investigator of Varimed, a database of variants associated with disease.

The company expects to complete a Series A funding round within the next few weeks, West said, with three venture capital firms as the main investors: Abingworth, an original seed investor in Solexa; Mohr Davidow, which also provided funding for Navigenics, Pacific Biosciences, and RainDance Technologies; and Lightspeed Venture Partners, which has traditionally invested in IT companies.

Personalis' website lists under "major investors" Jonathan MacQuitty, a partner at Abingworth; Chris Schaepe, founder of Lightspeed; Sue Siegel, general partner at Mohr Davidow and former president of Affymetrix; and Hermann Hauser, a founder of Amadeus Capital Partners, which invested in Solexa.

With funding in hand, the company plans to ramp up its staff over the next few months. West did not disclose the number of people he plans to hire but said that analyzing genomes "is not something that would be practical on the level of just five or 10 people — it needs to be a much more substantial team to take this on."

The company is already recruiting, with open positions in bioinformatics, curation, sequencing accuracy, finance and administration, intellectual property, and strategic marketing advertised on its website.

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As it aims to serve the international research market, Personalis plans to open an R&D and customer support site in the UK in order to be "reasonably close to customers," West said. The Cambridge office will also facilitate collaborations with European customers and conversations with European regulators. Other important potential customers are located in Asia, West added, and the firm might open an Asian office in the future as well.

Medical Interpretation

Within a year or less, Personalis plans to launch its first product. It has not yet disclosed exactly what this product will be, but its core capability will be the medical interpretation of human genomes, not sequencing technology. "There might be a variety of different ways that this could be implemented," West said.

The firm has also yet to disclose its business model, but "the most straightforward way for us would be a fee-for-service basis where [researchers] have genomes that have been sequenced by other companies, and they bring that kind of data, and we can analyze that," West said, adding that the company is "certainly open to other kinds of arrangements."

Personalis' strategic focus will be on interpreting whole human genomes, maybe supplemented with other information such as transcriptome data, West said, though a customer with a "substantial number of exomes" would also find its tools useful.

No pricing information for the interpretation of a human genome is available yet, but West said the time and effort involved is "extensive" and "not an insignificant cost." Pricing may vary according to the level of interpretation desired by the customer, and there will likely be volume-based discounts, he said.

Personalis expects to work closely with a variety of sequencing technology and service providers — including Illumina, Complete Genomics, and others — some of which are looking for third-party partners that offer interpretation services.

Illumina's individual genome sequencing service, for example, currently refers its customers to a variety of companies for the "secondary interpretation" of their genomes, including 23andMe, DeCode Genetics, Knome, Navigenics, and Pathway Genomics.

Initially, the Stanford startup plans to target the research community as its customers, but longer term, it wants to move into clinical applications where results would be returned to patients, which West said will require regulatory approval.

To that end, the company plans to have conversations with the US Food and Drug Administration and the European Medicines Agency about the best way to go about this.

"Our experience so far is that these agencies understand that this is something that's coming, it's coming faster than they originally anticipated, and they need some expert guidance on how to go about this," he said. "I think in many ways, the approaches that they have used all along are fitting, in the sense that if you have a medical result that a physician is going to rely on for treatment of a patient, you have to be pretty confident about the accuracy of that [result]."

The firm is not going to be offering its services directly to consumers, though. "The kind of work we're interested in doing will lead to quite serious medical diagnostic information, and that's appropriate in a medical setting with the guidance of physicians and in the full context of the other diagnoses and treatments," West said.

Providing accurate results will be a key focus of the company. The accuracy of next-gen sequencing technology has improved over the last several years, but different platforms still do not always produce concordant results.

"The scale of the problem is quite substantial," West said. For example, in an unpublished project where the same genome was sequenced on two different platforms, the two datasets differed in 400,000 single-nucleotide variants, or about 10 percent of the total number of SNPs. "To have 400,000 differences in an area where a single SNP can make a substantial medical difference … is a real problem," West said.

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Accuracy can be improved not only on the sequencing technology side but also using bioinformatics, he said. For example, sequencing and comparing the genomes of parents and children reduces the error rate about 10-fold, and using improved reference sequences that include the major alleles of the population studied further improves variant calling.

West said it is too early to talk about how Personalis will differ from competitors that are also providing clinical human genome interpretation services for researchers, such as Knome (CSN 8/9/2011) or Omicia (CSN 6/29/2011). "Once we have our product out, that will perhaps become more clear," he said.

Prior to launching its first product, Personalis will get its feet wet by analyzing "quite a few genomes" internally in order to validate its approaches and to build experience. It expects to present results from this work at conferences and in peer-reviewed publications.

Have topics you'd like to see covered in Clinical Sequencing News? Contact the editor at jkarow [at] genomeweb [.] com.