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Personalis Launches Cancer Assays, Updates Clinical Exome, Expands International Business

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This article was originally published Oct. 23.

NEW YORK (GenomeWeb) – Personalis has been expanding its human genome and exome sequencing and analysis business outside the US while broadening its reach into clinical and research markets with new and updated products for tumor research analysis and inherited disease diagnostics.

"Our expectation is that the clinical side of our business will grow and grow over time," CEO John West told Clinical Sequencing News, though in the short term, the majority of revenue will likely come from research and clinical trial services. Typically, Personalis launches a new product as a research service first before turning it into a clinical product after taking the necessary validation and regulatory steps, he said.

The Menlo Park, Calif.-based company has made a string of announcements recently pointing to a demand for its services. For example, earlier this month it said that it has partnered with the Garvan Institute of Medical Research in Sydney, Australia to provide human genome sequencing and interpretation services to researchers and clinicians worldwide.

Personalis also won a contract from the US Department of Veterans Affairs to provide clinical exome testing services, though West declined to provide further details about the contract, including its size, citing a request from the VA department. Under an earlier contract with the VA announced in 2013, Personalis has already sequenced several thousand samples for research purposes, including the Million Veteran Program. Most of these are exomes but they also include whole genomes, West said.

The firm also was recently shortlisted by Genomics England, along with nine other companies, as a potential service provider for the UK's 100,000 Genomes Project.

In addition to these partnerships, last week at the American Society of Human Genetics annual meeting Personalis introduced two new cancer sequencing and analysis services, the ACE Exome for Cancer and the ACE Extended Cancer Panel, following an update of its ACE Clinical Exome test for inherited genetic disease the previous week.

Expanding abroad

According to West, the company now has customers in 10 countries, including five in Asia, and continues to expand internationally. The Garvan Institute, one of the first customers of Illumina's HiSeq X Ten platform for human whole-genome sequencing, seemed like a good partner to access markets in Australia and other countries in the area, he said, as well as to broaden Personalis' services, which have been largely focused on exome sequencing, in the area of whole-genome sequencing.

While details of the joint services, including their start date, have not been finalized yet, the partners will likely have different offerings, including whole-genome and exome sequencing. Initially, these services will be for research, but "there is also an interest on both sides to explore clinical opportunities," West said.

Personalis has experience with diagnosing Mendelian diseases from whole-genome sequence data as part of research projects, he said, "and in the future, we expect that could become a clinical offering." However, a clinical whole-genome sequencing test would need to be validated first, which will take time, he cautioned.

Overall, international expansion has been "an important step for us," West said. Besides the partnership with Garvan, Personalis has distributors of its own services in several countries, in particular in Asia, and it opened a subsidiary in the UK last year.

Entering the cancer market

The introduction of two new services this week, the Accuracy and Content Enhanced, or ACE, Exome for Cancer and the ACE Extended Cancer Panel, marks Personalis' entry into the cancer analysis market, initially for research use only.

Both services analyze a set of more than 1,300 cancer-related protein-coding genes and more than 200 cancer-relevant miRNA genes, and both combine a DNA and an RNA assay from the same sample. However, one test covers the gene set deeply, while the other is an exome sequencing assay.

West said that customers have been asking for a cancer test that combines both DNA and RNA analysis. Depending on their research goals, they might choose either one or the other test. Personalis is not disclosing the price of the products, but he said they are "not as different in price as you might expect."

The ACE Extended Cancer Panel targets only the cancer gene set and provides more than 500x average sequencing coverage, enabling researchers to detect mutations in tumor subpopulations.

The ACE Exome for Cancer, on the other hand, sequences the entire exome, with enhanced coverage of more than 8,000 medically relevant genes, so researchers can use the additional information to discover new mutations in genes not previously associated with cancer.

Personalis has validated the tests internally using a variety of standard samples and different sample types, such as FFPE samples, fine needle aspirates, and core biopsies. A lot of effort has gone into methods to extract DNA and RNA from the same FFPE sample, he said.

The company has been offering the services to several early customers, including academic groups and pharmaceutical companies, and a "major pharmaceutical company" recently closed a multi-year, multi-million-dollar contract with Personalis to use the tests, West said.

For now, Personalis is offering the cancer services for research use only but is considering their development for clinical use in the future.

During the first half of 2015, the company plans to launch a "technical CLIA version" of the tests, which means they will comply with the quality standards required under CLIA but will not provide diagnostic interpretations of the results for individual patients.

The CLIA version of the assays, which would still be considered for research use only, would be of particular interest to pharmaceutical firms wanting to generate data to submit to the FDA, West said.

Sequencing for the cancer tests will be conducted in Personalis' own CLIA-certified and CAP-accredited laboratory, which also runs the ACE Clinical Exome, its only clinical test so far.

The clinical lab is now licensed in all US states except for New York, which Personalis plans to add in the future.

Updating rare disease clinical exome

A year ago, Personalis launched the ACE Clinical Exome test for the diagnosis of rare Mendelian disorders, its first clinical offering, and last week the company provided an update for the test.

Counting both clinical and research exomes, Personalis has now analyzed several thousand samples, West said, providing it with data to refine the test.

The diagnostic yield of the ACE Clinical Exome test has continued to exceed 50 percent, he said, which is more than what most other laboratories have reported. He declined to say how many clinical exomes the company has run so far but said that many of the patients were considered challenging cases and had undergone other genetic tests before.

The reason for the high diagnostic yield appears to be a combination of factors, he said, including the sequencing coverage, capture, enhanced human reference, curated database with links to the literature, and clinical expertise.

The updated test covers the entire exome but augments coverage for more than 8,000 medically relevant genes. Of those, more than 6,000 have at least 99 percent of their exons sequenced at more than 20-fold coverage.

This relatively high sequencing depth has allowed clinicians to detect mosaic variants, which have played a role in several diagnoses, West said, adding that there seems to be "a substantial underreported number" of patients with mosaic mutations. Those mutations would not have been found by a whole-genome sequencing assay, he added.

The test also includes disease-associated non-coding regions and analyzes "a large number" of medically relevant variants in untranslated regions, introns, and promoter regions, which West said the company has found "quite useful" clinically.

In addition to the exome, the test includes a separate, sequencing-based assay to detect structural variants throughout the genome.

The turnaround time for the test is 12 to 14 weeks, and the price continues to be $7,500 per case, which includes the exome of the proband and, if appropriate, of the parents. Other configurations of the test that only include the proband, or additional family members, are also possible.

On the analysis side, Personalis has tripled the size of its clinical team, which includes physicians, genetic counselors, and variant interpretation specialists. It has also formed a clinical review board, consisting of Personalis staff as well as outside clinical experts, that interprets patient cases and helps improve the clinical exome test.

The board, which is headed by Robert Nussbaum, a medical geneticist at the University of California, San Francisco, includes specialists in neurology, cardiology, hereditary cancer, immunology, and dysmorphology.

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