Precision medicine company Tempus has been expanding its data-driven approach to diagnostics even further over the past few months by entering the infectious disease market, starting with COVID-19.
In May, the Chicago-based company, which has grown to 1,600 employees, announced that it was launching a diagnostic COVID-19 PCR test at its CLIA-certified and CAP-accredited laboratories in Chicago and Atlanta while developing a sequencing-based respiratory pathogen panel. Earlier this month, Tempus received Emergency Use Authorization for its test – a modified version of the Thermo Fisher Scientific ABI TaqPath COVID-19 Combo Kit – from the US Food and Drug Administration.
In addition to offering diagnostic SARS-CoV-2 testing, Tempus started an initiative to structure and aggregate real-world clinical and genomic data from up to 50,000 COVID-positive patients, including RNA-seq transcriptome data from up to 10,000 patients, in collaboration with academic partners, with the goal to better understand the disease and how it affects different people.
In June, the company also appointed Christopher Mason, an associate professor of physiology and biophysics at Weill Cornell Medicine, as its VP of emerging genome technology, tasking him with developing and advising on technologies for next-gen sequencing, computational methods for linking clinical metadata to omics data, and studying the host response to COVID-19.
Mason said he is not permanently leaving Weill Cornell but plans to take a leave of absence for several months to focus on COVID-19-related research and development at Tempus and several other organizations. “I’m basically doing a COVID-19 mini-break to just help as many people as I possibly can,” he said.
Tempus CEO Eric Lefkofsky said the company’s machine learning and artificial intelligence approach to diagnostics, which adds different types of patient data to a test result, can be applied to many disease areas. While the company started out in cancer, it announced plans to move into depression and cardiology last year and felt ready to branch out even further. “We were looking to expand into other disease areas when COVID hit, so we just prioritized infectious disease,” he said.
“Any disease area where you have lots of heterogeneity in terms of patient populations who are being infected with these diseases, and where you have a variety of outcomes and possible therapeutics, are areas that can be enhanced with big data, machine learning, and artificial intelligence,” Lefkofsky said. The goal is to create “smart” laboratory tests, he said, by including and analyzing other types of data along with the test result, and by making the tests as personalized as possible.
While AI-enhanced diagnostics are the company’s overall aim, Tempus’ “standard” COVID-19 diagnostic business has already taken off over the past few months. Between its two laboratories, the firm now performs about 12,000 SARS-CoV-2 tests per day, Mason said, and has capacity to run 15,000 tests per day or more if needed.
Turnaround time from sample receipt to result is 24 to 48 hours, and the retail price of the test is $100, according to the firm’s website. Tempus has struck a variety of partnerships to make the test available to patients, Lefkofsky said, including with CVS Health, the Illinois Department of Public Health, universities, school systems, and agencies in other states.
“In addition to just running the test, we collect some amount of outcome and response data, and some amount of phenotypic data,” he said, which patients can provide on a voluntary basis when they receive their test result. About 75 percent of patients currently opt into providing this additional information, he said, which includes phenotypic data, drugs taken to treat COVID-19, and patient response to those drugs.
Over time, he said, Tempus hopes to use these data to built predictors of disease severity and therapy effectiveness. “It’s not just about a diagnostic, about whether you are COVID-19 positive or not, it’s about also arming the physician and the patient with data as to what therapeutics are most likely to work and how best to personalize therapy,” he said.
While the company could have implemented a SARS-CoV-2 test with EUA from a commercial provider in its labs, it opted to apply for its own EUA, mainly because at the time it started testing, not many tests had received EUA yet, Lefkofsky said.
Tempus is now working on a version of the test that enables at-home sample collection, which it hopes to bring to market soon. It is also in the midst of validating an assay that combines influenza and SARS-CoV-2 testing.
In addition, the firm is developing its sequencing-based respiratory pathogen panel, which it plans to launch later this year or early next year. Mason said the firm has been considering different versions and is in the process of teasing out which one is the best. A number of companies have put next-gen sequencing respiratory pathogen panels on the market, including Illumina, Twist Bioscience, and Agilent Technologies, and “we’ve been looking at all of these,” he said. Providing the respiratory panel with a short turnaround time will be very important, he added, so the test results remain meaningful for patients.
Meanwhile, Tempus’ COVID-19 data initiative is “moving along well,” Lefkofsky said. The company has signed up several undisclosed academic medical centers and large hospital systems as partners and has been collecting clinical data from more than 10,000 patients so far. For a fraction of these, Tempus will also perform RNA-seq profiling. According to Mason, viral sequencing data and whole-genome sequencing data is also available for some of the patients. The aim is structure and curate the clinical data along with the molecular data.
Mason said one of his primary goals at Tempus – though he is also involved in integrating RNA sequencing into the firm’s cancer diagnostics – is to build the network of patients for the COVID-19 initiative, which aims to grow to 50,000 patients. “My goal is to make it so it’s really a true public-private benefit, so there’s as much data as possible available to as many people as possible to learn as fast as possible about COVID-19,” he said. “It could be useful for vaccines, for treatments, for stratifying high-risk patients.”
Lefkofsky said the project doesn’t have a timeline or an endpoint. “This is simply building the first of its kind large dataset that we think can help answer some questions,” he said.
All of the COVID-19 work is not distracting Tempus from its oncology testing business, though, which has apparently not suffered from the pandemic. “Our cancer business continues to grow at triple-digit rates” and is ahead of plan for 2020, Lefkofsky said.