CHICAGO (GenomeWeb) – In the last three weeks, cancer informatics, molecular sequencing, and precision medicine company Tempus has landed $200 million in new investment, launched a clinical trial matching service, and teamed with a National Cancer Institute contractor to add structured clinical data to the Cancer Genome Atlas.
All this has happened as the fast-growing Chicago-based company has opened its first international office and is taking steps to bring its technology into additional disease areas.
Last week, Tempus announced that it was joining with National Cancer Institute contractor Leidos Biomedical Research to produce an "upgraded" TCGA dataset. Leidos Biomed helps manage the legal and administrative logistics of NCI projects like this one.
In this collaboration, Tempus will request current medical records from TCGA contributors for clinical data abstraction, then will clean and structure the data with its Tempus O informatics platform. After healthcare professionals verify the newly structured data, the clinical information will be matched with corresponding molecular data to enhance the TCGA dataset for researchers worldwide.
Tempus CEO and Founder Eric Lefkofsky said that only about one-third of the TCGA dataset contains any clinical data or clinical annotation. Lefkofsky said that the NCI contract is a validation of Tempus' ability to scale its technology platform.
"It's a big project. You have to go to all these people who contributed and see if the clinical data can be pulled and then have that sent the Tempus for us to do what we normally do, which is abstract those records and then pull out the key data elements," he said.
Tempus O combines optical character recognition, natural-language processing, and human intervention by a team of nearly 200 abstracters. These include data analysts, postdoctoral researchers, cancer registrars, and nurses, who comb records to extract "therapeutically relevant" data elements, Lefkofsky said.
During this month's American Society of Clinical Oncology meeting, Tempus introduced Tempus Integrated Molecular Evaluation (TIME) Trial, a service featuring a proprietary technology platform that analyzes molecular and clinical data on cancer patients in real time to find suitable and — importantly — convenient trials for individuals.
TIME Trial only sends patients to prequalified academic and community cancer centers so those who qualify can enroll right away.
Part of precision medicine, according to Lefkofsky, is finding appropriate, targeted clinical trials for as many patients as possible. "The challenge with that is that most of the trials are highly concentrated at academic medical centers," he said. TIME Trial is about bringing trials "to their front door," Lefkofsky added.
Tempus Senior Director of Operations Amy Franzen, who is heading up TIME Trial, said that the new program builds on the company's core strength, providing clinical decision support. Trial matching is one such support tool.
"When we match patients to clinical trials, often what we see is that those clinical trials are located far away from the patient, and that's a real problem for the patient," Franzen said.
On average, only 3 to 5 percent of adult cancer patients enroll in clinical trials, compared to about 70 percent in pediatrics. Franzen said that Tempus is able to match more than 70 percent of adults to biomarker-specific trials but still sees low enrollment rates, mostly because trials are in inconvenient locations for patients.
"We've identified that one of the largest gaps in that number is access to trials," Franzen said. "This service we provide actually brings the clinical trial to the patient."
Tempus sends lab reports to physicians then has an "onboarding" process that gets sites prequalified so they can open and start enrolling patients in trials within two weeks, Franzen said.
The company has a standard contract, a standard rate card, and a central, outsourced institutional review board to accelerate the process.
Scripps Health in La Jolla, California, is an early TIME Trial customer. The Scripps MD Anderson Cancer Center, a year-old partnership between Scripps and the University of Texas MD Anderson Cancer Center, currently has a trial accrual rate of 5 to 6 percent, slightly higher than the industry average.
Scripps and Tempus are currently negotiating data-sharing agreements and patient privacy agreements, and Michael Kosty, director of thoracic oncology at Scripps MD Anderson, expects the center to be up on TIME Trial in the next month or two.
Kosty said that he would like to see trial accrual double or triple in the first six months on TIME Trial and approach 33 percent in two to three years. He said that the goal is "very ambitious," but he has high hopes for the service.
"I think the clinical trial apparatus is really very cumbersome and inefficient," Kosty said. It typically takes three to five months for Scripps to negotiate with trial sponsors, get IRB approval, pass site qualification and initiation visits, then begin enrolling patients.
TIME Trial shifts that background work to Tempus. "You end up having a menu of trials," Kosty said.
"You have all these clinical trial options that are not necessarily active and open at your site because you don't yet have a patient. The patient walks in and you see they're eligible for this clinical trial and you start to process it and within a week or two, the patient is enrolled in the clinical trial," Kosty explained.
Trials are pre-approved but not actually activated until an appropriate subject comes in. "It makes clinical trials potentially accessible to many more patients," Kosty said. "That that really is unheard of in terms not only of clinical trials in oncology, but clinical trials in medicine."
Kosty called TIME Trial "revolutionary, as opposed to evolutionary" because it takes the burden of back-office work related to opening a clinical trial off the health system.
This is particularly useful for an organization like Scripps that lacks the massive research infrastructure of MD Anderson's flagship campus in Houston. MD Anderson itself can have more than 1,000 active clinical trials at any given time, something that the satellite Scripps MD Anderson facility in California cannot.
The Tempus service is more complementary than competitive with the MD Anderson affiliation, Kosty said. "We'd like to have as many clinical trials available for our patients as possible, and we see this as a way of accomplishing that much more efficiently, much more expeditiously, and really increasing the availability of trials for our patients," he said.
Scripps has an Epic Systems electronic medical record and will be creating an interface to Tempus to make sure patient data flows between platforms, Kosty said.
On the financial front, the $200 million Series F round brings Tempus' total venture capital to $520 million and valuation to $3.1 billion.
The four-year-old firm has built a library of molecular and clinical data alongside an operating system to make the data useful for clinicians and researchers alike. The company employs machine learning, next-generation sequencing, and artificial intelligence-assisted image recognition to enable scientific discovery and help physicians make real-time decisions to guide treatment of their patients. Tempus also has a sequencing laboratory in its sprawling headquarters, which processes samples for its cancer molecular diagnostics business.
The new funding will support general growth and expansion. "We'll be able to go faster and we'll be able to be more diverse in the investments we make," particularly in developing new analytics and AI technology, according to Lefkofsky.
Tempus employs about 700 and is adding about 10 employees a week. When GenomeWeb last visited in November, the headcount was closer to 500. Most of its employees work in Chicago, though Tempus has a growing presence in New York, a small office in Silicon Valley, and recently opened its first international outpost in Singapore.
After also considering Europe, the company chose Singapore to get a foothold in the Australasian market, which has lots of English speakers, a strong talent pool, and similar healthcare infrastructure to the US, Lefkofsky said.
"We still remain largely focused on cancer in the US, and we have a long way to go to for us to feel like we've fully saturated that opportunity," he said.
Meanwhile, the home office has been expanding. Tempus formerly occupied half a floor in the massive former Montgomery Ward catalog building on the Chicago River. The company took over the entire floor early this year. Among the additions is an under-construction sequencing lab that will house additional Illumina NovaSeq and HiSeq machines to keep up with demand.
Lefkofsky has set a goal of reducing turnaround time on Tempus' most popular test, a 596-somatic-gene Tempus xT panel, from the current 13 days to 10 days by the end of the year. The panel includes tumor-normal testing for cancer patients, then follows up with full transcriptomic profiling, variant classification, and calling, generating a total of 12 gigabytes of data per patient. An in-house pathologist signs off on each test.
"With more data comes more insight. The name of the game or the name of the problem in cancer is finding potentially actionable targets, especially for metastatic patients, late-stage, high-risk, high-mortality [patients]," Lefkofsky said. "The goal is to find for a physician anything that they can explore that might reverse what is otherwise going to be terminal."
"We think we can get [turnaround] to about 10 days by year end, in large part because we're getting to such a large scale as one of the largest sequencers in the country of cancer patients that we're able to automate more and more of the process," Lefkofsky said. "Every day we save is a big deal for patients."
Tempus also has started to "lightly explore" applying its technologies to diabetes and depression with small-scale projects in those areas with two undisclosed US academic medical centers, Lefkofsky said. The same system that structures clinical data and pulls in molecular and imaging reports in oncology can be used for other conditions.
"The core platform that we built in cancer is designed to work across disease areas, so it should work just as well in diabetes, in neurological disorders, in cardiovascular disease, in depression, and so on and so forth," Lefkofsky said.
Lefkofsky said that Tempus has not experienced some of the reimbursement frustrations that have plagued the likes of NantHealth, another deep-pocketed company offering sequencing and informatics services in oncology and beyond.
"We've seen reimbursement improving and we continue to think it will improve," Lefkofsky said.