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Tempus Aims to Bring Big Genomic Data Closer to Oncologists


Update: This article has been changed to correct the name of Tempus' sequencing panel. It is the Mi-Oncoseq panel not the Oncoseq panel as written previously.

NEW YORK (GenomeWeb) – Health technology company Tempus is building a business around offering access to genomic sequencing services and a proprietary analytical platform to clinicians to help them put together more effective treatment plans for patients with particularly problematic tumors that don't respond to conventional therapies.

Tempus' platform offers informatics tools for combining molecular data with phenotypic and therapeutic data from electronic medical records. Its internal algorithms assess variation and expression levels in tumor-normal samples to try to identify patterns that shed light on patients' responses to treatment.

The company also runs a CLIA-certified sequencing laboratory in Chicago that it claims can handle over 50,000 samples annually. From there it offers both whole-genome and whole-exome sequencing as well as two targeted panels, namely the Tempus xT panel, which is a 600-gene tumor panel that covers immediately actionable mutations, and the Tempus xO sequencing panel, which covers approximately 1,700 cancer-linked genes.

In the future, the company plans to offer proteomic, single-cell, liquid biopsy, and microbiome sequencing services. Healthcare providers that send patient blood and tissue samples to the company's lab receive reports approximately two weeks after the company receives the sample. Reports cover details about specific mutations present in the patients' sample including somatic variants, potentially effective FDA-approved and trial drugs, as well as relevant clinical trials based on patients' mutation profiles.

Tempus Cofounder and CEO Eric Lefkofsky told GenomeWeb that he launched the company to help clinicians access and use big data more effectively in patient care. Previously, Lefkofsky's wife was treated for breast cancer in a hospital at a major academic institution. "I was amazed at how little big data, the kind of big data that we were seeing and helping deploy in other industries, had made its way into the clinical setting and into her care," he told GenomeWeb. He further noted that while there were a lot of interesting NCI-funded research projects going on at various institutions, "[they] didn't exist at scale and very little of it was being used in the clinical context." Equally interesting to Lefkofsky was how few data and technology experts were actually involved in the clinical process. Prior to launching Tempus, Lefkofsky had cofounded companies such as Groupon and bagged more than 15 years of experience in building technology businesses that support industries such as printing, logistics, manufacturing, media, and commerce.

"A typical hospital in an academic institution on the oncology side has a great number of chemists and biologists involved in the patients' care but there are very few software engineers, data scientists, and the like that are working on this problem and that's unlike other industries," he said. "In almost every other industry where technology has had a big impact, you see a significant number of software engineers and data scientists enter that field."

Seeking to bridge that gap, Lefkofsky launched Tempus in 2015 and began building a team of data scientists, software engineers, bioinformaticians, computational biologists, research scientists, and other experts to build out the company's informatics infrastructure and testing services. The list includes Kevin White, a professor of human genetics and medicine at the University of Chicago who now serves as Tempus' president. White is also the founding director of U of Chicago's Institute for Genomics and Systems Biology. His lab uses genomics, computational biology, and systems biology approaches to improve molecular diagnostics and therapeutics in oncology among other areas.

Tempus has also tapped Arul Chinnaiyan, a Howard Hughes Medical Institute investigator and professor of pathology and urology at the University of Michigan, to serve as a scientific advisor for the company. The firm uses the Mi-Oncoseq panel developed in Chinnaiyan's lab in addition to other sequencing technologies in its portfolio to capture molecular data from patient samples.

Though the data may be different, most industries need to answer similar questions and as such rely on many of the same technology approaches to handle their big data needs. "How do you structure data that's unstructured? How do you look for algorithmically interesting patterns? How do you clean, normalize, and manage large datasets? How do you take these actionable insights and put them in the hands of people inside these industries that need to have that data?" Lefkofsky said. "It's exactly what we are doing in cancer and healthcare at Tempus."

Prior to joining the company, White ran the Chicago Pancreatic Cancer Initiative, an ongoing effort to use genetic information to improve treatment and outcomes for patients with the disease. One of the goals of the initiative, which brings together oncologists, pathologists, palliative care doctors, nurses, computational biologists, and other experts, is to identify factors that affect patients' fitness for surgery as well as quality-of-life outcomes post-surgery. To date, just over 300 pancreatic cancer patients have been enrolled in the study and benefitted from the expertise of the research team. However, scaling that approach out to reach the over 50,000 pancreatic cancer patients diagnosed in the US every year is more challenging, White noted.

Furthermore, "context is key" in cancer cases, he told GenomeWeb. "You're talking about multiple mutations at the DNA level that are driving the disease in each case and really wanting to bring together that expertise in understanding and interpreting that data [and] in building the tools on the software side. That's what Tempus is doing. … We're bringing together all these different domains under one roof and integrating them in a way that nobody has even done before," he added.

Pricing for the company's services varies depending on which tests physicians want performed, but Tempus claims its testing services provide significantly more information in its reports than existing providers do at a fraction of the cost. So, for example, Lefkofsky said, a competing firm might offer panels with 300 to 500 genes with no additional information — transcriptome data for instance — and charge on the order of $5,000. In contrast, Tempus claims to offer its panels for about half that cost. Included in that cost are detailed reports that offer access to "a tremendous amount of data," he said. This includes lists of somatic and germline variants, expression levels, available immunotherapies, and phenotypic and therapeutic information, among other information.

"We are able to gather large amounts of molecular data, combine that with therapeutic and phenotypic and outcome data, look for algorithmic patterns that might provide insight into why patients are responding a certain way, and then test that in biological models," Lefkofsky said. "[We also] package [the] informatics and analysis up in a way that clinicians can look at it, digest it, and make real-time decisions about how best to treat a patient when they are not responding to the standard of care."

Tempus recently announced two partnerships with Northwestern University's Robert H. Lurie Comprehensive Cancer Center and the Pancreatic Cancer Action Network. Specifically, Tempus will be a preferred platform for managing genomic sequencing and analysis for the Lurie Cancer Center's Onco-SET (Sequence, Evaluate, Treat) initiative, a program that aims to provide personalized care and treatments for patients with drug-resistant tumors. The program will combine genomic sequencing and molecular analysis with traditional pathology to identify tailored treatments for these patients as well as pertinent clinical trials. 

Leonidas Platanias, director of the Lurie Cancer Center, told GenomeWeb that the center tapped Tempus in part due to its proximity to the center but largely because it believes that the company shares its vision for precision medicine. "I really like the way they are thinking of broadening their efforts in other areas beyond just gene sequencing including proteomics, metabolomics," he said. "They may be a newer company, but they have put together a team with a lot of experience with [strong] track records."

Tempus is also partnering with the Pancreatic Cancer Action Network's Precision Promise Initiative, a large-scale precision medicine trial organized by the patient advocacy group that is designed to improve outcomes for patients with pancreatic cancer. That initiative will start enrolling patients in spring 2017. Patients in the initiative will receive advanced molecular profiling to figure out which sub-studies best match their individual needs. Once on treatment, researchers will monitor patients and reanalyze their samples to help them understand the effectiveness of the treatments that they are receiving.

Like the Lurie Cancer Center, the Pancreatic Cancer Action Network is using Tempus' platform to handle its sequencing and analysis needs. PCAN Chief Research Officer Lynn Matrisian told GenomeWeb that PCAN tapped Tempus because of the comprehensiveness of its portfolio as well as its experiences in the pancreatic space.

The PCAN initiative will initially focus on enrolling patients in three studies set up by expert working groups. One of these will focus on molecular alterations in a DNA damage repair pathway, and a second will focus on immunotherapies in pancreatic cancer. A third study will look for mechanisms of disrupting the dense stroma that forms around pancreatic tumors that make it difficult for drugs to penetrate the tumor.

"We want very robust molecular analysis in Precision Promise, we want a gene panel, we want the ability to have whole-genome and whole-exome sequencing, [and] we want other assays as well," Matrisian said. "[Tempus] had really excellent capabilities, ... and we were very impressed with a lot of the informatics basis that they were applying to this problem. It just seemed like a really good fit to have them become a partner for us."