Special Focus: Liquid Biopsies

Liquid Biopsies for Oncology to Gain Clinical Momentum in 2015 Liquid biopsy technology holds enormous potential to transform the medical management of oncology patients by providing noninvasive, real-time insights of disease status. Also known as a "molecular stethoscope," liquid biopsies are integral to personalizing cancer care. 2015 is predicted to be the year when liquid biopsy tests become commercially available and gain traction in clinical oncology care. "The applicability of a non-invasive cancer diagnostic and monitoring tool is immense," writes Doug Schenkel, managing director of the medical technology research group at Cowen and Company, in the equity research note Ahead of the Curve Series, published in November 2014. "Although the current field is somewhat nascent, liquid biopsies have a multi-billion dollar market potential that could eventually exceed $10 billion." Liquid biopsy technology is expected to ultimately permeate the entire continuum of cancer care - from early detection, treatment selection and treatment monitoring through recurrence surveillance. (Though there is scientific evidence the technology is applicable to other clinical areas including transplant monitoring, the most meaningful initial adoption is expected in oncology care.) Early forays into personalized cancer care focus on tailoring treatment based on the molecular makeup of tumors. But, this molecular assessment provides only a single snapshot and is based on analysis of tumor biopsy tissue. Such samples are derived from invasive procedures and may not be feasible in all patients either due to anatomical location of the tumor or due to advanced metastasis. Additionally, tumor samples may not reflect the true molecular heterogeneity both within the tumor and in distant metastases. Liquid biopsy affords many advantages over tumor sample analysis. Given its noninvasive nature, serial testing with liquid biopsies offers clinicians an ongoing opportunity to track disease status throughout treatment. This continuous monitoring enables clinicians to catch emerging mutations or disease progression and ensure treatment selection remains relevant much sooner than a radiological examination can. On the positive side, liquid biopsies can provide quick reassurance to patients and clinicians that treatment is working. "The beauty of circulating tumor DNA (ctDNA) monitoring is the speed," Paul B. Chapman, M.D., chair of the Medical Advisory Panel at the Melanoma Research Alliance (Washington, D.C.), told Medscape. "If you are looking for a change in a tumor, based on CT scan, you are talking about not only killing billions of tumor cells but also waiting for the resulting cell debris to be cleared by the body before the change shows up on imaging. That can take weeks. But cell death happens in minutes to hours, so you would expect the change in ctDNA to be a quick effect, and it is." CTCs versus ctDNA Circulating tumor cells (CTCs) were the lead target marker of liquid biopsies because they provide both genetic and cellular level data. However, these cells are relatively rare and require sensitive collection and enrichment methods. Experts say fewer than 10 CTCs are found among 1 million white blood cells and 1 billion red blood cells. CTCs have been detected in patients with breast, prostate, lung, and colon cancer. Importantly, CTCs have shown clinical value with many studies correlating higher CTC counts with a negative cancer prognosis. However, cell-free tumor nucleic acids (ctDNA and circulating cell-free tumor RNA), are emerging as effective alternatives to CTCs due to their easier collection and analysis. 2014 represented a "tipping point" industry watchers say, in which the focus, in terms of published papers and commercial plans shifted from CTCs towards ctDNA. Most ctDNA strands contain roughly 180 base pairs and can be detected in higher levels than CTCs (more than a 50-fold increase, experts say). Yet, ctDNA is believed to constitute as little as one ten thousandth of total circulating DNA. But, improved sensitivity of analysis techniques (next generation sequencing, and digital polymerase chain reaction) are overcoming that barrier, as can be seen with noninvasive prenatal testing (NIPT), which analyzes circulating fetal DNA from the mother's blood. Despite the rapid clinical adoption of NIPT, liquid biopsies for cancer are at a more nascent clinical state in part because ctDNA is harder to detect than fetal DNA and until recently, clinical use of sequencing for DNA analysis was not feasible. "Although the outlook is promising, the liquid biopsy field has significant technical and clinical hurdles to overcome," cautions Schenkel. "Technical challenges include sensitivity and specificity issues due to current isolation, enumeration, and enrichment methods. Furthermore, the diversity of approaches has obfuscated the path to clinical adoption; therefore, standardization is necessary to ensure a clear direction and future success." Commercialization Prospects Cowen and Company predicts that liquid biopsy represents a $10 billion market opportunity by the end of the decade ($4 billion of that in the United States). Cowen's estimate does not include the additional market potential for adjacent tests, instruments, and applications, so the full industry impact of liquid biopsy technology may be even greater. The true market size is also, of course, dependent upon test pricing and frequency. The $10 billion estimate is based on roughly a $500 price tag per test with testing once per year (for diagnosis of all new colorectal, lung, breast and prostate cancers and if all patients living with these cancers were tested annually). The market could again be higher if testing was performed serially more frequently and if liquid biopsy can penetrate the asymptomatic screening market. While the "holy grail" of liquid biopsy would be to apply the technology as an early-detection screening test, the more imminent commercial application is in patient monitoring of diagnosed cases. DTET's survey of the commercial landscape verifies that early entrants to the commercial liquid biopsy market are primarily developing applications for monitoring cancer treatment. Within the oncology market, it is estimated that liquid biopsies for monitoring will achieve routine clinical practice within five years, while the full potential of other liquid biopsy applications will take longer. Both test service providers and toolmakers stand to benefit from the clinical adoption of liquid biopsy technology. Among the commercial single cell analysis tools that could be utilized in liquid biopsy testing are Pacific Biosciences' (Menlo Park, Calif.) single molecule real-time sequencing (SMRT) products; Oxford Nanopore's (United Kingdom) nanopore-based readers to directly identify and sequence individual DNA bases; Fluidigm's (San Francisco) microfluidics-based C1 single cell sample preparation tool; and Nanostring’s (Seattle) nCounter, which digitally detects single molecules using multiplex profiling. As the dominant platform in the sequencing market, Illumina (San Diego) also of course stands to benefit on the equipment side from broader application of sequencing technology. But, Illumina is increasingly applying the technology itself. At the recent JP Morgan Healthcare Conference (San Francisco; Jan. 12-15), Illumina's CEO Jay Flatley stated that Illumina’s goal is to sell a research-use-only liquid biopsy product by the end of this year, while the company works toward U.S. Food and Drug Administration approval. Another sign of Illumina's interest in the liquid biopsy market is its December 2014 agreement with Sequenom to pool their patent portfolios and settle all outstanding legal disputes. The pooled patents are reported to include intellectual property around the use of ctDNA. Sequenom (San Diego) has recently reported that while performing NIPT testing, the company has identified over 20 significant incidental findings of confirmed maternal tumors, including breast cancer, colon cancer, and lymphomas. CEO Bill Welch said at JP Morgan that the company's lead oncology product will focus on advanced cancer patients with solid tumors (stage III-IV) and metastatic patients with (re)-biopsy of tumor. Welch said that the early access program for a research use test is expected in the second half of the year. Welch and Flatley were not the only large diagnostics players to speak of liquid biopsy test development plans at JP Morgan. Genomic Health (Redwood City, Calif.) is currently conducting larger-scale clinical trials to support the launch of its first liquid biopsy test in 2016, CEO Kim Popovits said at the conference. The company unveiled results from two feasibility studies in December — one assessing the application of liquid biopsy to detect bladder cancer from urine (2014 Society of Urologic Oncology ) and breast cancer in blood (2014 Annual San Antonio Breast Cancer Symposium). The company said that the results represent "important progress" in the development of a proprietary liquid biopsy platform. In mid-January Qiagen (Germany) received the first-ever CE mark of a lung cancer companion diagnostic based on liquid biopsies. The novel liquid biopsy-based companion diagnostic utilizes circulating nucleic acids obtained from plasma samples in patients with non-small cell lung cancer to assess EGFR mutations to determine eligibility for the drug IRESSA. The test was co-developed by Qiagen and the drug's maker AstraZeneca. While the potential of liquid biopsy has attracted interest from major diagnostics players, smaller startups are not conceding the market. Many small companies will be entering the commercial realm in 2015 as well. Thomas McLain, CEO of Exosome Diagnostics (Cambridge, Mass.), tells DTET that as liquid biopsy technology makes the transition into clinical care, his company is initially entering the market by selecting liquid biopsy tests for lung cancer markers such as the ALK and EGFR mutations (T790M) that are already covered by payers. He says that simultaneously introducing a new platform and new markers can complicate adoption efforts. "We are demonstrating that exosomes are diagnostically significant, so we are picking tests of accepted markers, so that clinicians can appreciate the performance difference," says McLain. The company's platform relies upon exosome analysis. Exosomes contain both RNA and DNA, which the company says can more comprehensively detect mutational shifts than ctDNA alone. McLain explains that ctDNA is reflective of therapeutic-related cell death, while ctRNA reflects the living process and may indicate metastasis. Also in 2015, the company plans to launch a solid tumor panel as a laboratory developed test that will target actionable 400 mutations (10 genes) in the most significant pathways in lung, colon, and breast cancers. The panel will focus on the most actionable mutations for current treatment and clinical trial eligibility. In early January, Personal Genome Diagnostics (Baltimore) launched its PlasmaSelect–R liquid biopsy test for cancer researchers. The test detects sequence alterations and translocations in 63 well-characterized genes that include all important known biologic and therapeutic cancer targets, the company says. The company, a spinout from Johns Hopkins University, plans to launch a clinical use version of the test in the second half of the year. "You will be able to overcome reimbursement barriers if you have a test that answers a clinical question that can't be answered another way. We spun out PGS to create high-value clinical tests that are 'must haves,'" Luis Diaz, M.D., the company's cofounder tells DTET. "Liquid biopsy must answer clinical questions — how will it help the patient live longer? How will it help oncologists decrease toxicity? How will it decrease the cost of patient care?" Those in the field believe adoption of liquid biopsy tests will be quicker than other genomic cancer risk assessment or prognostic tests because liquid biopsy reflects the real-time cancer dynamics — information that has been previously inaccessible. Chronix Biomedical (San Jose, Calif. and Germany) will begin offering liquid biopsies to assess minimal residual disease this year. The first of the company's anticipated launches will be a test for prostate cancer intended to supplement prostate serum antigen (PSA) testing. The $600 test, initially to be available in Germany, will guide clinician's decisionmaking in whether or not a man with marginally elevated PSA, in fact needs a biopsy. The hope, Chronix CEO Howard Urnovitz tells DTET, is that the test can help realize billions of dollars in savings by reducing unnecessary biopsies. In addition to the PSA test, the company is looking for partners to help bring to market its liquid biopsies for breast cancer, organ transplantation, and head/neck cancer. Takeaway: 2015 is expected to be the year that liquid biopsy technology penetrates the clinical oncology market. Uptake for the monitoring application is expected to be quick, with predictions that the liquid biopsy will become part of routine care within five years. Expanded applications of the technology to cancer screening and other clinical areas are expected to take longer.