Ultrasensitive 'Liquid Biopsy' May Detect Many Solid Tumors

Megan Brooks

April 07, 2014

Stanford University researchers say they have developed an ultrasensitive method to detect and quantify circulating tumor DNA (ctDNA) in patients with solid tumors.

The method could be used not only to diagnose many types of solid tumors using a blood sample but also to monitor treatment response, detect minimal residual disease and emerging resistance mutations to targeted therapies, "and potentially even for noninvasive cancer screening," co–senior author Maximilian Diehn, MD, PhD, assistant professor of radiation oncology at Stanford, told Medscape Medical News.

The research was published online April 6 in Nature Medicine.

Measuring ctDNA has shown promise as a "liquid biopsy" for assessing cancer burden, as reported previously by Medscape Medical News. But existing ctDNA detection methods are not sensitive enough or lack broad patient coverage for clinical application, Dr. Diehn and colleagues note in their article. Their aim was to develop a method that overcomes 2 major hurdles in the ctDNA field.

"First, the technique needs to be very sensitive to detect the very small amounts of tumor DNA present in the blood. Second, to be clinically useful, it's necessary to have a test that works off the shelf for the majority of patients with a given cancer," Dr. Diehn said in a Stanford news release.

Gaining Momentum

Approached for comment, Luis Diaz Jr, MD, of the Johns Hopkins Sidney Kimmel Comprehensive Cancer Center in Baltimore, Maryland, said, "I think this is a really cool area. It's something I have been involved in for about 10 years, and it's now catching momentum."

Dr. Diaz, who was not involved in the Stanford research, said this article does a "good job, like many before it, to show that circulating tumor DNA is a viable diagnostic test, not only for tracking mutations in advanced patients but possibly also for screening. I really think there is a future for this in cancer."

 
I think this is poised to hit the clinic, but now we have to start the heavy lifting. Dr. Luis Diaz Jr
 

The method is "complicated," he admitted, "but no more complicated than sequencing the tumor. It will have to be refined. This is version 1.0. Version 2.0 is going to get better and better. I think we are going to see that. I think this is poised to hit the clinic, but now we have to start the heavy lifting. By heavy lifting I mean larger clinical trials with thousands of patients."

But Frank J. Rauscher III, PhD, deputy director for basic science at the Wistar Institute Cancer Center in Philadelphia, Pennsylvania, has reservations about whether this approach will ever reach the clinic.

 
I don't see physicians making treatment decisions based on this type of data. Dr. Frank Rauscher III
 

"It's a technical feat," he said, "but I don't see physicians making treatment decisions based on this type of data. I am still a skeptic about DNA markers in blood. A protein marker will likely be much more specific and easier to detect and quantify," Dr. Rauscher told Medscape Medical News. "And unless it can detect small stage I tumors in non-high-risk people, it's not going to be much use."

The CAPP-Seq Method

The method developed by the Stanford researchers ― dubbed CAncer Personalized Profiling by deep Sequencing, or CAPP-Seq ― is the first next-generation sequencing-based method for ctDNA analysis that achieves "both an ultra low detection limit and broad patient coverage at a reasonable cost," the researchers say.

"Technically, CAPP-Seq involves sequencing a small portion of the genome that contains recurrent mutations in the cancer of interest. In its most basic implementation, we first identify the unique set of mutations in a patient's tumor by sequencing its DNA and then measure the presence of those mutations in circulating DNA," Dr. Diehn told Medscape Medical News.

"CAPP-Seq creates a personalized biomarker for every patient. We designed the approach to be directly applicable to the vast majority of patients with a given cancer type so that no patient- specific optimization is required to use it. We believe that this will be very important for facilitating clinical implementation of circulating tumor DNA analysis," he added.

In the article, the researchers describe the technical performance and explore the clinical utility of CAPP-Seq in patients with early and advanced non-small-cell lung cancer (NSCLC).

They detected ctDNA in all patients with stage II-IV NSCLC and in 50% of patients with stage I, with 96% specificity for mutant allele fractions down to approximately 0.02%. Absolute levels of ctDNA correlated with tumor volume and distinguished between residual disease and treatment-related imaging changes.

They say CAPP-Seq is sensitive enough to detect 1 molecule of tumor DNA in 10,000 healthy DNA molecules in blood.

They also demonstrated the prognostic potential of CAPP-Seq. In 1 patient treated with radiotherapy for stage IIB NSCLC, follow-up imaging showed a large mass that was thought to represent residual disease. However, ctDNA at the same time point was undetectable, and the patient remained disease free 22 months later, the researchers report.

A separate patient was treated with chemoradiotherapy for stage IIIB NSCLC, and follow-up imaging revealed a near-complete response. However, the ctDNA concentration increased slightly following treatment, suggesting progression of occult microscopic disease, the researchers say. Indeed, clinical progression was detected 7 months later, and the patient ultimately died of their disease, they say.

"If we can monitor the evolution of the tumor and see the appearance of treatment-resistant subclones, we could potentially add or switch therapies to target these cells," Dr. Diehn said in the news release. "It's also possible we could use CAPP-Seq to identify subsets of early-stage patients who could benefit most from additional treatment after surgery or radiation, such as chemotherapy or immunotherapy," he added.

The researchers are now designing clinical trials to see whether CAPP-Seq can improve patient outcomes and decrease costs.

Although this study focused on NSCLC, the researchers think their method could be applied to other tumors for which recurrent mutation data are available. "This approach could, theoretically, work for any tumor. We expect it to be broadly applicable across cancers," Ash Alizadeh, MD, PhD, assistant professor of medicine at Stanford, and co–senior author, said in the release.

Dr. Diehn told Medscape Medical News, "From a technical standpoint, CAPP-Seq is ready for clinical implementation. Of course, there are important regulatory requirements that have to be followed for tests that could be used to alter patient management, and we are already working to address these. Additionally, while CAPP-Seq is relatively inexpensive, widespread clinical use would require insurance coverage."

The research was supported by the Department of Defense, the National Institutes of Health, the Ludwig Institute for Cancer Research, the Radiological Society of North America, the Association of American Cancer Institutes' Translational Cancer Research Fellowship, the Siebel Stem Cell Institute, the Thomas and Stacey Siebel Foundation, and Doris Duke Clinical Scientists Development Awards. The authors, Dr. Diaz, and Dr. Rauscher have disclosed no relevant financial relatinships. Dr. Rauscher is related to the writer of this news article.

Nat Med. Published online April 6, 2014. Abstract

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