Liquid Biopsy Technique May Allow Early Screening

A new method for performing liquid biopsies can detect the majority of early-stage tumors without large amounts of tumor DNA or foreknowledge of cancer mutations, a recent study reveals (Sci Transl Med 2017;9:eaan2415).

Liquid biopsies can be used to examine cell-free DNA in the bloodstream of patients with cancer, some of which comes from the tumor. Through DNA sequencing, researchers have been able to discern characteristic mutations in circulating tumor DNA (ctDNA). In some of the previous studies of this technique, however, researchers had already sequenced the tumor tissue, so they knew which mutations to look for in the blood. In addition, these analyses mainly included patients with late-stage cancer, who have more ctDNA than do patients with early-stage disease.

Victor Velculescu, MD, PhD, of Johns Hopkins University School of Medicine in Baltimore, MD, and colleagues developed a technique to profile the smaller amounts of ctDNA present in early-stage cancer. After isolating DNA fragments from a patient's blood, the researchers tagged each one with a different DNA barcode. These identifiers allowed the researchers to keep track of each fragment as they sequenced it around 30,000 times. By comparing many sequences at each position to each other and to a reference genome, the researchers could confirm whether a detected mutation was genuine or a false positive.

The scientists' approach, called targeted error correction sequencing (TEC-Seq), detects 55 genes that are frequently mutated in cancer, as well as three genes that are often altered in certain benign blood conditions and can confound the identification of tumor-specific mutations. They used the technique to analyze blood samples from 194 patients with breast, colorectal, lung, or ovarian cancers. TEC-Seq correctly identified 56%, 83%, 62%, and 71% of these patients, respectively, pinpointing gene alterations in blood samples for each case. TEC-Seq was sensitive enough to detect early-stage tumors. Overall, it identified 62% of 138 patients whose tumors were stage I or II.

One concern about liquid biopsies is that mutations present in the blood may not be tumor-derived. When the researchers analyzed matched tumor and blood samples from 100 patients, however, they found that in 82% of cases, a mutation detected in the blood was also present in the tumor. In a further test, the researchers applied TEC-Seq to blood samples from 44 healthy individuals. None of them came up positive for ctDNA.

TEC-Seq may also be useful for predicting cancer recurrence. The researchers applied the method to blood samples from 38 patients with colorectal cancer who had undergone surgery to remove their tumors. Patients with large amounts of ctDNA at diagnosis had shorter progression-free survival and overall survival than did patients with less ctDNA.

The study shows that “you can use DNA changes in blood to identify cancer at an early stage,” says Velculescu. He notes that this technique can't determine what type of tumor a patient has; further mutation analyses or imaging would be necessary to determine tumor identity and location. Velculescu and colleagues have begun clinical trials to verify TEC-Seq's capabilities in larger groups of patients.

“What's exciting is that they did de novo mutation calling without prior knowledge of the changes in tumor DNA,” says Pedram Razavi, MD, PhD, of Memorial Sloan Kettering Cancer Center in New York, NY. His colleague Jorge Reis-Filho, MD, PhD, agrees that this method is promising and “a significant step forward.” –Mitch Leslie

For more news on cancer research, visit Cancer Discovery online at http://cancerdiscovery.aacrjournals.org/content/early/by/section.