Noninvasive ctDNA Test Sensitive to Early-Stage Cancer

Researchers from the United States, Netherlands, and Denmark have collaborated on developing a new liquid biopsy test that can detect circulating cell-free DNA (cfDNA) in patients with early-stage colorectal (CRC), breast, lung, or ovarian cancer.

Lack of clinically proven biomarkers to detect early stage cancer remains a foreboding problem in oncology. Those that exist, including cancer antigen 125 or prostate-specific antigen, can be quite non-specific and are also expressed in healthy individuals, which raises the risk of false positives. Analysis of circulating tumor DNA (ctDNA) is a viable, noninvasive option that uses a combination of next-generation sequencing (NGS) and computational methods to genotype patient tumors. However, so far, analysis of ctDNA has found widespread application only for mutational analysis in the blood or in patients with advanced-stage tumors.

In their current study, the authors used an extremely sensitive targeted error correction sequencing (TEC-Seq) method to evaluate sequence changes in ctDNA in 58 cancer-related genes in the plasma from 44 healthy and 200 patients with stage I or II CRC, breast, lung, or ovarian cancer.

Researchers analyzed 194 plasma samples from treatment-naïve patients with breast cancer (n = 45), CRC (n = 42), lung cancer (n = 65), and ovarian cancer (n = 42)., who had localized or metastatic disease. Average cfDNA levels were much higher in the patient samples (29 ng/ml) than in samples from healthy individuals (7 ng/ml). TEC-Seq analysis of the 194 patient samples found that about 75% of the CRC samples, 66% of ovarian cancer samples, and most of the lung and breast cancer samples had detectable driver gene mutations.

The amount of ctDNA varied across the cancer types, with breast cancer showing the lowest mutant allele fraction, the authors wrote (P = .028). Similar to the trend observed with cfDNA, ctDNA was higher in metastatic disease compared with earlier-stage disease across all 4 cancer types (P <.0001). The genetic alternations in driver genes matched previous reports, according to the researchers.

“On average, 2.1 alterations, including 0.9 changes at hotspot positions, were observed in each patient with detectable ctDNA, with lung and colorectal cancers having a higher number of alterations per case,” they wrote.

Notably, limiting the analysis to specific gene hotspots reduced the fraction of cases detected by the TEC-Sec method to less than 60%, which the authors explain, emphasizes the importance of avoiding such restrictions. Comparing mutations in the plasma ctDNA with those in the patients’ matched tumor and normal tissue (n = 152), detected using an independent NGS approach, confirmed that ctDNA can be used to detect germline changes.

“This study shows that identifying cancer early using DNA changes in the blood is feasible and that our high accuracy sequencing method is a promising approach to achieve this goal,” said Victor Velculescu, MD, PhD, professor of oncology at the Johns Hopkins Kimmel Cancer Center and senior study author.

Overall, their test could detect 86 of 138 (6%) stage I and II cancers:

• Of the 42 patients with CRC, the test correctly predicted cancer in 4 of the 8 (50%) patients with stage I disease, 8 of 9 (89%) with stage II disease, 9 of 10 (90%) with stage III, and 14 of 15 (93%) with stage IV disease.
• Of 71 people with lung cancer, TEC-Seq identified cancer among 13 of 29 (45%) with stage I disease, 23 of 32 (72%) with stage II disease, 3 of 4 (75%) with stage III disease, and 5 of 6 (83%) with stage IV cancer.
• For 42 patients with ovarian cancer, 16 of 24 (67%) with stage I disease were correctly identified, as well as 3 of 4 (75%) with stage II disease, 6 of 8 (75%) with stage III cancer, and 5 of 6 (83%) with stage IV disease.
• Among 45 patients with breast cancer, the test spotted cancer-derived mutations in 2 of 3 (67%) patients with stage I disease, 17 of 29 (59%) with stage II disease, and 6 of 13 (46%) with stage III disease.

The authors concluded that their approach, in addition to being noninvasive, is highly specific for tumor DNA, unlike other blood-based biomarkers which may also be detected in individuals without cancer.

Reference

Phallen J, Sausen M, Adleff V, et al. Direct detection of early-stage cancers using circulating tumor DNA. Sci Trans Med. 2017;9(403):eaan2415. doi: 10.1126/scitranslmed.aan2415.