Mutation detection with a liquid biopsy 96 mutation assay in cancer patients and healthy donors

Abstract

Aim: Detection of circulating tumor DNA (ctDNA) holds promise as an adjunct to traditional cancer screening methods. To determine the sensitivity and specificity of ctDNA measurements, levels were measured in plasma from patients with a cancer diagnosis and a low-risk, healthy population. Methods: We validated a plasma assay for detection of 96 ctDNA mutations in nine cancer genes (BRAF, CTNNB1, EGFR, FOXL2, GNAS, KRAS, NRAS, PIK3CA, and TP53). The assay reliably detects low levels of ctDNA, >2 copies. A total of 183 plasma samples from cancer patients were obtained along with plasma from 102 healthy individuals. Results: ctDNA was detected in 24.0% of cancer patients (14.7% stage I, 18.8% II, 33.3% III, and 50.0% IV). ctDNA was not detected in 96% of low-risk subjects. Three subjects tested positive for one mutation and one subject tested positive for two mutations. ctDNA levels in positive subjects were followed for a year, and levels remained steady with small fluctuation. Multiple lung nodules found in the subject with two mutations have remained stable for 1 year. None of the healthy individuals was diagnosed with cancer in the year following study entry. Conclusion: The sensitivity of the ctDNA assay was 24.0% in the mixture of cancers. The specificity was 96.1%. In the low cancer risk population, the apparent false positive detection rate for ctDNA at 1 year is 3.9%.