Identification of Circulating Tumor DNA for the Early Detection of Small-cell Lung Cancer

Abstract

Circulating tumor DNA (ctDNA) is emerging as a key potential biomarker for post-diagnosis surveillance but it may also play a crucial role in the detection of pre-clinical cancer. Small-cell lung cancer (SCLC) is an excellent candidate for early detection given there are no successful therapeutic options for late-stage disease, and it displays almost universal inactivation of TP53. We assessed the presence of TP53 mutations in the cell-free DNA (cfDNA) extracted from the plasma of 51 SCLC cases and 123 non-cancer controls. We identified mutations using a pipeline specifically designed to accurately detect variants at very low fractions. We detected TP53 mutations in the cfDNA of 49% SCLC patients and 11.4% of non-cancer controls. When stratifying the 51 initial SCLC cases by stage, TP53 mutations were detected in the cfDNA of 35.7% early-stage and 54.1% late-stage SCLC patients. The results in the controls were further replicated in 10.8% of an independent series of 102 non-cancer controls. The detection of TP53 mutations in 11% of the 225 non-cancer controls suggests that somatic mutations in cfDNA among individuals without any cancer diagnosis is a common occurrence, and poses serious challenges for the development of ctDNA screening tests.

Keywords: Early detection; Screening; Small-cell lung cancer; TP53 mutations; cfDNA; ctDNA.

Fig. 1

Characteristics of TP53 mutations in cases and controls (a) Two examples of variants called using Needlestack's regression model of sequencing error. Each dot represents a sequenced library (two dots per sample) colored according to its phred-scaled q-value. The black regression line shows the estimated sequencing-error rate along with the 99% confidence interval (black dotted lines) containing samples. Colored-dotted lines correspond to the limits of regions defined for different significance q-value thresholds. Both technical duplicates appear as outliers from the regression (in red), and are therefore classified as carrying the given mutation; (b) Percentage of TP53 mutated samples in the cfDNA of Russian cases and controls, and replication controls; (c) Distribution of TP53 mutations found in SCLC tumors (George et al., 2015) and in our series of cases and controls across the different p53 protein domains; (d) Type of mutations and functional impact of missense ones based on the IARC TP53 database: F (functional), PF (partially functional), NF (non-functional); (e) Percentage of allelic fractions of the TP53 mutations detected in the cfDNA of Russian cases and controls, and replication controls. The whiskers represent the minimum and maximum values.