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.

Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA)

“…Hence, we performed a new series of sequencing with an increase flow of 850 and detected a significant increase rate in coverage. This observation suggests to use other analytical variants, raising coverage until to 3000× in order to overcome troubles such as the reported low efficiency (24,32,33).…”

Emerging concepts in liquid biopsies

“…This was shown in a recent study that used an assay specifically designed to accurately detect TP53 mutations at very low allelic fractions, in which cfDNA TP53 -mutated fragments were found in 11.4% of 123 matched non-cancer controls [70] (Fig. 1c).…”

Blood-Based Analysis of Circulating Cell-Free DNA and Tumor Cells for Early Cancer Detection

“…As an example, Fernandez-Cuesta and colleagues [12] recently used a pipeline specifically designed to accurately detect sequence variants present at very low fractions in cfDNA from patients with small-cell lung cancer (SCLC), addressing TP53 mutations, which are known to occur in the majority of cases of SCLC [13]. TP53 mutations were detected in only 35.7% of early-stage cases, indicating limited sensitivity as marker for detection of early SCLC.…”

“…Recent reports have shown that cancer-associated mutations are not restricted to cancer patients. For example, TP53-mutated cfDNA fragments were observed in 11.4% of 123 matched noncancer controls [12], and Krimmel and colleagues demonstrated very low levels of TP53 mutations in the peritoneal fluid and peripheral blood of women with benign ovarian lesions [14]. Likewise, leukemia-associated mutations have been shown to occur with increasing age and, although such mutations pose a statistically significant risk for a person to develop leukemia, most individuals (>90%) with these mutations never developed leukemia during their lifetime [15].…”