The potential of liquid biopsies for the early detection of cancer

Abstract

Precision medicine refers to the choosing of targeted therapies based on genetic data. Due to the increasing availability of data from large-scale tumor genome sequencing projects, genome-driven oncology may have enormous potential to change the clinical management of patients with cancer. To this end, components of tumors, which are shed into the circulation, i.e., circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), or extracellular vesicles, are increasingly being used for monitoring tumor genomes. A growing number of publications have documented that these "liquid biopsies" are informative regarding response to given therapies, are capable of detecting relapse with lead time compared to standard measures, and reveal mechanisms of resistance. However, the majority of published studies relate to advanced tumor stages and the use of liquid biopsies for detection of very early malignant disease stages is less well documented. In early disease stages, strategies for analysis are in principle relatively similar to advanced stages. However, at these early stages, several factors pose particular difficulties and challenges, including the lower frequency and volume of aberrations, potentially confounding phenomena such as clonal expansions of non-tumorous tissues or the accumulation of cancer-associated mutations with age, and the incomplete insight into driver alterations. Here we discuss biology, technical complexities and clinical significance for early cancer detection and their impact on precision oncology.

Fig. 1

Plasma DNA diagnostics in physiologic and pathologic conditions. a Pregnancy is a physiologic scenario which results in a relatively constant and reproducible, i.e., similar in different pregnancies, release of fetal or placental DNA into the circulation. Hence, diagnostic procedures are easy to standardize. The graph at the bottom indicates the fetal plasma DNA fraction as a function of gestational age and shows a positive correlation. In the majority of pregnancies fetal fractions of more than 4%, which is considered to represent a threshold for reliable non-invasive prenatal testing, are already present at 10^th week of pregnancy (graph adapted from ref. 126). b In contrast, cancer is a pathologic process, which is often heterogeneous (various clones within the primary tumor are depicted in different colors and furthermore metastatic sites, which also contribute) including multiple parameters, e.g., the microenvironment (indicated here by tumor infiltrating lymphocytes) and access to blood vessels, which affect the release of tumor DNA and which may cause significant variation from one patient to the next. At the bottom, average ctDNA levels for tumor stages I to IV are depicted. However, as indicated by the bars, these values may vary tremendously for each stage (graph adapted from ref. 42) and are frequently below 4% required for NIPT. For clarity, we only show DNA fragments in the blood vessels, although other factors, e.g., extracellular vesicles, or modifications of the DNA either by epigenetic changes or alterations in the nucleic acid sequence can also be detected in the systematic circulation

Fig. 2

Tumors, clonal expansions and their respective lead times. a In breast cancer, tumors with “favorable” biological features (grade 1) may have extensive lead times of up to 19 years and these tumors contribute to significant overdiagnosis by screening mammography. Even if detected at a late stage, these tumors often have an excellent prognosis. In contrast, breast cancers with unfavorable biological features (grade 2–3) usually have short lead times (<2 years) and are therefore less frequently identified by screening mammography. However, because of their biology, early diagnosis would be mandatory to significantly reduce mortality. b In CRC, tumors develop through well-defined stages (i.e., stages I–IV), a process which may take up to 20–40 years and is the result of the accrual of specific mutations in tumor driver genes (image adapted from refs. 127,128). As survival rates are stage-dependent, the earlier the diagnosis is made the better. In the two scenarios depicted in a and b, the primary clinical challenge remains to determine the fate of the specific lesions so that they do not always differ fundamentally, but transitions exist. c Clonal expansions are best characterized in hematopoietic systems and are frequently associated with known driver gene mutations. Their lead time is hard to determine. For CHIP (clonal hematopoiesis of indetermined potential), the odds of progression to overt neoplasia were estimated to be approximately 0.5–1% per year

Fig. 3

The three early cancer detection scenarios. a The detection of relapse after surgery with curative intent is facilitated by the option to profile the resected tumor and to use this information for the design of personalized assay panels, which can be used for high-resolution monitoring approaches. b In individuals at-risk, i.e., due to a cancer-predisposition germline mutation, chronic exposure to toxic agents, or due to viral infections, systemic screening approaches can be extended by proximal sampling, i.e., the analysis of other body fluids than blood which are close to the organ with high-risk of malignant transformation. c In the “general population”, i.e., persons without a family history of cancer or known risks for tumors at certain sites, liquid biopsy concepts for screening may include the search for mutations, somatic copy number alterations, or analyses of methylation and chromatin patterns. However, generally accepted strategies do not yet exist. Naturally occurring phenomena such as the aging associated mutation rate or clonal expansions of non-tumorous tissue may hamper early detection efforts (see also Table 1)