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Circulating tumor cells and circulating tumor DNA in precision medicine
Published in Debmalya Barh, Precision Medicine in Cancers and Non-Communicable Diseases, 2018
Recent advances in genomics technologies are paving the way for the analysis of ctDNA. NGS technologies are now being used for plasma DNA analysis to allow more comprehensive detection of mutations across wider genomic regions. Types of tumor-specific aberrations that have been detected in ctDNA include somatic single nucleotide variants (SNVs), chromosomal rearrangements, and epigenetic alterations (Leon et al., 1977; Esteller et al., 1999; Silva et al., 1999; Wong et al., 1999; Lecomte et al., 2002; Hanley et al., 2006; Umetani et al., 2006; Warton and Samimi, 2015). The detection of SNVs in plasma DNA has been achieved by the use of a variety of PCR approaches (Nawroz et al., 1996; Tomita et al., 2007; Zhai et al., 2012), but digital PCR has now emerged as a sensitive analytical tool for the detection of mutations at low allele fractions (Diaz and Bardelli, 2014). Methods involving the use of digital PCR include droplet-based systems; microfluidic platforms; and the use of beads, emulsions, amplification, and magnetics (BEAMing) (Yoshimasu et al., 1999; Ito et al., 2002; Hanley et al., 2006; Heitzer et al., 2013b; Lipson et al., 2014); Targeted deep sequencing using PCR-based (e.g., TAm-Seq, Safe-Seq, Ion AmpliSeq™) or capture-based (e.g., CAPP-seq) approaches have been used to sequence specified genomic regions in plasma DNA (Leon et al., 1977; Vasioukhin et al., 1994; Shinozaki et al., 2007; Heyn and Esteller, 2012; Schwarzenbach et al., 2012). Additionally, whole-exome analysis of plasma DNA has opened up new opportunities to carefully characterize mutation profiles, without the need to focus on predefined or existing mutations (Esteller et al., 1999). Chromosomal rearrangements such as translocations or gains/losses of chromosomal regions can also be detected in ctDNA, providing excellent sensitivity and specificity as tumor biomarkers (Umetani et al., 2006; Bidard et al., 2014). Personalized analysis of rearrangement ends (PARE) is a method that involves the identification of specific somatic rearrangements in tumor tissue and the subsequent design of PCR-based assays to detect these alterations in plasma DNA (Leon et al., 1977). Moreover, in selected cases, whole-genome sequencing has now been directly applied to plasma DNA analysis to view somatic chromosomal alterations and copy number aberrations in ctDNA genome-wide (Silva et al., 1999; Wong et al., 1999; Kawakami et al., 2000).
The current status of the clinical utility of liquid biopsies in cancer
Published in Expert Review of Molecular Diagnostics, 2019
Anson Snow, Denaly Chen, Julie E. Lang
The most significant advantage of NGS is the ability to identify novel tumor mutations and track changes temporally with treatments. However, these techniques require a large amount of ctDNA, ≥10% in a blood sample, to reconstruct tumor-specific copy numbers consistently [53]. Low ctDNA concentrations are problematic as it was mentioned earlier that the total concentration of ctDNA obtained in a sample is generally <1% of total cfDNA. Another method of detection is Cancer Personalized Profiling by deep Sequencing (CAPP-Seq), which has been successfully applied in NSCLC [54] but may be applied to any cancer type with a known pattern of genetic mutations. Instead of targeting recurrent point mutations that may or may not be present in all patients, CAPP-Seq designs a library based on databases such as The Cancer Genome Atlas (TCGA) that targets reoccurring mutated regions in the cancer of interest [54].
Circulating tumor DNA: an important tool in precision medicine for lymphoma
Published in Expert Review of Precision Medicine and Drug Development, 2018
Vincent Camus, Elodie Bohers, Sydney Dubois, Hervé Tilly, Fabrice Jardin
CAncer Personalized Profiling by deep Sequencing (CAPP-seq) is a highly sensitive modern technique for measuring ctDNA that runs high-performance, high-throughput sequencing and allows the prompt quantification of rare circulating somatic variants in numerous tumors [25]. In their report, the authors established the presence of ctDNA in all patients with stage II–IV non-small cell lung cancer (NSCLC) and in 50% of patients with small tumor burden (stage I), with 96% specificity for the mutant allele fractions down to ~0.02%. In an additional notable study, CAPP-seq was performed to investigate tumor biopsies and ctDNA from 92 lymphoma patients and 24 healthy subjects [26]. The study spots different modes of clonal evolution that distinguish indolent follicular lymphomas (FL) and those that transformed into DLBCL, which may hopefully lead to a noninvasive way of appraising histological transformation in the coming years. In addition, the same authors were able to precisely establish the DLBCL Cell of Origin (COO) subtypes by testing somatic mutations that were detectable in ctDNA using the CAPP-seq method. In this study including 146 DLBCL patients [27], COO classification determined by tumor immunohistochemistry or ctDNA was highly concordant (88%). In comparison to dPCR, CAPP-seq can not only discern point mutations but is also capable of discriminating indels as well as structural variations including translocations and copy number variations and is able to examine many loci in the same experiment [28]. CAPP-seq seems to be a promising method that overcomes some of the restraints of the GEP- and IHC-based techniques, including the requirement of tumor biopsies, scarcity of tissue, and unequal assay efficiency. Furthermore, it is striking that the ctDNA measurements obtained by this CAPP-seq method are highly robustly correlated with the tumor volume evaluated using PET scan during treatment, and there was an outstanding homogeneity between the plasma ctDNA changes, the response after two cycles of chemotherapy and the clinical consequence in DLBCL patients [29].
Liquid biopsy in newly diagnosed patients with locoregional (I-IIIA) non-small cell lung cancer
Published in Expert Review of Molecular Diagnostics, 2019
Kezhong Chen, Guannan Kang, Heng Zhao, Kai Zhang, Jian Zhang, Fan Yang, Jun Wang
Monitoring the treatment response is also important, as clinicians will decide on further treatment by evaluating the current treatment response. Traditional strategies for treatment response evaluation are based on radiological methods, which have substantial limitations. For patients who undergo R0 resection, radiological methods are difficult to assess and analyze the treatment response of adjuvant therapy, while liquid biopsy can evaluate the therapeutic effect by quantitative detection of components derived from tumor. In addition, evaluation by CT scanning can be lack of accuracy, especially when patients are receiving immune checkpoint inhibitors. Patients treated with immune checkpoint inhibitors may exhibit pseudoprogression, which is difficult to distinguish from progression by radiological methods and requires subsequent imaging. Promisingly, longitudinal ctDNA detection has been shown to predict response and survival in patients treated with anti-programmed cell death 1 (PD-1) antibodies [54,55]. Moreover, the treatment response should be evaluated in real time so that clinicians can decide the treatment strategy, but radiological methods cannot meet this requirement. Previous studies have shown that ctDNA levels decrease rapidly after radical resection of the tumor, indicating that quantitative ctDNA detection can reflect the tumor burden. Chen et al. investigated the mutation frequency variance of plasma ctDNA during perioperative period. ctDNA obtained before and during surgery had the same mutations with a low variance in mutation frequency. And as expected, ctDNA frequency reduced sharply after curative surgery [26]. Similarly, Guo et al. analyzed preoperative and postoperative plasma ctDNA frequencies among 23 stage Ⅰ NSCLC patients, and the average mutation frequency declined from 8.88% to 0.28% [56]. As a result, the dynamic characteristics of ctDNA can be used to monitor the treatment response. Newman et al. showed that the ctDNA levels detected by CAPP-Seq were significantly correlated with tumor volume and could provide an earlier response assessment than radiographic approaches [52]. As CAPP-Seq has relatively high sensitivity and specificity, evaluation of the therapeutic response by ctDNA detection may be applied clinically in the future.