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Global Translational Medicine ctDNA in management of patients with NSCLC

disease. Liquid biopsy is a noninvasive and convenient test, time and money to run a test and also requires professional
which can be used for multiple times in a short period of researchers equipped with abundant relevant knowledge
time. In the meantime, the short half-life of ctDNA further and sufficient training to manipulate the detection. Cancer
makes real-time surveillance a possibility. Fourth, ctDNA personalized profiling by deep sequencing (CAPP-Seq) and
can act as a reference to tumor’s volume. In ctDNA-positive tagged-amplicon deep sequencing are classical and widely
patients, the mean plasma variant allele frequency (VAF) of recognized NGS-based methods [18,19] . PCR-based method
clonal SNVs correlated with tumor volume tested by three- is a high-throughput technique that involves the selection
dimensional reconstruction technology of spiral computed of targeted main mutation driver genes or the detection
tomography (CT). A linear relationship was found between of specific mutation spots, which can be meaningful
log-transformed tumor size and log-transformed mean to the outcome of adjuvant therapy, while NGS-based
clonal VAF values in ctDNA-positive cohort. Based on the method has high sensitivity, especially in early diagnosis,
TRACERx data, a plasma VAF of 0.1% is corresponding to a for its ability in detecting unknown mutations . As for
[20]
tumor burden of 10 cm 3[15] . Finally, ctDNA has the potential structural variations, NGS-based technology is the only
to be utilized throughout the whole clinical treatment means for detection. The analytical tools which extract
course. The potential of ctDNA has been explored under different features from NGS outputs allow for the detection
different circumstances and the outcome lived up to our of CNVs by low-coverage (0.1×) sequencing of the genome
expectations. The use of ctDNA is advantageous to many accompanied by normalization algorithms . Since CNVs
[21]
fields, including lung cancer screening and early detection as are also originally present in healthy individuals and
well as monitoring of MRD for both prognostic evaluation susceptible to tumor conditions , CNVs in ctDNA are
[22]
and prediction of therapeutic effect (Table 1) . quite difficult to discern. Recent technical development
[16]
on CNVs detection, within-sample aneupLoidy detection
1.3. ctDNA mutation classification and detection (WALDO), has set the detection threshold to 1% of cfDNA
technology
[23]
fragment concentration in sample plasma , but there is
ctDNA can barely be detected in peripheral blood. The still insufficient proof for its clinical applications. NGS is
precision of detection technology restricts the outcome of also applicable to the detection of genomic rearrangements.
liquid biopsy analysis. Various highly sensitive methods that
can be used to detect different mutational types have emerged. 1.3.2. Fragmentomics characters
ctDNA has unique mutation patterns compared Gel electrophoresis and electron microscopy were the
with normal tissue DNA and the following biomarkers first detection methods used to detect the length of
have been reported in the previous research: (i) Genetic cfDNA, and NGS-based methods are mainly used to
[20]
mutations and structural variations, such as SNVs and work out the fragmentomics characters at present .
copy number variations (CNVs); (ii) fragmentomics Except for fragment coverage and size, various innovative
characters, including motif, fragment length distribution, fragmentation patterns can be delineated by corresponding
and nucleosome distribution patterns; and (iii) epigenetic analytical techniques. DNA evaluation of fragments
changes, including DNA methylation, histone modification, for early interception (DELFI) used ~1× low-coverage
and amount of special non-coding RNA (ncRNA). whole-genome sequencing (WGS) to detect genomic
fragment abnormalities, including fragment coverage,
1.3.1. Genetic mutations and structural variations size distribution chromosome-arm copy number, and
[24]
To detect DNA mutations, polymerase chain reaction mitochondrial aligned reads from cfDNA . Ulz et al.
(PCR) and next generation sequencing (NGS) are developed another detection method to estimate the overall
recommended . Real-time PCR, droplet digital PCR, binding affinity of the transcription factor by cfDNA WGS.
[9]
amplification refractory mutation system, and BEAMing Transcription factors at specific genetic spots are protected
(that stands for beads, emulsion, amplification, magnetics) from endonuclease and transcription factor’s affinity
can be classified as PCR-based methods. These techniques consequently influenced ctDNA’s fragment distribution.
have high sensitivity and specificity with temperate cost The score of binding affinity exhibited its ability in early
[25]
for limited known mutation spot, but with a disability of detection and primary classification of cancer .
discerning structural variations, such as copy variations
and gene fusions . NGS-based method can overcome 1.3.3. Epigenetic changes
[17]
this problem by determining the order of nucleotides in Epigenetics refer to heritable chromatin modifications that
entire genomes or targeted regions of ctDNA and spotting impact gene expression without a direct effect on the coding
every DNA mutation a sample may have. However, with sequence of the DNA . DNA methylation is the most studied
[26]
the width of NGS-based detection, it inevitably costs more epigenetic regulatory mechanism and the methylation

Volume 1 Issue 1 (2022) 4 https://doi.org/10.36922/gtm.v1i1.96