The Role Of Circulating Tumor DNA In Therapeutic Resistance

Figures & data

Table 1 Comparison Of Strengths And Limitations Between ctDNAs And Other Circulating Biomarkers

	Strengths	Limitations	References
Similarities	-Noninvasive -High specificity for multiple types of cancer -Vital function in the diagnosis, progression monitoring, and prognosis of cancer	-Lack of standardization in isolation, enrichment, or detection techniques -Combined application is necessary for a more comprehensive insight into cancer specificity	^Citation19,Citation68,Citation69
ctDNAs	-Allowing for early detection and high sensitivity -Relatively higher detection rates -Tracing tumor heterogeneity temporally and spatially	-Analysis limited to segments of DNA -Functional genomic testing cannot be performed -No co-localization of signal	^Citation70^–^Citation73
CTCs	-Fully showing the molecular profile of RNAs and proteins -Achievable structural evaluation of intact tumor cells -Show alterations in the whole genome -Co-localization of signal -Available for ex-vivo functional studies	-Influence of heterogeneity on selection methods -Low signal-to-noise rate, especially in early stage cancer -Detection limited to metastasis period	^Citation74^–^Citation76
Exosomes	-Extractable from many biological fluids -Allowing for early detection and stable -mRNA and miRNAs enriched from exosomes, as well as lipids and metabolites, can serve as reliable biomarkers	-Lack of large scale in vivo studies -Function in immune response and interplay with the tumor environment require further research into the mechanism	^Citation77^–^Citation80
miRNAs	-Exist in different biological fluids and benefit the early detection of cancer -More stable and resistant to storage and handling -Detectable in low quantity of sample with high specificity	-Hemolysis causing specific miRNAs mixed with ruptured erythrocytes containing miRNAs -Difficulty in accurately measuring the expression level	^Citation81^–^Citation83
Proteins	-Easy detection and quantification -Proved efficiency in the prediction of recurrence and monitoring of therapeutic efficacy	-Low accuracy for early clinical diagnosis	^Citation68
lncRNAs	-Stable and levels indicative of severity -Wide range of expression patterns in various cancers	-Low quantity and quality resulting in low signal-to-noise ratios -Development of efficient detection technologies is required -Lack of clinical trials	^Citation84^–^Citation86

Abbreviations: CTC, circulating tumor cell; ctDNA, circulating tumor DNA; lncRNA, long non-coding RNA; miRNA, microRNA.

Table 2 Sequencing Technologies For ctDNA Analysis

Categories Of Sequencing Technologies		Type Of Alterations	Cancer Types	References	Advantages		Limitations
PCR-based
Nested real-time PCR		Genomic rearrangements	Breast cancer, osteosarcoma	^Citation87	-Ease of use -Lowest cost		-Lower sensitivity -Only detect limited genomic loci
ARMS-Scorpion PCR		PIK3CA mutation	Breast cancer	^Citation88
PAP-A amplification		TP53 mutation	Breast cancer	^Citation89
		EGFR deletion	Non-small cell lung cancer
Digital PCR-based
BEAMing		NRAS, KRAS mutation	Colorectal cancer	^Citation90	-Ease of use		-Only detect limited genomic loci or single nucleotide variants
		KRAS mutation	Pancreatic cancer	^Citation91
		EGFR mutation	Non-small cell lung cancer	^Citation92
Droplet-based digital PCR		NPY methylation	Colorectal cancer	^Citation93	-High sensitivity
Microfluidic digital PCR		TP53 and PTEN mutation	Ovarian, pancreatic cancer	^Citation94	-Clinically validated
Targeted deep sequencing
Safe-SeqS		KIT mutation	Gastrointestinal stromal tumor	^Citation95	-High sensitivity -Relatively inexpensive	For selected alterations across targeted regions
TAm-Seq		TP53 mutation	Ovarian cancer	^Citation96
		EGFR mutation	Non-small cell lung cancer
CAPP-Seq		KRAS, APC, and TP53 mutation	Ovarian cancer	^Citation97
Ion-AmpliSeq		TP53, KRAS, and EGFR mutation	Non-small cell lung cancer	^Citation98,Citation99
Whole-genome sequencing (with NGS)	Copy number aberrations		Non-small cell lung cancer	^Citation100	-Broad application	-Expensive -Low sensitivity
	Alterations in DNA repair deficiency genes and biallelic inactivation		Prostate cancer	^Citation101
	KRAS and BRAF mutation		Colorectal cancer	^Citation102
Whole-exome sequencing (with NGS)	SNVs and copy number aberrations		Wilms’ tumor, neuroblastoma	^Citation103,Citation104	-Broad application	-Expensive -Low sensitivity -Lack of standardization
	EGFR mutation		Non-small cell lung cancer	^Citation105

Abbreviations: ARMS, amplification refractory mutation system; BEAMing, beads, emulsion, amplification, magnetics; CAPP-seq, cancer personalized profiling by deep sequencing; NGS, next generation sequencing; PAP-A, pyrophosphorolysis-activated polymerization allele-specific-amplification; PCR, polymerase chain reaction; Safe-SeqS, safe-sequencing system; SNV: single-nucleotide variants; TAm-Seq, tagged amplicon deep sequencing.

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