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Table 1 Technologies for circulating tumor DNA (ctDNA) detection

From: Cell-free circulating tumor DNA in cancer

Principle of detection Method Type of alteration Advantage(s) Limitation(s) Selected reference(s)
PCR-based Nested real-time PCR Known point mutations such as KRAS, EGFR, and PIK3CA hotspot alterations Ease of use, lowest cost Lower sensitivity, only detect limited genomic loci [70]
ARMS/Scorpion PCR [116]
PCR-SSCP [117]
Mutant allele-specific PCR [118]
Mass spectrometry [119]
Bi-PAP-A amplification [120]
Digital PCR BEAMing Known point mutations, genomic rearrangements High sensitivity Only detect limited genomic loci [59]
Droplet-based digital PCR [56]
Microfluidic digital PCR [10]
Targeted deep sequencing SafeSeq Selected SNVs, CNVs, and rearrangements across targeted regions High sensitivity, relatively inexpensive Less comprehensive than WES methods [64]
TamSeq [57]
Ion-AmpliSeq™ [66, 68]
CAPP-Seq [68]
OnTarget [121]
Whole-genome sequencing Digital karyotyping Genome-wide SNVs, CNVs, and rearrangements Broad application Expensive [73]
PARE [70, 72, 74]
  1. PCR polymerase chain reaction, ARMS amplified refractory mutation system, SSCP single-strand conformation polymorphism, Bi-PAP-A amplification bidirectional pyrophosphorolysis-activated polymerization allele-specific amplification, BEAMing beads, emulsion, amplification, and magnetics, SafeSeq safe sequencing system, TamSeq tagged amplicon deep sequencing, CAPP-Seq cancer personalized profiling by deep sequencing, PARE personalized analysis of rearranged ends, KRAS Kirsten rat sarcoma viral oncogene homolog, EGFR epidermal growth factor receptor, PIK3CA phosphatidylinositol-4,5-biphosphate 3-kinase, catalytic subunit alpha, SNV single-nucleotide variants, CNVs copy number variations, WES whole-exome sequencing