Table 1.

NGS platforms designed for biomarkers in liquid biopsy.

Technology	Brief Description	References
Non Targeted
WES	Whole Exome Sequencing sequences all exons in ctDNA for mutation detection. Less expensive than WGS (lower coverage). Sample requirement not always feasible in liquid biopsy.	[107,108,109]
Digital Karyotyping	Uses WGS to sequence short DNA tags and then aligns these tags to the reference genome to identify genomic alterations, e.g., CNVs, SNVs and SVs. The short DNA tags are typically generated by restriction enzyme digestion. Requires high-quality genomic DNA.	[43,110,111,112]
FAST-SeqS	Fast Aneuploidy Screening Test-sequencing System uses individual primer pairs to amplify the repeat regions of interest. The WGS version, called mFAST-SeqS, identifies any somatic mutations in the tumor and then uses those mutations as unique markers for monitoring the disease.	[113,114,115]
PARE	Personalized Analysis of Rearranged Ends uses WGS data to identify rearranged ends in ctDNA. Detects structural variations, e.g., translocations and inversions.	[111,116,117]
Targeted panel
Tam-seq	Tagged-Amplicon deep sequencing uses primers targeting regions of interest for a pre-amplification step. Templates undergo individual amplification, aiding purification.	[44]
Safe-SeqS	Safe-Sequencing System is a method for profiling low-frequency mutations. The method combines PCR amplification of targeted genomic regions with UMIs and deep sequencing to achieve high accuracy and sensitivity. The use of UMIs reduces errors introduced by PCR amplification and sequencing.	[118]
CAPP-Seq	Cancer Personalized Profiling by Deep Sequencing uses a library that generates many hybrid affinities captures of recurrently mutated genomic regions to create the selector, which is used to identify individual-specific mutations in the tumor DNA. The selector is then applied to ctDNA for quantification.	[119]
Ion AmpliSeq™	Customized multiplex PCR amplifies target regions for analysis with the Ion Torrent sequencing platform.	[120]
Guardant360®	Analyzes 73 genes commonly mutated in cancer. Digital sequencing technology for mutation detection with 99.5% sensitivity and 99.999% specificity. FDA approval for use in patients with advanced cancer without treatment options.	[100,101]
Foundation One®CDx	Analyzes 324 genes and selects genomic signatures, including MSI and TMB. Detects single nucleotide variants, small in/dels, copy number alterations and gene fusions. FDA-approved for use in patients with solid tumors, including NSCLC, to sort patients for specific targeted therapies.	[102,103]
iDES	In Integrated Digital Error Suppression, DNA is tagged with UIDs and tracked through library preparation and sequencing for error correction. By incorporating UIDs into NGS, iDES can improve the accuracy and sensitivity of NGS assays, particularly in low-frequency variant detection.	[121]
TEC-Seq	Targeted Error Correction Sequencing is a method for profiling low-frequency mutations in cfDNA. Utilizes molecular barcoding to distinguish true mutations from false positive variants. Before any amplification, DNA fragments are tagged with different “exogenous” DNA barcodes. Additionally, the start and end genome mapping positions of paired-end sequenced fragments are used as “endogenous barcodes” to differentiate between individual molecules. This combination of barcodes enables tracking each fragment, allowing for the detection of rare mutations with high accuracy and sensitivity.	[98]

Abbreviations: CNVs: Copy Number Variations; ctDNA: circulating tumor DNA; FDA: US Food and Drug Administration; mFAST-SeqS: Mutation-focused Assessment of Sequencing and Tracking by Sequencing; MSI: microsatellite instability; SNVs: Single Nucleotide Variations; SVs: Structural Variations; TMB: Tumor Mutational Burden; UIDs: Unique Identifiers; UMIs: Unique Molecular Identifiers; WGS: Whole-Genome Sequencing.