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Table 1 Platforms used to analyze cell-free DNA in circulation

From: Liquid biopsy: a step forward towards precision medicine in urologic malignancies

Method Platform Applications Advantages Limitations Reference
PCR-based Nested real-time PCR • Known point mutations
• Methylated genes
• Ease of use
• Low cost
• Low sensitivity
• Detect limited genomic loci
[129131]
Mutant allele-specific PCR
Mass spectrometry
Digital PCR Droplet digital PCR • Known point mutations
• Methylation
• Very high sensitivity
• Quantitative
• Detect limited genomic loci [132, 133]
Microfluidic digital PCR
Targeted Sequencing Safe-SeqS • Selected SNVa, SCNAb and rearrangements • High sensitivity
• Low cost
• Less comprehensive than next gen sequencing [134136]
Tam-Seq
CAPP-Seq
Whole genome sequencing karyotyping • Genome wide SNV, SCNA and rearrangements • Detect all genomic loci • Expensive
• Time consuming
[137139]
PAREc
  1. aSingle nucleotide variant, bSomatic copy number alteration, cPersonalized analysis of rearranged ends