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Table 3 Comparison of different approaches for ctDNA detection

From: Next Generation-Targeted Amplicon Sequencing (NG-TAS): an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA

  NG-TAS Digital PCR TAm-Seq Oncomine™ Breast cfDNA Assay
Approx. cost per sample (GBP) 3 × 10 2–3 10 200
Time (96 reactions) 7 h 3 h × 2 2 days 2 days
Number of amplicons 377 1 48 n/a
Amplicon size (bp) < 160 n/a < 200 < 170
Number of genes 20 1 (hotspot) 6 10
Choice of targets Flexible Limited Flexible Limited
Median depth 3064 770 650 (avg) n/a
Limit of detection (%) 1–2 > 0.1 1–2 0.6–0.1
Library material as input Yes Not tested Not tested Not tested
Ideal input (ng) 3 × 10 2–5 50 20
Multiplex 8plex No No n/a
Number of samples per sequence run 384 n/a 96 12
Platform Fluidigm Access Array Fluidigm qdPCR Fluidigm Access Array Ion Chef System
Sequencing Illumina HiSeq 4000 n/a Illumina GAIIx Ion S5/S5XL™