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Table 3 Overview of the cfDNA extraction and variant analysis methods methods used by the participants

From: International pilot external quality assessment scheme for analysis and reporting of circulating tumour DNA

  # participants to KRAS analysis (%) (n = 23) # participants to NRAS analysis (%) (n = 20) # participants to EGFR analysis (%) (n = 31)
cfDNA extraction method
 QIAamp Circulating Nucleic AcidKit (Qiagen) 14 (60.9) 13 (65.0) 17 (54.8)
 Cobas cfDNA Sample Preparation Kit (Roche) 4 (17.4) 3 (15.0) 8 (25.8)
 MagMAX Cell-Free DNA Isolation Kit (Thermo Fisher Scientific) 3 (13.0) 3 (15.0) 3 (9.7)
 Maxwell® RSC ccfDNA Plasma Kit (Promega) 1 (4.3) 0 (0.0) 1 (3.2)
 Nucleospin Plasma XS (Macherey-Nagel) 1 (4.3) 1 (5.0) 1 (3.2)
 QIAamp DSP DNA Blood Mini Kit (Qiagen) version 2 0 (0.0) 0 (0.0) 1 (3.2)
Variant analysis method
 NGS 13 (56.5) 13 (65.0) 12 (38.7)
 Commercial Kit 4 (17.4) 3 (15.0) 11 (35.5)
 LDT 1 (4.3) 0 (0.0) 1 (3.2)
 BEAMing 1 (4.3) 1 (5.0) 0 (0.0)
 ddPCR 4 (17.4) 3 (15.0) 7 (22.6)
  1. The LDT consisted of a 5’nuclease polymerase-chain reaction (Taqman) with peptide nucleic acid probe. For a detailed breakdown of the used methods see Additional file 2: Table S2. Abbreviations: BEAMing Beads, emulsification, amplification, and magnetics, ddPCR Droplet digital polymerase chain reaction, LDT Labroratory-developed test, NGS Next-generation sequencing
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BMC Cancer

ISSN: 1471-2407

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