Step-wise validation results for a selected subset of 25 marker candidates derived from the discovery process and from the literature.1
Gene symbol (HUGO) | Methylation array | Real-time PCR | ||||||
---|---|---|---|---|---|---|---|---|
AUC, CRC vs all controls | AUC, CRC vs colon controls | PBL: median PMR, % | PBL: median PMR, % | Healthy colon: median PMR (90% range), % | CRC: median PMR, (90% range), % | AUC | Exclusion criteria | |
BCL6 | 0.73 | 0.78 | 25 | Failed chip-selection criteria | ||||
DNAJC5 | 0.67 | 0.73 | 23 | |||||
DUX2 | 0.75 | 0.70 | 17 | |||||
ESTG0208962 | 0.64 | 0.63 | 9 | |||||
MSH63 | 0.58 | 0.64 | 0 | |||||
ESTG23086092 | 0.62 | 0.56 | 22 | |||||
DLX5 | 0.84 | 0.83 | 0 | PBL+ | Failed PBL filter | |||
NPBWR1 (GPR7) | 0.73 | 0.82 | 0 | PBL+ | ||||
APBA23 | NT4 | NT | NT | PBL+ | ||||
SLC32A1 | 0.85 | 0.89 | 0 | 1.0 | ||||
SLITRK1 | 0.86 | 0.85 | 1 | 0.3 | ||||
KCTD12 | 0.67 | 0.77 | 0 | 0.0 | 0 (0–0) | 0 (0–28) | 0.53 | Insufficient CRC methylation |
ONECUT2 | 0.72 | 0.77 | 2 | 0.0 | 1 (0–1) | 0 (0–2) | 0.24 | |
RNF4 | 0.79 | 0.84 | 0 | 0.0 | 0 (0–0) | 0 (0–0) | 0.52 | |
SMAD7 | 0.68 | 0.71 | 0 | 0.0 | 0 (0–0) | 0 (0–1) | 0.59 | |
TUSC33 | 0.82 | 0.74 | 1 | 0.2 | 3 (1–10) | 11 (1–32) | 0.71 | Failed LOD test |
TMEFF2 | 0.90 | 0.94 | 0 | 0.1 | 4 (1–9) | 30 (1–81) | 0.81 | |
ZDHHC22 | 0.88 | 0.87 | 9 | 0.0 | 0 (0–1) | 3 (0–27) | 0.78 | HM assay failed |
VTN | 0.93 | NT | 1 | 0.0 | 2 (0–4) | 20 (0–77) | 0.81 | Plasma positive |
FOXL2 | 0.67 | NT | 0 | 0.0 | NT | 7 (0–38) | NT | Candidates for plasma testing |
NGFR | 0.83 | 0.87 | 0 | 0.0 | 0 (0–2) | 3 (0–60) | 0.69 | |
ALX4 | 0.65 | 0.83 | 0 | 0.1 | 1 (0–2) | 11 (0–58) | 0.74 | |
SIX6 | 0.77 | 0.85 | 0 | 0.0 | 0 (0–0) | 16 (0–46) | 0.83 | |
EYA4 | 0.66 | 0.81 | 4 | 0.0 | 2 (0–4) | 26 (0–76) | 0.88 | |
SEPT9 | 0.84 | NT | 0 | 0.0 | 2 (1–7) | 26 (0–89) | 0.87 |