Table 3. Targeted analysis in plasma.
Targeted analysis in WISECONDOR data of 61 selected genomic regions and genes (reported in S2 Table). All regions with a Z-score 3.0 or higher and their corresponding findings in the whole-genome targeted plasma analyses and tissue array-CGH are presented. The “Ratio” column contains the normalized coverage difference in the targeted analysis, corresponding to effect size in the whole-genome analysis.
| Individual | Target region | Targeted analysis | Whole genome analysis | |||
|---|---|---|---|---|---|---|
| Z-score | Ratio | WC | Ichor | Tissue | ||
| P01 | CD44 | 14 | 63% | Amp | Gain | 0 a |
| P01 | ZNF217 | 7.0 | 27% | Amp | Amp | Gain |
| P01 | 15q26.1 | 6.9 | 32% | Amp | Amp | Amp |
| P01 | VEGFA | 5.7 | 21% | Amp | Amp | Gain |
| P02 | CDK6 | 33 | 71% | Amp | Amp | Amp |
| P02 | CCND1 | 12 | 26% | Amp | Gain | Amp |
| P03 | EGFR | 160 | 439% | Amp | 0 | Amp |
| P03 | MYC | 4.7 | 11% | Gain | Amp | Amp |
| P04 | 2q32.1 | 8.6 | 21% | Amp | Amp | Amp |
| P05 | MYC | 28 | 50% | Amp | 0 | Amp |
| P06 | KLF5 | 8.1 | 16% | Amp | 0 | Gain |
| P07 | CCND1 | 12 | 24% | Amp | 0 | 0 |
| P08 | MYC | 79 | 114% | Amp | Amp | Gain |
| P09 | KRAS | 11 | 20% | Amp | 0 | Gain |
| P09 | MYC | 9.6 | 18% | Amp | Amp | Amp |
| P11 | 21q11.2 | 3.2 | 5% | 0 | 0 | 0 |
| P13 | MYC | 12 | 20% | Amp | Amp | 0 |
| P33 | FGFR2 | 3.2 | 6% | 0 | 0 | 0 |
| P37 | KDR | 3.3 | 6% | 0 | 0 | 0 |
| P40 | CD44 | 3.7 | 6% | 0 | 0 | 0 |
| P44 | FGFR2 | 124 | 382% | Amp | Amp | 0 |
| P44 | CD44 | 81 | 317% | Amp | Amp | 0 |
| P44 | KLF5 | 6.5 | 20% | Amp | Gain | 0 |
Amp; amplification, indicates an approximated gain of 5 or more copies. The ratio corresponds to the effect size and is the difference in the normalized sequencing coverage for the target bin/region. WC; WISECONDOR (whole-genome plasma analysis). ichor; ichorCNA (whole-genome plasma analysis). Tissue; array-CGH in tumour tissue biopsy.
a; The gain on chromosome 11 detected in tissue array-CGH does not include the CD44 gene.