Table 3.
SNPs with possible discordance >10% in FFPE‐T.
| Study label | Gene | rsID | # FFPE‐T strict discordant calls | # FFPE‐T no‐calls | # blood no‐calls | Possible discordancea |
|---|---|---|---|---|---|---|
| 4E | VEGFC | rs1485766 | 1 | 8 | 3 | 10.5% |
| 6O | ESR1 | rs2046210 | 5 | 7 | 1 | 11.4% |
| 6T | ESR1 | rs3853250 | 3 | 8 | 1 | 10.5% |
| 6Z | ESR1 | rs1709181 | 4 | 8 | 1 | 11.4% |
| 6BD | OPRM1 | rs1799971 | 1 | 70 | 0 | 62.3% |
| 7A | Intergenic | rs2097903 | 2 | 10 | 0 | 10.5% |
| 7F | ABCB1 | rs2032582 | 2 | 15 | 3 | 17.5% |
| 7G | CYP3A | rs10273424 | 0 | 27 | 1 | 24.6% |
| 9A | SLC28A3 | rs7853758 | 0 | 44 | 2 | 40.4% |
| 10M | CYP2C8 | rs11188172 | 0 | 25 | 1 | 22.8% |
| 10Q | CYP17A1 | rs4919687 | 0 | 12 | 0 | 10.5% |
| 11Bb | PGR | rs500760 | 6 | 6 | 0 | 10.5% |
| 12M | NCOR2 | rs1812730 | 1 | 10 | 1 | 10.5% |
| 13J | HTR2A | rs6311 | 2 | 18 | 4 | 21.1% |
| 13L | SLC10A2 | rs2301159 | 3 | 7 | 3 | 11.4% |
| 14I | ESR2 | rs1952585 | 1 | 18 | 1 | 17.5% |
| 14R | AKT1 | rs2494732 | 3 | 10 | 5 | 15.8% |
| 15Eb | CYP19A1 | rs9806371 | 11 | 22 | 2 | 30.7% |
| 15S | CYP19A1 | rs730154 | 0 | 10 | 2 | 10.5% |
| 15U | CYP19A1 | rs4774585 | 2 | 5 | 5 | 10.5% |
| 16D | SPG7 | rs12960 | 4 | 10 | 0 | 12.3% |
| 17A | PELP1 | rs9436 | 2 | 11 | 0 | 11.4% |
| 22D | COMT | rs6269 | 1 | 12 | 0 | 11.4% |
| 22Eb | COMT | rs4633 | 8 | 6 | 0 | 12.3% |
| 22F | COMT | rs4818 | 3 | 10 | 0 | 11.4% |
| 22L | EP300 | rs20551 | 1 | 8 | 5 | 12.3% |
| 22Q | NDUFA6 | rs1801311 | 4 | 10 | 0 | 12.3% |
| 22R | CYP2D6 | rs28371738 | 1 | 13 | 5 | 16.7% |
a
Calculated as: # of strict discordant calls + FFPE‐T no‐calls + blood no‐calls/number of patients (n = 114).
b
Also failed due to strict discordance >5% in FFPE‐T (Table 2).