Table 2.
Top ranking SNPs for meta-analysis using cumulative dose to first instance of Grade 2 or higher peripheral neuropathy event.
| CALGB 40101 | CALGB 40502 | Meta | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| SNP* | Alleles† | Gene | Location | MAF | Effect‡ | P | MAF | Effect‡ | P | P |
| rs74497159 | T>G | S1PR1 | 168 kb 3’ | 0.065 | 0.591 | 5.96E-04 | 0.055 | 0.693 | 1.59E-04 | 3.62E-07 |
| rs3110366 | T>A | ZFPM2 | 142 kb 5’ | 0.204 | −0.394 | 1.20E-03 | 0.198 | −0.446 | 2.51E-04 | 1.07E-06 |
| rs77526807 | G>T | C9orf106 | 39 kb 3’ | 0.053 | 0.818 | 4.32E-04 | 0.059 | 0.764 | 1.14E-03 | 1.66E-06 |
| rs17076837 | C>G | SLITRK1 | 382 kb 3’ | 0.135 | 0.578 | 7.72E-06 | 0.124 | 0.304 | 2.78E-02 | 1.85E-06 |
| rs61963755 | T>A | KLHL1 | intron | 0.050 | 0.674 | 3.60E-04 | 0.055 | 0.630 | 1.56E-03 | 1.88E-06 |
| rs2342780 | T>A | ZFPM2 | 68 kb 5’ | 0.069 | −0.788 | 8.07E-06 | 0.064 | −0.432 | 3.81E-02 | 2.06E-06 |
| rs10771973 | G>A | FGD4 | intron | 0.311 | 0.451 | 3.91E-06 | 0.301 | 0.203 | 3.65E-02 | 2.15E-06 |
| rs2342791 | T>C | ZFPM2 | 43 kb 5’ | 0.164 | −0.414 | 1.03E-03 | 0.162 | −0.430 | 7.43E-04 | 2.53E-06 |
| rs11076190 | T>C | CX3CL1 | 8 kb 3’ | 0.060 | 0.738 | 3.18E-05 | 0.063 | 0.453 | 1.38E-02 | 2.55E-06 |
| rs78777495 | A>T | SUGCT | 67 kb 3’ | 0.107 | 0.602 | 1.11E-05 | 0.097 | 0.328 | 4E-02 | 2.99E-06 |
| rs9623812 | A>T | SCUBE1 | intron | 0.330 | −0.340 | 3.70E-03 | 0.335 | −0.387 | 2.60E-04 | 3.23E-06 |
| rs2060717 | G>A | CALU | intron | 0.069 | 0.496 | 4.35E-03 | 0.066 | 0.735 | 1.61E-04 | 3.48E-06 |
| rs6788186 | T>C | ZBBX | 696 kb 3’ | 0.267 | 0.282 | 2.11E-02 | 0.257 | 0.476 | 4.11E-05 | 5.08E-06 |
| rs78017515 | A>G | SUGCT | 87 kb 3’ | 0.069 | 0.621 | 1.43E-04 | 0.059 | 0.488 | 1.14E-02 | 5.72E-06 |
| rs13168251 | T>G | LOC100129716 | 718 kb 3’ | 0.111 | 0.295 | 4.18E-02 | 0.105 | 0.664 | 1.13E-05 | 6.54E-06 |
| rs777619 | T>C | ADGRB3 | 487 kb 5’ | 0.193 | 0.416 | 1.54E-04 | 0.189 | 0.315 | 1.48E-02 | 8.13E-06 |
| rs2188156 | G>A | SEPT5 | 65 kb 5’ | 0.051 | 0.800 | 1.90E-05 | 0.052 | 0.394 | 5.28E-02 | 8.23E-06 |
| rs57940640 | G>A | CNGB1 | intron | 0.064 | 0.552 | 1.65E-03 | 0.068 | 0.607 | 1.64E-03 | 8.74E-06 |
SNP, single nucleotide polymorphism; Chr, chromosome; MAF, minor allele frequency
*
SNPs listed are filtered for P < 10−5 and LD-pruned (r2 ≥0.7) to the top-ranking SNP within each genomic region.
†
Alleles are denoted Major>Minor allele
‡
Positive effects represent increased risk to MTA-induced peripheral neuropathy