Table 2.
Single-nucleotide polymorphisms (SNPs) associated with risk for chemotherapy-induced neutropenia (p < 1.0E-04) in women with breast cancer recruited to the SUCCESS-A trail (n = 3252) and expression quantitative trait loci (eQTL) analysis in lymphoblastoid cell lines (LCLs).
| SNP rs ID | Chr. | Common allele | Minor allele | OR | MAF | p-value | Gene | Pathway | eQTL in LCLs |
|---|---|---|---|---|---|---|---|---|---|
| rs144991623 | 13 | C | T | 69.8 | 0.002 | 5.98E-06 | FOXO1 | Checkpoint, PI3K | NA |
| rs9389568 | 6 | T | C | 0.59 | 0.049 | 7.10E-06 | PERP | P53 | Yes |
| rs8110364 | 19 | G | A | 3.09 | 0.011 | 2.23E-05 | PIK3R2 | mTOR, PI3K, P53 | Yes |
| rs56022120 | 19 | C | T | 3.12 | 0.011 | 2.29E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs150688309 | 19 | C | G | 2.87 | 0.013 | 2.67E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs58695150 | 19 | C | T | 3.07 | 0.011 | 3.15E-05 | PIK3R2 | mTOR, PI3K, P53 | Yes |
| rs299293 | 5 | C | T | 1.36 | 0.133 | 3.19E-05 | HMMR/CCNG1 | P53 | Yes |
| rs138602176 | 19 | G | A | 2.97 | 0.011 | 3.24E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs148235907 | 19 | G | A | 3.06 | 0.011 | 3.35E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs117951771 | 19 | C | T | 3.06 | 0.011 | 3.37E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs299314 | 5 | T | C | 1.35 | 0.138 | 3.60E-05 | HMMR/CCNG1 | P53 | Yes |
| rs299313 | 5 | G | A | 1.35 | 0.139 | 3.72E-05 | HMMR/CCNG1 | P53 | Yes |
| rs115457081 | 2 | G | A | 5.04 | 0.012 | 3.89E-05 | IRS1 | mTOR | No |
| rs117341846 | 19 | C | T | 3.03 | 0.011 | 3.93E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs4968187 | 17 | C | T | 0.10 | 0.004 | 4.09E-05 | TP53 | 5FU, Apoptosis, Checkpoint, Doxorubicin, PI3K, P53 | NA |
| rs142244113 | 19 | C | T | 1.72 | 0.039 | 4.59E-05 | INSR | mTOR | No |
| rs79430272 | 19 | C | T | 2.94 | 0.011 | 4.80E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs118129530 | 19 | G | A | 3.00 | 0.011 | 4.82E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs77769901 | 14 | A | G | 0.31 | 0.012 | 4.99E-05 | CCNK | P53 | No |
| rs145623321 | 19 | C | T | 3.01 | 0.010 | 5.35E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs148013902 | 19 | C | T | 3.01 | 0.010 | 5.46E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs55633228 | 19 | C | T | 3.00 | 0.010 | 5.59E-05 | PIK3R2 | mTOR, PI3K, P53 | No |
| rs141084494 | 22 | G | A | 0.05 | 0.003 | 6.26E-05 | RBX1 | Checkpoint | NA |
| rs41412545 | 19 | C | A | 1.70 | 0.038 | 6.36E-05 | INSR | mTOR | No |
| rs3805945 | 6 | T | C | 1.68 | 0.040 | 6.81E-05 | PPP2R5D | mTOR | No |
| rs117101815 | 6 | G | T | 0.63 | 0.051 | 7.17E-05 | PERP | P53 | Yes |
| rs9402944 | 6 | G | T | 0.63 | 0.051 | 7.20E-05 | PERP | P53 | Yes |
| rs181501757 | 17 | G | A | 4.77 | 0.008 | 7.75E-05 | TOP2A | Doxorubicin | NA |
| rs149212925 | 12 | A | G | 0.00 | 0.001 | 8.33E-05 | NOS1 | Doxorubicin | NA |
| rs112783657 | 21 | C | T | 0.49 | 0.027 | 8.65E-05 | CBR3 | Doxorubicin | No |
| rs74743371 | 21 | G | T | 0.49 | 0.027 | 8.68E-05 | CBR3 | Doxorubicin | No |
| rs117458836 | 10 | G | A | 2.53 | 0.014 | 8.85E-05 | CYP2C8 | Cyclophosphamide | No |
| rs118088833 | 11 | C | T | 0.26 | 0.009 | 8.99E-05 | TP53AIP1 | P53 | NA |
| rs112242273 | 3 | C | T | 0.52 | 0.038 | 9.58E-05 | GNL3 | Checkpoint, P53 | No |
| rs78428806 | 6 | G | A | 0.63 | 0.048 | 9.79E-05 | PERP | P53 | Yes |
Chr., chromosome; OR, odds ratio; MAF, minor allele frequency; NA, not applicable, because SNP MAF is too low to find LCLs with variant SNP allele. The three SNPs in HMMR gene were highlighted in bold.