Table 1.
Results of logistic regression test of association in African-American NBL patients for most significant SNPs in European-American GWAS
| Gene | Chr. | SNP (bp) | Alleles (m/M) | MAF cases | MAF controls | p-value | Emp-p | OR | 95% CI |
|---|---|---|---|---|---|---|---|---|---|
| FLJ22536 | 6 | rs4712653 (22233943) | T/C | 0.19 | 0.19 | 0.56 | 1.00 | 0.94 | 0.77–1.15 |
| rs9295536 (22239908) | C/A | 0.19 | 0.19 | 0.30 | 1.00 | 0.90 | 0.73–1.10 | ||
| rs6939340 (22247983) | A/G | 0.17 | 0.18 | 0.77 | 1.00 | 0.97 | 0.79–1.19 | ||
| BARD1 * | 2 | rs3768716 (215344039) | G/A | 0.10 | 0.07 | 0.007 | 0.14 | 1.45 | 1.11–1.90 |
| rs17487792 (215351745) | T/C | 0.10 | 0.06 | 0.009 | 0.19 | 1.45 | 1.10–1.93 | ||
| rs7587476 (215362132) | T/C | 0.42 | 0.34 | 2.4×10−6 | 0.0003 | 1.47 | 1.25–1.72 | ||
| rs6712055 (215375149) | C/T | 0.22 | 0.17 | 0.006 | 0.14 | 1.31 | 1.08-1.59 | ||
| rs6435862 (215380791) | G/T | 0.34 | 0.26 | 1.8×10−5 | 0.0005 | 1.44 | 1.22–1.70 | ||
| LMO1 | 11 | rs4758051 (8195215) | A/G | 0.20 | 0.18 | 0.77 | 1.00 | 1.03 | 0.84–1.27 |
| rs10840002 (8199602) | G/A | 0.27 | 0.25 | 0.79 | 1.00 | 1.03 | 0.85–1.23 | ||
| rs110419 (8209429) | G/A | 0.22 | 0.23 | 0.18 | 0.99 | 0.88 | 0.72–1.07 | ||
| rs204938 (8234773) | T/C | 0.34 | 0.31 | 0.27 | 1.00 | 1.10 | 0.93–1.30 |
*
SNP rs6715570 reported by Capasso et al. (6) was removed from our analysis for missing rate greater than 5% in cases.
m/M = minor allele/major allele
MAF = minor allele frequency
Emp-p = empirical p-value from permutation test
OR = odds-ratio for the minor allele
CI = confidence interval