Table 1.
Lead SNPs near SP4, 8q24, and IKZF3 reaching genome-wide significance in discovery analyses of CCRLP acute lymphoblastic leukemia patients, including replication analyses in the Children’s Oncology Group and the California Childhood Leukemia Study Latino Participants
| SP4—rs2390536 risk allele Aa | 8q24.1—rs4617118 risk allele Gb | IKZF3—rs2290400 risk allele Tc | |||||||
|---|---|---|---|---|---|---|---|---|---|
| RAFd | P value | OR (95% CI) | RAFa | P value | OR (95% CI) | RAFa | P value | OR (95% CI) | |
| CCRLP meta-analysise | 3.59 × 10 −8 | 1.20 (1.13–1.29) | 3.05 × 10 −9 | 1.27 (1.17–1.38) | 2.05 × 10 −8 | 1.18 (1.11–1.25) | |||
| CCRLP Latinos | 0.26 | 1.42 × 10−4 | 1.19 (1.09–1.31) | 0.15 | 2.90 × 10−5 | 1.25 (1.12–1.38) | 0.57 | 4.33 × 10−6 | 1.20 (1.11–1.30) |
| CCRLP Whites | 0.35 | 5.69 × 10−5 | 1.23 (1.11–1.35) | 0.18 | 1.74 × 10−3 | 1.26 (1.09–1.45) | 0.50 | 2.72 × 10−3 | 1.15 (1.05–1.26) |
| CCRLP African Americans | 0.22 | 0.73 | 1.07 (0.73–1.58) | 0.23 | 1.55 × 10−3 | 1.54 (1.18–2.01) | 0.52 | 0.18 | 1.19 (0.92–1.53) |
| Replication meta-analysis | 0.075 | 1.10 (0.99–1.23) | 1.29 × 10 −4 | 1.30 (1.14–1.49) | 0.013 | 1.14 (1.03–1.26) | |||
| COG Replication (European) | 0.36 | 0.025 | 1.15 (1.018–1.31) | 0.17 | 0.011 | 1.22 (1.05–1.43) | 0.45 | 0.13 | 1.10 (0.97–1.25) |
| CCLS Replication (Hispanic) | 0.2133 | 0.74 | 0.96 (0.77–1.20) | 0.1069 | 1.03 × 10−3 | 1.58 (1.20–2.07) | 0.6135 | 0.030 | 1.22 (1.02–1.46) |
| Combined datasets | 1.77 × 10 −8 | 1.18 (1.11–1.24) | 1.76 × 10 −12 | 1.28 (1.19–1.37) | 1.06 × 10 −9 | 1.17 (1.11–1.23) | |||
RAF risk allele frequency, CCLS California Childhood Leukemia Study, CCRLP California Cancer Records Linkage Project, COG Children’s Oncology Group.
Bold values indicate P values lower than genome-wide significance (P<5 × 10−8) for CCRLP GWAS and combined datasets, and nominal significance (P<0.05) for replication meta-analysis.
a Rs2390536 was genotyped “on array” for all sample sets apart from COG Replication (Imputed INFO score = 0.99)
b rs4617118 was genotyped “on array for CCRLP datasets, and imputed for COG Replication (INFO = 0.96) and CCLS Replication (INFO = 0.88)
c rs2290400 was genotyped “on array” for all sample sets apart from COG replication (INFO = 0.88)
d RAF calculated among ethnicity-matched controls
e Sample sizes for all analyses: CCRLP Latinos: 1949 cases, 8584 controls; CCRLP whites: 1184 cases, 3551 controls; CCRLP African Americans: 130 cases, 3842 controls. For the replication: COG: 959 cases, 2624 controls; CCLS: 530 cases and 511 controls