Table 3. Results for two associated regions based on a 3-SNP haplotype sliding window analysis of BCP-ALL cases and controls.
| Frequency |
Compare to reference haplotype |
Compared to all other haplotypes |
||||||
|---|---|---|---|---|---|---|---|---|
| Haplotype | Cases (%) | Controls (%) | OR | 95% CIa | OR | 95% CIa | p-value | p-value(FWE) b |
| Region A | ||||||||
| rs1237485-rs3118361-rs2032502c | ||||||||
| A-A-G | 0.06 | 0.06 | 1.03 | (0.72-1.48) | 1.16 | (0.82-1.62) | 0.406 | |
| A-G-A | 0.10 | 0.13 | 0.84 | (0.65-1.08) | 0.74 | (0.58-0.94) | 0.015 | |
| A-G-G | 0.37 | 0.33 | 1.22 | (1.02-1.45) | 1.14 | (0.97-1.34) | 0.109 | |
| G-A-G | 0.06 | 0.03 | 2.44 | (1.54-3.88) | 2.18 | (1.41-3.38) | 2.9 x10-4 | |
| G-G-G | 0.41 | 0.45 | 1.00 | Ref | 0.89 | (0.76-1.04) | 0.136 | |
| Global p-valued | 3.2x10-4 | 0.046 | ||||||
| Region C | ||||||||
| rs423639-rs7754316-rs9296068c | ||||||||
| A-A-A | 0.07 | 0.08 | 0.82 | (0.61-1.11) | 0.93 | (0.69-1.23) | 0.576 | |
| G-A-A | 0.27 | 0.32 | 0.77 | (0.63-0.93) | 0.80 | (0.67-0.95) | 9.1x10-3 | |
| G-A-C | 0.39 | 0.34 | 1.00 | Ref | 1.25 | (1.07-1.46) | 6.0x10-3 | |
| G-G-A | 0.24 | 0.25 | 0.82 | (0.67-1.00) | 0.91 | (0.76-1.10) | 0.331 | |
| G-G-C | 0.04 | 0.02 | 1.98 | (1.08-3.63) | 2.47 | (1.38-4.43) | 1.7x10-3 | |
| Global p-valued | 9.2 x10-5 | 0.014 | ||||||
Abbreviations: CI, confidence interval; FWE, family-wise type I error; OR, odds ratio; SNP, single nucleotide polymorphism
a ORs and 95% CI for each haplotype were derived using logistic regression modeling haplotype probabilities and adjusting for child’s age, sex, and race/ethnicity (non-Hispanic white versus Hispanic).
b Adjustment for multiple testing was performed with 10,000 permutations of case-control status on 393 haplotype windows and using FWE rate of 0.05. An adjusted p-value of less than 0.05 was considered statistically significant.
c The associated region A haplotype is located in the extended class I region and the SNPs are at chromosomal positions 29,002,323 (rs1237485), 29,006,266 (rs3118361), and 29,009,544 (rs2032502). The associated region C haplotype is located in the class II region and the SNPs are chromosomal positions 33,095,752 (rs423639), 33,095,976 (rs7754316), and 33,096,673 (rs9296068).
d Global p-values were derived based on a likelihood ratio test of association based on the null hypothesis of no effect of any haplotype at that position.