Table 1. Association of GATA3 SNPs with Ph-like ALL in the discovery GWAS and replication cohorts1.
| Chr | Position2 | SNP | Alleles3 | Cohort4 | Risk allele frequency (total number of subjects) |
Ph-like ALL vs. non-ALL | Ph-like ALL vs. non-Ph-like ALL | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Ph-like ALL | non-Ph-like ALL | non-ALL5 | P-value5 | OR (95%, CI)5 | P-value5 | OR (95%, CI)5 | |||||
| 10 | 8144214 | rs3824662 | A/C | Discovery | 58% (75) | 29% (436) | 20% (6,661)−14 | 2.17×10 | 3.85 (2.71-5.47) | 1.05×10−8 | 3.25 (2.16-4.89) |
| Replication | 50% (32) | 30% (139) | 18% (5,755) | 3.69×10−5 | 3.14 (1.18-5.44) | 0.01 | 2.16 (1.18-3.97) | ||||
| 10 | 8141933 | rs3781093 | C/T | Discovery | 52% (75) | 26% (436) | 22% (6,661) | 4.94×10−12 | 3.45 (2.42-4.93) | 2.62×10−7 | 2.89 (1.92-4.34) |
| Replication | 46% (32) | 25% (139) | 18% (5,755) | 0.0001 | 2.95 (1.68-5.16) | 0.004 | 2.55 (1.33-4.88) | ||||
Abbreviations: Chr, chromosome; OR, odds ratio; CI, confidence interval.
1
Association of SNP genotype and Ph-like ALL was evaluated by comparing allele frequency between Ph-like ALL and non-ALL, also between Ph-like ALL and non-Ph-like ALL, after adjusting for genetic ancestry.
2
Chromosomal locations are based on hg18.
3
Bold indicates risk allele for Ph-like ALL.
4
Discovery cohort: COG AALL0232, Replication cohort: COG P9906.
5
P-values were estimated by the logistic regression test and OR represents the increase in risk of developing Ph-like ALL for each copy of the risk allele compared with subjects who don't carry the risk allele.