Table 2. Association of GATA3 SNP rs3824662 with somatic lesions in CRLF2, JAK and IKZF11.
| COG AALL0232 | COG P9906 | COG P9905 | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| ||||||||||||
| Genomic lesions |
Subjects with lesion (RAF) |
Subjects without lesion (RAF) |
P-value2 | OR (95% CI)2 | Subjects with lesion (RAF) |
Subjects without lesion (RAF) |
P-value2 | OR (95% CI)2 | Subjects with lesion (RAF) |
Subjects without lesion (RAF) |
P-value2 | OR (95% CI)2 |
|
| ||||||||||||
|
CRLF2 genomic
lesion |
39 (62%) | 472 (30%) | 9.64×10−7 | 3.68 (2.18-6.23) | 23 (50%) | 150 (32%) | 0.08 | 1.87 (0.99-3.87) | 66 (34%) | 711 (24%) | 0.009 | 1.70 (1.13-2.57) |
| JAK mutation | 23 (67%) | 488 (31%) | 2.06×10−5 | 4.31 (2.18-8.52) | 18 (58%) | 155 (32%) | 0.008 | 2.89 (1.29-6.44) | 21 (38%) | 610 (25%) | 0.05 | 1.89 (0.96-3.71) |
| IKZF1 deletion | 84 (45%) | 371 (30%) | 0.00026 | 1.97 (1.36-2.86) | 45 (50%) | 122 (30%) | 0.002 | 2.30 (1.23-3.96) | 89 (37%) | 519 (23%) | 0.0002 | 1.94 (1.35-2.78) |
Abbreviations; RAF, risk allele frequency (i.e., allele A at rs3824662); OR, odds ratio; CI, confidence interval.
1
Association of SNP genotype with CRLF2 genomic lesions (either IGH@-CRLF2 or P2RY8-CRLF2), JAK mutation (JAK1, JAK2 or JAK3) or IKZF1 deletion was evaluated by comparing allele frequency between ALL cases with vs. without the specific lesion or mutation, after adjusting for genetic ancestry.
2
P-values were estimated by logistic regression test and OR represents the increase in the likelihood of CRLF2, JAK or IKZF1 somatic lesions/mutations for each copy of the A allele compared with subjects who don't carry the A allele at this SNP.