Association of GATA3 SNPs with AYA ALL susceptibility in the discovery GWAS and replication cohort
| Chr . | Position* . | SNP . | Alleles† . | Cohort . | RAF§ in AYA cases (%) . | Genotype count in cases‡ . | RAF§ in non-ALL controls (%) . | Genotype count in controls‡ . | AYA ALL vs non-ALL . | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RR . | RW . | WW . | RR . | RW . | WW . | P|| . | OR|| . | 95% CI . | |||||||
| 10 | 8144214 | rs3824662 | A/C | Discovery | 35 | 36 | 145 | 125 | 20 | 341 | 2078 | 4242 | 2.84 × 10-10 | 1.77 | 1.48-2.12 |
| Replication | 39 | 24 | 78 | 59 | 18 | 226 | 1651 | 3876 | 1.52 × 10-10 | 2.21 | 1.72-2.83 | ||||
| 10 | 8141933 | rs3781093 | C/T | Discovery | 33 | 34 | 137 | 136 | 22 | 380 | 2254 | 4025 | 3.20 × 10-9 | 1.73 | 1.44-2.08 |
| Replication | 35 | 18 | 75 | 64 | 18 | 236 | 1702 | 3809 | 1.00 × 10-7 | 1.96 | 1.52-2.54 | ||||
| Chr . | Position* . | SNP . | Alleles† . | Cohort . | RAF§ in AYA cases (%) . | Genotype count in cases‡ . | RAF§ in non-ALL controls (%) . | Genotype count in controls‡ . | AYA ALL vs non-ALL . | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RR . | RW . | WW . | RR . | RW . | WW . | P|| . | OR|| . | 95% CI . | |||||||
| 10 | 8144214 | rs3824662 | A/C | Discovery | 35 | 36 | 145 | 125 | 20 | 341 | 2078 | 4242 | 2.84 × 10-10 | 1.77 | 1.48-2.12 |
| Replication | 39 | 24 | 78 | 59 | 18 | 226 | 1651 | 3876 | 1.52 × 10-10 | 2.21 | 1.72-2.83 | ||||
| 10 | 8141933 | rs3781093 | C/T | Discovery | 33 | 34 | 137 | 136 | 22 | 380 | 2254 | 4025 | 3.20 × 10-9 | 1.73 | 1.44-2.08 |
| Replication | 35 | 18 | 75 | 64 | 18 | 236 | 1702 | 3809 | 1.00 × 10-7 | 1.96 | 1.52-2.54 | ||||
Association of SNP genotype and ALL was evaluated by comparing allele frequency between ALL and non-ALL, after adjusting for genetic ancestry.
Chr, chromosome.
Chromosomal locations are based on hg18.
Bold indicates risk allele for ALL.
Genotype is denoted by RR (homozygous for the risk allele), RW (heterozygous), or WW (homozygous for the wild-type allele).
RAF, risk allele frequency (allele A at rs38246623 and allele C at rs3781093).
P values were estimated by the logistic regression test and OR represents the increase in risk of developing ALL for each copy of the risk allele compared with participants who don’t carry the risk allele.