Table 1. Summary of the childhood ALL-associated SNPs investigated and the corresponding tumor DNA allelic imbalance results.
| Gene | Tumor-associated SCNA (predicted %) | SNP | Genomic location (hg19) | Genotyped ALL cases n (GWAS/ replication) | Tumor heterozygote samples n * | Samples with AI n (%) | Risk allele PAI n | Protective allele PAI n | p-value (1-sided) |
|---|---|---|---|---|---|---|---|---|---|
| CDKN2A | Deletion (~28%) | rs3731217 | chr9:21984661 | 653 (321/332) | 50 | 17 (34.0) | 11 | 6 | 0.17 |
| IKZF1 | Deletion (~15%) | rs4132601 | chr7:50470604 | 543 (297/246) | 142 | 29 (20.4) | 17 | 12 | 0.23 |
| CEBPE | Gain of chr14 (~91%)‡ | rs2239633 | chr14:23589057 | 570 (297/273) | 42† | 32 (76.2) | 19 | 13 | 0.19 |
| ARID5B | Gain of chr10 (~67–76%)‡ | rs7089424 | chr10:63752159 | 543 (297/246) | 61† | 35 (57.4) | 20 | 15 | 0.25 |
| PIP4K2A | Gain of chr10 (~67–76%)‡ | rs10764338 | chr10:22866892 | 297 (297/0) | 19† | 9 (47.4) | 4 | 5 | 0.5 |
| GATA3 | Gain of chr10 (~67–76%)‡ | rs3824662 | chr10:8104208 | 297 (297/0) | 37† | 19 (51.4) | 10 | 9 | 0.5 |
* Number of heterozygous samples (for each SNP) with available bone marrow (i.e. tumor) DNA.
‡ % of HeH ALL samples with gains of that chromosome, based on data from Paulsson et al. (2010) [21] and Dastugue et al. (2013) [22].
† High hyperdiploid samples only.
Significant p-values highlighted in bold.