Table 2.
Chromosomal locations of GWAS-verified SNPs or genuine germline gene defects that predispose to the development of particular types of childhood ALL.
| Chromosome region | Candidate genes | Type | Function | All subset | References |
|---|---|---|---|---|---|
| 2(q22.3) | Not specified | SNP | – | ETV6–RUNX1 | (24) |
| 3(q28) | TP63 | SNP | P53 family of transcription factors | ETV6-RUNX1 | (325) |
| 7(p12.2) | IKZF1 | SNP, gene defects | Ikaros family of Zinc finger transcription factors | Not specified | (32, 172, 326, 327) |
| 8(q24.1) | MYC? | SNP | Proto-oncogene, BHLH transcription factor | Not specified | (24, 25) |
| 9(p12) | PAX5 | Gene defects | Paired box transcription factor | Not specified | (48, 328) |
| 9(p21.3) | CDKN2A & CDKN2B | SNP | Cyclin-dependent kinase Inhibitors | Not specified | (329–331) |
| 9(p24.1) | JAK2 | SNP | Tyrosine kinase | BCR-ABL1-like | (49) |
| 10(p12.2) | PIP4K2A | SNP | Kinase | Not specified | (329, 332) |
| 10(p14) | GATA3 | SNP | GATA family of transcription factors | BCR-ABL1-like | (332, 333) |
| 10(q21.2) | ARID5B | SNP | Transcription coactivator | Hyperdiploid | (26, 32, 326, 327) |
| 10(q26.13) | LHPP | SNP | Phosphatase | Not specified | (28) |
| 11(p11.2) | PTPRJ | SNP | Family of protein tyrosine phosphatases | ETV6-RUNX1 | (325) |
| 12(p13.2) | ETV6 | Gene defects | Proto-oncogene, ETS domain family of transcription factor | Hyperdiploid | (334–338) |
| 12(q23.1) | ELK3 | SNP | ETS domain family of transcription factor | Not specified | (28) |
| 12(q24.1) | PTPN11 | Gene defects* | Family of protein tyrosine phosphatases | Hyperdiploid | (297) |
| 14(q11.2) | CEBPE | SNP | bZIP transcription factor | Hyperdiploid | (23, 25, 32, 327) |
| 16(p13.3) | CREBBP | Gene defects** | Histone acetyltransferase | Hyperdiploid | Haas, unpublished observation |
| 17(p13.1) | TP53 | Gene defects*** | Tumor-suppressor, transcription factor | Hypodiploid | (339–341) |
| 17(q12) | IKZF3 | SNP | Ikaros family of Zinc finger transcription factors | Not specified | (25) |
| 17(q21.2) | STAT3 | SNP | Signal transducer and transcription activator | BCR-ABL1-like | (49) |