Table 5. p-values obtained in the swine GWAS for genes associated with human melanoma.
| Human Gene Name | Associated Phenotypes | Human Locus | Location on pig genome | Nb of SNPs within 1Mb, with a MAF >0,1 | Nb of SNPs with a p-value <10–2 | Minimal p-value found in the 1Mb interval | SNP ID | Position on pig genome | MAF |
|---|---|---|---|---|---|---|---|---|---|
| ATM | Ulceration | 11q22.3 | 9:40925895–40945439 | 11 | 1 | 9.38E-03 | ALGA0056075 | 9: 40925224 | 0.181 |
| CCND1 | Tumor occurrence | 11q13.3 | 2: 2342270–2343202* | 20 | 1 | 7.40E-03 | INRA0008096 | 2: 2666056 | 0.43 |
| Ulceration | 22 | 1 | 8.47E-03 | ALGA0112306 | 2: 1868626 | 0.132 | |||
| CDKAL1 | Tumor occurrence | 6p22.3 | 7:16819884–17481027 | 35 | 2 | 7.68E-04 | H3GA0020098 | 7: 16370134 | 0.389 |
| Ulceration | 35 | 10 | 5.48E-04 | ASGA0031451 | 7: 16354696 | 0.482 | |||
| Metastasis | 35 | 1 | 3.20E-05 | H3GA0020098 | 7: 16370134 | 0.389 | |||
| CLPTM1L-TERT | Tumor occurrence | 5p15.33 | 16:85904690–85932895 | 7 | 1 | 9.24E-03 | H3GA0047553 | 16: 85723254 | 0.429 |
| Ulceration | 8 | 2 | 7.00E-04 | ||||||
| FTO | Ulceration | 16q12.2 | 6: 28248675–28592703* | 39 | 5 | 3.48E-04 | ASGA0085552 | 6: 28115104 | 0.16 |
| Metastasis | 25 | 2 | 1.52E-03 | ||||||
| Locus ARNT, SETDB, LASS2 | Ulceration | 1q21.3 | 4:107510690–107636206 | 30 | 1 | 4.67E-03 | ALGA0027243 | 4: 108252729 | 0.453 |
| MX2 | Metastasis | 21q22.3 | 13:215028064–215059085 | 17 | 2 | 7.12E-03 | ALGA0074008 | 13: 214911346 | 0.383 |
| OBFC1 | Tumor occurrence | 10q24.33 | 17 | 3 | 7.49E-03 | ASGA0066225 | 14: 124353052 | 0.288 | |
| PARP1 | Metastasis | 1q42.12 | 10: 16598158–16636256 | 28 | 1 | 4.09E-03 | ASGA0085873 | 10: 16744185 | 0.21 |
| PLA2G6 | Tumor occurrence | 22q13.1 | 5: 6996414–7059756 | 14 | 1 | 7.07E-03 | MARC0059533 | 5: 7491676 | 0.359 |
| Metastasis | 19 | 1 | 4.47E-04 | ||||||
| SLC45A2 | Ulceration | 5p13.3 | 16:20718194–20758825 | 34 | 7 | 3.84E-04 | ASGA0100023 | 16: 20279413 | 0.121 |
| TMEM38-RAD23B | Tumor occurrence | 9q31.2 | 1:276767826–278948163 | 51 | 4 | 4.12E-03 | H3GA0004197 | 1: 279069362 | 0.247 |
| Ulceration | 51 | 5 | 5.11E-04 | INRA0006959 | 1: 278401825 | 0.352 | |||
| Metastasis | 51 | 1 | 3.53E-03 | H3GA0004197 | 1: 279069362 | 0.247 |
approx. location*
Data correspond to the Fisher’s exact test on the 3 phenotypes Tumor occurrence, ulceration, and metastasis). *Approximate location estimated by comparative genomics between human and pig genomes.