Appendix 2 Detailed information on the polymorphisms in 11 HCC susceptibility genes in humans
| Gene location . | Accession no. . | SNP: position . | Size (bp) . | Primer 1 . | Primer 2 . | Annealing temperature . | Scoring . |
|---|---|---|---|---|---|---|---|
| EPHX1-3e | L29766 | Exon 3, codon | 147 | GCTGCTTCCACTATGGCTTC | GGCGTTTTGCAAACATACCT | 66°C | 11 (CC:GG) |
| 1q42.1 | AF253417 | 113, T to C | 12 (CT:GG) | ||||
| (exon 3) | (Tyr to His) | 13 (CT:GA) | |||||
| T/C: 17673 | 22 (TT:GG) | ||||||
| 23 (TT:GA) | |||||||
| A/G: 17693 | 33 (TT:AA) | ||||||
| EPHX1-4e | L29766 | Exon 4, codon 139, A to G, | 381 | CAGAGCCTGACCGTGCAG | GGTCACCCCGCCGGAAGG | 67°C | 11 (AA) |
| 1q42.1 | AF253417 | 22 (GG) | |||||
| (exon 4) | (His to Arg) | 12 (GA) | |||||
| A/G: 24448 | |||||||
| EPHX2 | L05779 | A/G: 1742 | 291 | CGGTGGTCTCAAAGATGTAGA | TGTCCCCCTACAGGACACTA | 60°C | 11 (AA) |
| 8p21-p12 | 22 (GG) | ||||||
| 12 (AG) | |||||||
| GSTP1 | M37065 | STRs | 230-295 | CACGCACCTATAATTCCACC | GCTTAGAGGAAAGGAAATTGC | 54°C | NA |
| 11q13 | (AAAAT): | ||||||
| 1856–1942 | |||||||
| GSTT1 | Z67376 | STRs (CA repeats): 110-155 | 268 | CAACTTCATCCACGTTCACC | GAAGAGCCAAGGACAGTTAC | 54°C | NA |
| 22q11.23 | |||||||
| GSTT2 | Z84718 | G/T: 66094 | 527 | TAAAACACTGATGACATTTGCC | AGGTGACACTGGCTGATCTC | 56°C | 11 (TT) |
| 22q11.23 | 22 (GG) | ||||||
| 12 (TG) | |||||||
| MGST1 | J03746 | G/A: 560 | 325 | TTCCATGGCTTACAGGTTG | AGTGAGGTGTTGTGTGAATGTT | 66°C | 11 (AA) |
| 12p12.3-p12.1 | 22 (GG) | ||||||
| 12 (AG) | |||||||
| GSTA1 | L13269 | C/T: 3962 | 287 | CCAACCTTGAAAAGGAACAC | CTAGACAGGAGGGTGTAAGGC | 66°C | 11 (CC) |
| 6p12 | 22 (TT) | ||||||
| 12 (CT) | |||||||
| GSTA4 | AL121969 | T/G: 97161 | 397 | TGTAAAACGACGGCCAGTGGCCA TAAAACAACACATCC | CAGGAAACAGCTATGACCGAGA GCAGAAAGACGCTCAG | 62°C | 11 (TT) |
| 6p12 | 22 (GG) | ||||||
| 12 (TG) | |||||||
| GSTM1 | X68676 | C/G: 534 | 132 | GCTTCACGTGTTATGAAGGTTC | TTGGGAAGGCGTCCAAGCGC/ TTGGGAAGGCGTCCAAGCAG | 56°C | 11 (CC) |
| 1p13.3 | GSTM1B | ||||||
| 22 (GG) | |||||||
| GSTM1A | |||||||
| 12 (GC) | |||||||
| GSTM1AB | |||||||
| GSTM2 | M63509 | G/A: 905 | 284 | GCCCTTTAAAGCAGACACAA | GAGTGAGGAGCCCATACTCA | 56°C | 11 (AA) |
| 1p13.3 | 22 (GG) | ||||||
| 12 (GA) | |||||||
| GSTM3 | AF043105 | AGG/—: | 273 | CCTCAGTACTTGGAAGAGCT | CACATGAAAGCCTTCAGGTT | 58°C | 11 GSTM3*A |
| 1p13.3 | 4596–4598 | 22 GSTM3*B | |||||
| 12 GSTM3*AB |
| Gene location . | Accession no. . | SNP: position . | Size (bp) . | Primer 1 . | Primer 2 . | Annealing temperature . | Scoring . |
|---|---|---|---|---|---|---|---|
| EPHX1-3e | L29766 | Exon 3, codon | 147 | GCTGCTTCCACTATGGCTTC | GGCGTTTTGCAAACATACCT | 66°C | 11 (CC:GG) |
| 1q42.1 | AF253417 | 113, T to C | 12 (CT:GG) | ||||
| (exon 3) | (Tyr to His) | 13 (CT:GA) | |||||
| T/C: 17673 | 22 (TT:GG) | ||||||
| 23 (TT:GA) | |||||||
| A/G: 17693 | 33 (TT:AA) | ||||||
| EPHX1-4e | L29766 | Exon 4, codon 139, A to G, | 381 | CAGAGCCTGACCGTGCAG | GGTCACCCCGCCGGAAGG | 67°C | 11 (AA) |
| 1q42.1 | AF253417 | 22 (GG) | |||||
| (exon 4) | (His to Arg) | 12 (GA) | |||||
| A/G: 24448 | |||||||
| EPHX2 | L05779 | A/G: 1742 | 291 | CGGTGGTCTCAAAGATGTAGA | TGTCCCCCTACAGGACACTA | 60°C | 11 (AA) |
| 8p21-p12 | 22 (GG) | ||||||
| 12 (AG) | |||||||
| GSTP1 | M37065 | STRs | 230-295 | CACGCACCTATAATTCCACC | GCTTAGAGGAAAGGAAATTGC | 54°C | NA |
| 11q13 | (AAAAT): | ||||||
| 1856–1942 | |||||||
| GSTT1 | Z67376 | STRs (CA repeats): 110-155 | 268 | CAACTTCATCCACGTTCACC | GAAGAGCCAAGGACAGTTAC | 54°C | NA |
| 22q11.23 | |||||||
| GSTT2 | Z84718 | G/T: 66094 | 527 | TAAAACACTGATGACATTTGCC | AGGTGACACTGGCTGATCTC | 56°C | 11 (TT) |
| 22q11.23 | 22 (GG) | ||||||
| 12 (TG) | |||||||
| MGST1 | J03746 | G/A: 560 | 325 | TTCCATGGCTTACAGGTTG | AGTGAGGTGTTGTGTGAATGTT | 66°C | 11 (AA) |
| 12p12.3-p12.1 | 22 (GG) | ||||||
| 12 (AG) | |||||||
| GSTA1 | L13269 | C/T: 3962 | 287 | CCAACCTTGAAAAGGAACAC | CTAGACAGGAGGGTGTAAGGC | 66°C | 11 (CC) |
| 6p12 | 22 (TT) | ||||||
| 12 (CT) | |||||||
| GSTA4 | AL121969 | T/G: 97161 | 397 | TGTAAAACGACGGCCAGTGGCCA TAAAACAACACATCC | CAGGAAACAGCTATGACCGAGA GCAGAAAGACGCTCAG | 62°C | 11 (TT) |
| 6p12 | 22 (GG) | ||||||
| 12 (TG) | |||||||
| GSTM1 | X68676 | C/G: 534 | 132 | GCTTCACGTGTTATGAAGGTTC | TTGGGAAGGCGTCCAAGCGC/ TTGGGAAGGCGTCCAAGCAG | 56°C | 11 (CC) |
| 1p13.3 | GSTM1B | ||||||
| 22 (GG) | |||||||
| GSTM1A | |||||||
| 12 (GC) | |||||||
| GSTM1AB | |||||||
| GSTM2 | M63509 | G/A: 905 | 284 | GCCCTTTAAAGCAGACACAA | GAGTGAGGAGCCCATACTCA | 56°C | 11 (AA) |
| 1p13.3 | 22 (GG) | ||||||
| 12 (GA) | |||||||
| GSTM3 | AF043105 | AGG/—: | 273 | CCTCAGTACTTGGAAGAGCT | CACATGAAAGCCTTCAGGTT | 58°C | 11 GSTM3*A |
| 1p13.3 | 4596–4598 | 22 GSTM3*B | |||||
| 12 GSTM3*AB |