Huang et al. 10.1073/pnas.0609954104. |
Table 5. Haplotype analysis of all SNPs in IFN-a-treated patients (cohort 1)
Haplotype | CA (%) | AA (%) | CMH race-adjusted | ||||||
No. | Pattern* | All | SVR | NR | All | SVR | NR | P | OR (95% CI) |
1 | TCAATCAG | 32 (7.5) | 11 (6.1) | 21 (8.5) | 23 (16.2) | 2 (12.5) | 21 (16.7) | 0.344 | 0.71 (0.35-1.45) |
2 | TGAATCAG | 29 (6.8) | 18 (10.0) | 11 (4.5) | 4 (2.8) | 1 (6.3) | 3 (2.4) | 0.013 | 2.65 (1.2-5.85) |
3 | TCTATCAG | 1 (0.2) | 0 | 1 (0.4) | 0 | 0 | 0 | 0.392 |
|
5 | TCAATTAG | 0 | 0 | 0 | 1 (0.7) | 0 | 1 (0.8) | 0.722 |
|
6 | CCAATTAG | 18 (4.2) | 7 (3.9) | 11 (4.5) | 17 (12.0) | 1 (6.3) | 16 (12.7) | 0.541 | 0.76 (0.31-1.84) |
7 | CCAGTTAG | 3 (0.7) | 0 | 3 (1.2) | 8 (5.6) | 0 | 8 (6.3) | 0.071 |
|
9 | CCAGCTAG | 116 (27.2) | 49 (27.2) | 67 (27.2) | 18 (12.7) | 1 (6.3) | 17 (13.5) | 0.726 | 0.91 (0.54-1.54) |
10 | CGAGCTAG | 4 (0.9) | 2 (1.1) | 2 (0.8) | 0 | 0 | 0 | 0.752 | 1.38 (0.19-9.95) |
11 | CCTGCTAG | 1 (0.2) | 1 (0.6) | 0 | 0 | 0 | 0 | 0.242 |
|
12 | TCAATCGG | 0 | 0 | 0 | 2 (1.4) | 1 (6.3) | 1 (0.8) | 0.081 | 8.86 (0.50-157.76) |
13 | TCTATCGG | 182 (42.7) | 78 (43.3) | 104 (42.3) | 31 (21.8) | 6 (37.5) | 25 (19.8) | 0.691 | 1.12 (0.65-1.98) |
15 | TCAATTGG | 0 | 0 | 0 | 1 (0.7) | 0 | 1 (0.8) | 0.722 |
|
18 | TCAATTAA | 38 (8.9) | 13 (7.2) | 25 (10.2) | 18 (12.7) | 3 (18.8) | 15 (11.9) | 0.602 | 0.84 (0.43-1.63) |
19 | CCAATTAA | 0 | 0 | 0 | 18 | 1 (6.3) | 17 (13.5) | 0.529 | 0.50 (0.06-4.41) |
20 | TGAATTAA | 1 (0.2) | 1 (0.6) | 0 | 0 | 0 | 0 | 0.242 |
|
25 | TCAATCGA | 1 (0.2) | 0 | 1 (0.4) | 1 (0.7) | 0 | 1 (0.8) | 0.361 |
|
Total | 426 | 180 | 246 | 142 | 16 | 126 |
|
| |
*The order of SNPs is rs2069705, rs2069707, rs2430561, rs1861494, rs1861493, rs2069718, rs2069727, and rs2069728. Allele G of SNP rs2069707 is underlined.
Table 6. Treatment regimens of IFN-a-treated patients (cohort 1)
Treatment regimen | All | SVR (%) | NR (%) |
IFN-a* | 27 | 7 (25.9) | 20 (74.1) |
IFN-a + Rbv* | 83 | 39 (47.0) | 44 (53.0) |
IFN-a + Rbv (NR to IFN-a)† | 28 | 9 (32.1) | 19 (67.9) |
Peg-IFN-a + Rbv* | 106 | 38 (35.8) | 68 (64.2) |
Peg-IFN-a + Rbv (NR to IFN-a and/or IFN-a + Rbv)† | 40 | 5 (12.5) | 35 (87.5) |
Total | 284 | 98 (34.5) | 186 (65.5) |
Rbv, ribavirin.
*Naive patients who had no previous exposure to IFN-based therapy.
†
Retreated patients who were either virologic nonresponders or relapsers after previous treatments (indicated in parentheses).Table 7. Sequences of primers used for genotyping
SNP ID* (Alleles) | Amplification primers (5' to 3') | Allele-specific probes | |
rs2069705 (T/C) | F | CAGGTAAGGAGACTGAGTCATAGAAGATT | AAGAAGTTAACTCACAATC |
R | CTGTGTACATAACAGTATTGCAGTTATGG | AGAAGCTAACTCACAATC | |
rs2069707 (C/G) | F | GCCTCAACCTCCCAAAGTG | TGGGAATATTCTCTACACTG |
R | TAAACCAATATATCCCAAATAGTACTTCAG | TGGGAATATTCTGTACACTG | |
rs2430561 (T/A) | F | TCAGACATTCACAATTGATTTTATTCTTAC | CAAAATCAAATCTCACACACA |
R | CCTTCCTGTAGGGTATTATTATACGAGC | CACAAAATCAAATCACAC | |
rs1861494 (A/G) | F | TGAGCAAGGGACAATGAGAGAA | AAGAAGCAGGGAGT |
R | AAGACAGGTGAGTTGACAAATCCA | AGAAGCGGGGAGT | |
rs1861493 (T/C) | F | GCTCAGTTTCCTCATCTTAAAAGGA | ACTGTTAGGTTCACTGTAT |
R | GGAGCAAAGAAGGTCATCAAACTT | CTGTTAGGCTCACTGTA | |
rs2069718 (C/T) | F | GGCAGAGCCAAGAGGAAGGT | CCACATCTTATGAAGCAT |
R | CACTCTAACCAATAGGGCCATTTAG | CCACATTTTATGAAGCAT | |
rs2069727 (A/G) | F | GCCCCTTCTCCACCTTCCTA | CCTCCTTCATTTCAG |
R | ATTGGATGAGGGAGAGGAAGATT | CCTCCTTCGTTTCAG | |
rs2069728 (G/A) | F | GGTGATTGGTGTCATGGAAAAA | AGTTAAAGGAGAGCAGGA |
R | CTCCACCATACATAGGACTCCTAATTT | AGTTAAAGAAGAGCAGGAC | |
F, forward; R, reverse.
*The ID is according to National Center for Biotechnology Information dbSNP database reference number.