Table 2 |
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|
Association of 40F and 43E with thymidine analogue-associated mutations |
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| pos1 |
pos2 |
phi |
OR |
% pos2 in pos1 |
P value |
|
|
|||||
| 40F |
43E |
0.287 |
38.2 |
84% |
<10E-09 |
| 40F |
41L |
0.125 |
6.9 |
99% |
<10E-09 |
| 40F |
210W |
0.162 |
11.2 |
97% |
<10E-09 |
| 40F |
215Y |
0.124 |
7.2 |
94% |
<10E-09 |
| 40F |
67N |
0.107 |
6.6 |
79% |
<10E-09 |
| 40F |
70R |
0.001 |
1.1 |
9% |
NS |
| 40F |
215F |
-0.001 |
0.9 |
4% |
NS |
| 40F |
219E |
0.032 |
4.6 |
14% |
<10E-09 |
| 40F |
219Q |
-0.003 |
0.8 |
4% |
NS |
|
|
|||||
| 43E |
40F |
0.287 |
38.2 |
10% |
<10E-09 |
| 43E |
41L |
0.326 |
6.3 |
91% |
<10E-09 |
| 43E |
210W |
0.367 |
9.0 |
78% |
<10E-09 |
| 43E |
215Y |
0.31 |
6.4 |
82% |
<10E-09 |
| 43E |
67N |
0.211 |
4.8 |
58% |
<10E-09 |
| 43E |
70R |
-0.002 |
0.9 |
9% |
NS |
| 43E |
215F |
0.014 |
1.4 |
7% |
9.7E-08 |
| 43E |
219E |
0.009 |
1.4 |
4% |
NS |
| 43E |
219Q |
0.004 |
1.1 |
6% |
NS |
|
|
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|
Binomial correlation coefficients (phi) and Odds Ratios (OR) were calculated for 57 amino acid substitutions at 34 reverse transcriptase codons to study the association of E40F and K43E with each other and with known thymidine analogue associated mutations. Phi: binomial correlation coefficient (1.0 = perfect pairwise correlation). OR: Odds Ratio – the observed frequency of the pair divided by the product of the individual mutation frequencies. P-value: chisquare probability was evaluated for significance at a Benjamini-Hochberg false discovery rate (FDR) of 0.01 for 1,566 multiple comparisons. NS: Not significant at FDR 0.01. Sequences with a phi value of 0.15 or greater, an odds ratio of > 2 and FDR of 0.01 were considered to be co-varying. |
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|
Huigen et al. Retrovirology 2008 5:20 doi:10.1186/1742-4690-5-20 |
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