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jodyphelan / tbdb

Standard database for the TBProfiler tool
GNU Lesser General Public License v3.0
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Add following mutations #15

Closed malare closed 4 years ago

malare commented 4 years ago

I thought these mutations were worth considering:

Gene | Mutation | Drug | Literature |   rpoB | p.His445Tyr | rifampicin | 10.1128/AAC.01343-16 rpoB | p.His445Leu | rifampicin | 10.1128/JCM.01599-17 rpoB | p.Ser450Leu | rifampicin | 10.1128/AAC.01093-18 katG | p.Arg632Cys | isoniazid | 10.1128/AAC.01691-09 katG | p.Met420Thr | isoniazid | 10.1128/AAC.01691-09 katG | p.Trp351STOP | isoniazid | 10.5588/ijtld.18.0095 katG | p.Asp329Ala | isoniazid | 10.1128/AAC.06418-11 eis | G-6T | kanamycin | 10.1093/jac/dkr109 eis | G-10C | kanamycin | 10.1016/j.ijmyco.2015.09.001 eis | A-13G | kanamycin | 10.1073/pnas.0907925106 eis | C-15T | kanamycin | 10.1093/jac/dkr109 ethA | p.Asn345Lys | ethionamide | 10.1111/j.1469-0691.2009.02838.x; 10.1111/j.1365-2672.2010.04840.x ethA | p.Ser266Arg | Ethionamide | 10.1128/AAC.01030-10

jodyphelan commented 4 years ago

Thanks, I'll have a look at these!

jodyphelan commented 4 years ago

I've added in those mutations which passed review!

malare commented 4 years ago

Thank you very much. I have additionally some mutations:

gid | p.Gly73Ala | Streptomycin | 10.1128/AAC.02175-18 gid | p.Leu79Ser | Streptomycin | 10.1128/AAC.02175-18 gid | p.Leu108Arg | Streptomycin | 10.1128/AAC.02175-18 ethA | p.Cys137Arg | Ethionamide | 10.1128/AAC.02175-18 embB | p.Ala505Val | Ethambutol | 10.1128/AAC.02175-18 ahpC | p.Cys-57Thr | Pyrazinamide | 10.1016/S1473-3099(15)00062-6

I am sorry for the individual messages.. Best

jodyphelan commented 4 years ago

No Problem! I'll take a look at these, thanks for the suggestions!

jodyphelan commented 4 years ago

Can you double-check the last mutation? As far as I know ahpC is only associated with isoniazid resistance.

malare commented 4 years ago

I made a mistake. Of course the following is true: ahpC | p.Cys-57Thr | isoniazid | 10.1016/S1473-3099(15)00062-6

Sorry and thank you!

jodyphelan commented 4 years ago

The mutations have undergone review and high-confidence mutations have been merged in. Thanks for the suggestions!

Jody