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jodyphelan / tbdb

Standard database for the TBProfiler tool
GNU Lesser General Public License v3.0
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added new mutations #20

Closed jodyphelan closed 4 years ago

jodyphelan commented 4 years ago

added new mutations from #15

jodyphelan commented 4 years ago

Here are my thoughts:

Drug Gene Mutation Extra info --------Comment-------- Recommendation
ethambutol embB p.Ala505Val image Very rare mutation as it is not found in WGS data. Isolate with p.Ala505Val has no other mutations in ethambutol resistance genes and an elevated resistance level, although this does overlap with the top-end of the wild-type distribution. Potentially not enough evidence yet. Exclude
isoniazid ahpC c.-57C>T Convergent evolution in strains and good statistical evidence Include
ethionamide ethA p.Cys137Arg image Convergent evolution. In publication (suppl figure) it seems as though it is only present in combination with inhA c.-8T>C to give a high MIC although in table s3 it does not appear together with this mutation. Potentially not enough evidence yet Exclude
streptomycin Rv3919c p.Leu108Arg image Convergent evolution. Positive odds ratio. Two instances of elevated MIC in publication. Include
streptomycin Rv3919c p.Gly73Ala image Convergent evolution. Positive odds ratio. Elevated MIC Include
streptomycin Rv3919c p.Leu79Ser Convergent evolution. Could not find in publication however there is strong statistical evidence Include
camusnimmo commented 4 years ago

Agree with all of the above.

Ala505Val in embB does not give high MGIT MIC, and think in lack of any corroborative data should be excluded. Likewise Cys137Arg as was only assoc with high MIC with known resistance mutation.

jodyphelan commented 4 years ago

Great I'll merge them in!