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jodyphelan / tbdb

Standard database for the TBProfiler tool
GNU Lesser General Public License v3.0
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add mutations #18

Closed jodyphelan closed 4 years ago

jodyphelan commented 4 years ago

Added mutations from https://github.com/jodyphelan/tbdb/issues/9

jodyphelan commented 4 years ago

Here are my thoughts:

Drug Gene Mutation Tree Comment Reccomendation
delamanid ddn p.Gly81Asp Not found in WGS dataset however stong evidence from literature Include
delamanid ddn p.Gly81Ser image Arose twice independently: 1) In an XDR transmission chain and 2) In a branch located deep in the phylogeny (potentially phylogenetic mutation). Literature finds this mutation in sensitive strains. Exclude

The p.Gly81Ser mutation is interesting as it seems associated to XDR clade bed also looks like a phylogenetic mutaion in another clade. It was found in strains with and MIC ≤0.0125 mg/L. Could be an issue with the MIC results or potentially this mutation by itself is not enough to confer resistance and interacts with others?

camusnimmo commented 4 years ago

Agree with this, though I assume it is Gly81Ser that appears phylogenetic and we are proposing to exclude?

jodyphelan commented 4 years ago

Oh yeah, will fix that typo!