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jodyphelan / tbdb

Standard database for the TBProfiler tool
GNU Lesser General Public License v3.0
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Resistance to Bedaquiline and Delamanid #9

Closed malare closed 4 years ago

malare commented 4 years ago

Hi @jodyphelan,

I was wondering why mutations like the following are not included in the database:

Mutations

Thank you very much

jodyphelan commented 4 years ago

Hi @malare,

Thanks for highlighting this. I'll take a look.

Jody

jodyphelan commented 4 years ago

Hi @malare Is the table generated from only those two references? I can't some such as the Lys250STOP. I can also see a number of synonymous mutations, what is their role in resistance?

malare commented 4 years ago

Dear @jodyphelan I have checked the table (see above), excuse me. Best

jodyphelan commented 4 years ago

Great, I've created a pull request to add in the new mutations here. After we can a couple of reviews we can add them in.

jodyphelan commented 4 years ago

Hi @malare I've added in the mutations now thanks for the contribution!

malare commented 4 years ago

I have found some additional mutations leading to delamanid resistance: ddn | Rv3547 | p.Leu107Pro | L107P | delamanid | 10.1016/j.tube.2017.12.006 ddn | Rv3547 | 51-101 deletion |   | delamanid | 10.1016/j.tube.2017.12.006 Best

jodyphelan commented 4 years ago

Hi @malare, thanks for highlighting these mutations. Do you know if the deletion refers to nucleotide positions or codon positions?

malare commented 4 years ago

Unfortunately, this is not entirely clear. I thought they were codon positions.

jodyphelan commented 4 years ago

Ah right.. I'll try contact the authors. If it is codon positions then there are several possible indels on the nucleotide level.

jodyphelan commented 4 years ago

Got a reply... it's on the nucleotide level

jodyphelan commented 4 years ago

They have now been added in now!

malare commented 4 years ago

Some additional delamanid resistance conferring mutations: Gly81Asp dnn delamanid 10.3343/alm.2018.38.6.563 Gly81Ser dnn delamanid 10.3343/alm.2018.38.6.563

Thank you and Best,

jodyphelan commented 4 years ago

Thanks! I will take a look.

Jody

jodyphelan commented 4 years ago

The mutations have been reviewed and Gly81Asp has been added, thanks again for the recommendation!