Which is the best way to find novel mutation in the sequence of single gene?

Question

[azeem839839]

I have sequenced 96 samples of a single gene involved in the resistance to PZA dug. I got the sequenced data and I extracted all the non synonymous mutations from all the sequences. Now which is the easy and reliable method to find which are novel mutations in my sequence. any could help please?

[GenoMax]

Depends. All mutations you found could be novel, if they have not been described in literature before.

I am not aware of gene specific mutation databases for bacteria but perhaps someone else on the forum may have an idea.

Here is a database for TB gene mutations.

Answer 1

[Michael]

Mutation or variant databases for prokaryotes are unfortunately not as well established as for eukaryotes. The following cite describes the ugly situation well:

Currently, mutation and drug-resistance data for M. tuberculosis are scattered across multiple independent databases, journal articles, and their Supplementary Materials. We sought to identify data on isolates appropriate to integrate into a single database to enable querying data across study sources. The purpose of this work was to determine (i) the challenges to integrating mutation and DST data from multiple sources, and (ii) if data, once integrated, allow for systematic analysis that could inform diagnostics development.

Salamon H, Yamaguchi KD, Cirillo DM, et al. Integration of Published Information Into a Resistance-Associated Mutation Database for Mycobacterium tuberculosis. The Journal of Infectious Diseases. 2015;211(Suppl 2):S50-S57. doi:10.1093/infdis/jiu816. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366577

Unfortunately, the article does not alleviate the problem at all because there is no link to the DB in the paper, or I did not find it. Googling for TBDR gets me here: https://tbdreamdb.ki.se/Info/ which cites a different paper and was apparently last updated in 2014.

So even though you can use the resources listed, to help, you will have to do a full literature search for those mutations, because there is no warranty that the databases are complete.

[azeem839839]

Thanks dear Michael. This is big issue still present. a bid database is needed to be created continuously registering all the identified mutation in Mycobacterium drug resistance isolates.