Reference Data Elements
Some elements are available from the QIAGEN Sets tab in the Reference Data Manager (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=References_management.html).
- WHO Mycobacterium Tuberculosis. The WHO database is a variant track with all variants from the WHO's Mycobacterium tuberculosis mutation catalogue [WHO, 2023]. Variants called with the variant detection tools (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Variant_Detection_tools.html) can be matched against this database using Filter against Known Variants or Annotate from Known Variants.
The variant table contains five columns unique to this reference data element:
- Graded variant. The name(s) of the variant as given by WHO. The name consists of the gene the variant is in, along with the corresponding position and change, either as a nucleotide or amino acid change.
- Drug. The antimicrobial resistance drug(s) for which the variant is graded.
- Gene. The gene with which the variant is associated, as given by WHO.
- Grade. The grade of drug resistance determined for the variant. See figure 17.1 for a schematic of the resistance grades.
- Comment. In case any comments on the variants resistance are given by WHO, these are listed here.
In some cases of variants being associated with multiple "Graded variant" names, not all of the names are graded for a drug. This leads to instances of N/A in the "Drug" column. In the "Grade" column, this will be listed as "Ungraded". See figure 17.2 for an example of this.
Figure 17.1: The five levels of resistance as given by WHO (from fig. 1, page 5 of [WHO, 2023]).
Figure 17.2: An example of a single variant with multiple instances of "Graded variant". In this case the third "Graded variant", embB_c.927C>G, is not graded for a drug, so the third "Drug" is N/A and the third "Grade" is Ungraded. The last "Graded variant", embB_p.Met306Ile, is graded for Ethambutol and has received a grade of 1.