TB-Insight: Run TB-Lineage

Run TB-Lineage [Please cite]

A tool to determine the major genetic lineage of a Mycobacterium tuberculosis isolate given its spoligotypes and optionally MIRU locus 24 through various methods.

Tools: Octal to Binary / Binary to Octal

The TB-Insight suite provides the RULE and CBN methods to predict the folllowing major MTBC genetic lineages:

Modern Lineages
- East-Asian (Beijing)
- Euro-American
- East-African Indian
Ancestral Lineages
- Indo-Oceanic
- M. africanum
  - West African 1
  - West African 2
- M. bovis

Major Lineage by Rules

Uses rule-based system for major MTBC phylogenetic lineages.
Refines and clarifies rules developed by Dr. Lauren Cowan, U.S. Centers for Disease Control and Prevention (Atlanta, Georgia).
Utilizes rules with two types of features:

Deletion of contiguous spacers
MIRU locus 24 (if MIRU 24< 2 then modern, else ancestral.)

Evaluates rules sequentially until a rule determines lineage.

Major Lineages by CBN

Employs a hierarchical Bayesian network that uses multiple biomarkers obtained from PCR-based typing methods, spoligotyping and MIRU typing.
The design of the probability-based model exploits known properties about the structure, position and mutation mechanisms of spoligotypes and MIRU.
Predictions can be made using one or more types of biomarkers based on availability. Classification can be done based on:
- Spoligotype only
- MIRU only
- Spoligotype and MIRU
CBN does not currently discriminate between West African 1 and West African 2. CBN returns M. africanum for both.

KBBN for SITVIT CLADES

Predictive model for 69 MTBC clades found in the SITVIT international collection.
Probability-based model incorporates expert rules into Bayesian networks for classification of MTBC clades.
KBBN uses data to refine rule-based classifiers when the rule set is incomplete or ambiguous.
Predictions are done using spoligotypes only. MIRU is not considered.
The 69 SITVIT Clades that are predicted can be found here