MycoVarP: Mycobacterium Variant and Drug Resistance Prediction Pipeline for Whole-Genome Sequence Data Analysis

Area of Science:

• Genomics
• Microbiology
• Bioinformatics

Background:

• Whole-genome sequencing (WGS) is crucial for analyzing bacterial genomes, including Mycobacterium tuberculosis (Mtb), for genotype-phenotype correlations, variant diversity, and evolution.
• Existing WGS analysis tools for Mtb are often too general or limited in scope, failing to adequately address bacterium-specific issues like gene variations, INDELs/synonymous variants, PE-PPE family genes, and drug resistance.
• Accurate identification and prioritization of variants are essential for therapeutic intervention, particularly for drug resistance and lineage-specific characteristics.

Purpose of the Study:

• To introduce Mycobacterium variant pipeline (MycoVarP), an end-to-end solution for Mtb WGS data analysis.
• To address the limitations of existing pipelines by providing specific insights into Mtb-related genetic variations and drug resistance.
• To enhance the identification of true-positive, drug resistance-associated variants, including those in the PE-PPE/PGRS family.

Main Methods:

• MycoVarP processes raw WGS reads, performing quality checks before trimming and after alignment to a reference genome.
• The pipeline incorporates user-defined and default filters for variant prioritization.
• Annotated variants are mapped to a drug-susceptible (DS) database to remove false positives, followed by lineage identification and drug resistance prediction.

Main Results:

• Re-analysis of existing Mtb WGS data using MycoVarP identified additional variants not previously reported.
• MycoVarP demonstrated effectiveness in identifying nonsynonymous, true-positive variants associated with drug resistance.
• The pipeline successfully identified variants within the PE-PPE/PGRS family (IDP).

Conclusions:

• MycoVarP provides a more effective and comprehensive approach to identifying critical Mtb variants compared to current pipelines.
• The tool facilitates better prioritization of variants for therapeutic targeting, especially for drug resistance.
• MycoVarP enhances the analysis of complex genetic variations within Mtb, including those in the PE-PPE/PGRS family.