UVP

UVP processes Mycobacterium tuberculosis complex (MTBC) whole genome sequencing (WGS) data to identify genetic variants and assign lineages for analysis of drug-resistant tuberculosis and integration with phenotypic drug susceptibility testing (DST) in the ReSeqTB platform.

Key Features:

• Variant Identification: Detects genetic variants in MTBC isolates from WGS using stringent thresholds and quality-control measures.
• Lineage Assignment: Assigns MTBC lineages with reported 100% concordance to conventional methods.
• Data Standardization and Aggregation: Standardizes and aggregates global MTBC variant data with phenotypic DST and clinical metadata for incorporation into the ReSeqTB platform.

Scientific Applications:

• Drug Resistance Prediction: Predicts phenotypic drug resistance with reported accuracy exceeding 94% when compared to DST across 4,636 publicly available MTBC isolates covering all seven major lineages.
• Reference Standard Development: Supports establishment of confidence-graded mutations statistically associated with phenotypic drug resistance to inform molecular diagnostic assay development.
• Public Health Reference: Provides a reference standard to aid researchers, public health agencies, and clinicians in the control and management of drug-resistant tuberculosis.

Methodology:

Standardizes and aggregates WGS-derived MTBC variant data alongside phenotypic DST and clinical information; applies stringent thresholds and quality-control measures for variant detection; assigns lineage; validated on 90 diverse MTBC isolates with comparison to conventional DST and DNA Sanger sequencing (98.9% agreement) and evaluated across 4,636 public isolates from all seven major lineages for drug resistance prediction (>94% accuracy).