MiDRMpol

MiDRMpol quantifies HIV-1 drug resistance mutations in the pol region (protease, reverse transcriptase, and integrase) from high-throughput sequencing data to detect and report resistance-associated variants including low-abundance minority variants.

Key Features:

• High-Throughput Sequencing Compatibility: Processes HTS data generated from Illumina HiSeq2500 for comprehensive analysis of large datasets.
• Target Regions: Targets the HIV-1 pol region and incorporates data from amplification/sequencing of the gag-vpu region from plasma samples as reported.
• Computational Efficiency: Implements a computationally efficient pipeline that minimizes required computational resources.
• Integrated Preprocessing: Performs adapter trimming and sequence read processing using custom in-house scripts.
• Validation and Benchmarking: Validated against PASeq (Polymorphism Analysis by Sequencing) and benchmarked with Sanger sequencing data from Swedish and Ethiopian cohorts.
• Sensitivity for Minor Variants: Demonstrated sensitivity for detecting minor viral populations with mutations at levels below 5%.
• Error-Rate Thresholding: Applies a stringent error-rate threshold of less than 1% for variant reliability.

Scientific Applications:

• Surveillance of HIV-1 Drug Resistance: Enables large-scale surveillance studies to detect and quantify DRMs across populations, including low-frequency variants.
• Clinical Resistance Profiling: Supports profiling of dominant and minor viral populations to inform antiretroviral therapy decisions.
• Viral Evolution and Research: Facilitates research on viral evolution and the emergence of resistant strains across diverse genetic backgrounds.

Methodology:

Adapter trimming and analysis are performed using custom in-house scripts, with an applied error-rate filter of <1% for calling reliable variants.