PASeq

PASeq identifies and quantifies HIV drug resistance mutations from sequencing data to determine mutation presence and frequency.

Key Features:

• Mutation identification: Identifies HIV drug resistance mutations, including M184V and M184I.
• Frequency quantification: Reports mutation frequencies and detects variants at frequencies greater than 1%.
• Sequencing input: Analyzes paired-end MiSeq reads covering the first 855 base pairs of the HIV reverse transcriptase gene from PBMC samples.
• Validation and concordance: Compares outputs to an in-house bioinformatics pipeline and demonstrated concordance up to 99.5%.

Scientific Applications:

• Clinical variant detection: Identification and frequency measurement of M184V and M184I in clinical MOBIDIP trial samples.
• Archived resistance assessment: Assessing reduction or persistence of archived M184V between initial treatment failure and trial enrollment.
• Pipeline validation: Cross-validation of variant calls and frequency estimates against an in-house bioinformatics pipeline.
• Clinical-trial interpretation: Providing molecular evidence to interpret virological outcomes in comparisons of PI/r monotherapy versus PI/r + 3TC.
• APOBEC-related analysis: Detection of M184I and its association with stop codons consistent with APOBEC-targeted sites.

Methodology:

PASeq analyzed paired-end MiSeq reads spanning the first 855 bp of the HIV reverse transcriptase gene from PBMC samples to identify and quantify drug resistance mutations and to compare results with an in-house bioinformatics pipeline, yielding concordance up to 99.5% for variants detected above 1% frequency.