Abstract
Over the past decade, there has been an increase in the adoption of next generation sequencing (NGS) technologies for HIV drug resistance (HIVDR) testing. NGS far outweighs conventional Sanger sequencing as it has much higher throughput, lower cost when samples are batched and, most importantly, significantly higher sensitivities for variants present at low frequencies, which may have significant clinical implications. Despite the advantages of NGS, Sanger sequencing remains the gold standard for HIVDR testing, largely due to the lack of standardization of NGS-based HIVDR testing. One important aspect of standardization includes external quality assessment (EQA) strategies and programs. Current EQA for Sanger-based HIVDR testing includes proficiency testing where samples are sent to labs and the performance of the lab conducting such assays is evaluated. The current methods for Sanger-based EQA may not apply to NGS-based tests because of the fundamental differences in their technologies and outputs. Sanger-based genotyping reports drug resistance mutations (DRMs) data as dichotomous, whereas NGS-based HIVDR genotyping also reports DRMs as numerical data (percent abundance). Here we present an overview of the need to develop EQA for NGS-based HIVDR testing and some unique challenges that may be encountered.
Highlights
Next-generation sequencing (NGS) or high throughput sequencing has revolutionized DNA sequencing methodology
In HIV drug resistance (HIVDR) genotyping, next generation sequencing (NGS) could detect drug-resistance mutations (DRMs) present at frequencies below 20%, known as minority resistance variants (MRVs), which are mostly undetectable by Sanger sequencing (SS) methods [1,3,4]
NGS is a powerful tool with the ability to detect variants at low-frequency levels that were otherwise undetectable by Sanger sequencing
Summary
Next-generation sequencing (NGS) or high throughput sequencing has revolutionized DNA sequencing methodology. As more labs are implementing NGS as the preferred platform for HIVDR genotyping, the need to develop appropriate external quality assessment (EQA) strategies suitable for such assays is urgent. As with all other molecular clinical laboratory tests, NGS-based HIVDR assays must implement quality management systems to ensure high-quality test results [12,13,14,15,16]. Performance monitoring includes internal and external quality controls, as well as participation in an EQA program [14,20]. EQA programs establish the comparison of assay performance amongst different participating labs, helping to identify analytical or interpretive errors, flag areas that need improvement, and identify training needs. EQA program, participant labs receive blind-coded samples, process the samples as they would do for clinical specimens, and submit the results to the EQA administrator for performance assessments.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
