Application of a Sanger-Based External Quality Assurance Strategy for the Transition of HIV-1 Drug Resistance Assays to Next Generation Sequencing

Viruses

NeilT. Parkin¹  Cheryl Jennings²  JamesW. Bremer²  Hezhao Ji³  Rupert Capina³  Paul Sandstrom³  DanielJ. Zaccaro⁴  DonaldJ. Brambilla⁵ 

[1] Data First Consulting, Inc., Sebastopol, CA 95472-2129, USA;Department of Molecular Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA;National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada;Research Triangle Institute (RTI) International, Research Triangle Park, NC 27709-2194, USA;Research Triangle Institute (RTI) International, Rockville, MD 20852, USA;

关键词: HIV-1 drug resistance;    next-generation sequencing;    external quality assurance;    Sanger sequencing;   

DOI  :  10.3390/v12121456

来源: DOAJ

【 摘 要 】

The National Institute of Allergy and Infectious Diseases (NIAID) Virology Quality Assurance (VQA) established a robust proficiency testing program for Sanger sequencing (SS)-based HIV-1 drug resistance (HIVDR) testing in 2001. While many of the lessons learned during the development of such programs may also apply to next generation sequencing (NGS)-based HIVDR assays, challenges remain for the ongoing evaluation of NGS-based testing. These challenges include a proper assessment of assay accuracy and the reproducibility of low abundance variant detection, intra- and inter-assay performance comparisons among laboratories using lab-defined tests, and different data analysis pipelines designed for NGS. In collaboration with the World Health Organization (WHO) Global HIVDR Laboratory Network and the Public Health Agency of Canada, the Rush VQA program distributed archived proficiency testing panels to ten laboratories to evaluate internally developed NGS assays. Consensus FASTA files were submitted using 5%, 10%, and 20% variant detection thresholds, and scored based on the same criteria used for SS. This small study showed that the SS External Quality Assurance (EQA) approach can be used as a transitional strategy for using NGS to generate SS-like data and for ongoing performance while using NGS data from the same quality control materials to further evaluate NGS assay performance.

【 授权许可】

Unknown