| Autor: |
Jennings C; Department of Molecular Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA., Parkin NT; Data First Consulting, Inc., Sebastopol, CA 95472-2129, USA., Zaccaro DJ; Research Triangle Institute (RTI) International, Research Triangle Park, NC 27709-2194, USA., Capina R; National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada., Sandstrom P; National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada.; Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada., Ji H; National HIV and Retrovirology Laboratories at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada.; Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada., Brambilla DJ; Research Triangle Institute (RTI) International, Rockville, MD 20852, USA., Bremer JW; Department of Molecular Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA. |
| Abstrakt: |
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. |
