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Quality Control of Next-Generation Sequencing-Based HIV-1 Drug Resistance Data in Clinical Laboratory Information Systems Framework
Commentary

Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing

1
IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, Catalonia, 08196 Badalona, Spain
2
Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic, Central University of Catalonia, Can Baumann. Ctra. de Roda, 70, 08500 Vic, Spain
3
National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
4
Stanford University Medical School, Stanford, CA 94305, USA
5
Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02903, USA
6
Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
*
Author to whom correspondence should be addressed.
Received: 28 May 2020 / Revised: 18 June 2020 / Accepted: 18 June 2020 / Published: 20 June 2020
(This article belongs to the Special Issue Next Generation Sequencing for HIV Drug Resistance Testing)
External quality assessment (EQA) is a keystone element in the validation and implementation of next generation sequencing (NGS)-based HIV drug resistance testing (DRT). Software validation and evaluation is a critical element in NGS EQA programs. While the development, sharing, and adoption of wet lab protocols is coupled with the increasing access to NGS technology worldwide, rendering it easy to produce NGS data for HIV-DRT, bioinformatic data analysis remains a bottleneck for most of the diagnostic laboratories. Several computational tools have been made available, via free or commercial sources, to automate the conversion of raw NGS data into an actionable clinical report. Although different software platforms yield equivalent results when identical raw NGS datasets are analyzed for variations at higher abundance, discrepancies arise when variations at lower frequencies are considered. This implies that validation and performance assessment of the bioinformatics tools applied in NGS HIV-DRT is critical, and the origins of the observed discrepancies should be determined. Well-characterized reference NGS datasets with ground truth on the genotype composition at all examined loci and the exact frequencies of HIV variations they may harbor, so-called dry panels, would be essential in such cases. The strategic design and construction of such panels are challenging but imperative tasks in support of EQA programs for NGS-based HIV-DRT and the validation of relevant bioinformatics tools. Here, we present criteria that can guide the design of such dry panels, which were discussed in the Second International Winnipeg Symposium themed for EQA strategies for NGS HIVDR assays. View Full-Text
Keywords: HIV; drug resistance testing; next generation sequencing; external quality assessment; dry panel HIV; drug resistance testing; next generation sequencing; external quality assessment; dry panel
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MDPI and ACS Style

Noguera-Julian, M.; Lee, E.R.; Shafer, R.W.; Kantor, R.; Ji, H. Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing. Viruses 2020, 12, 666. https://0-doi-org.brum.beds.ac.uk/10.3390/v12060666

AMA Style

Noguera-Julian M, Lee ER, Shafer RW, Kantor R, Ji H. Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing. Viruses. 2020; 12(6):666. https://0-doi-org.brum.beds.ac.uk/10.3390/v12060666

Chicago/Turabian Style

Noguera-Julian, Marc, Emma R. Lee, Robert W. Shafer, Rami Kantor, and Hezhao Ji. 2020. "Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing" Viruses 12, no. 6: 666. https://0-doi-org.brum.beds.ac.uk/10.3390/v12060666

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