Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based 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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-06-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/12/6/666 |
| _version_ | 1797564704445431808 |
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| author | Marc Noguera-Julian Emma R. Lee Robert W. Shafer Rami Kantor Hezhao Ji |
| author_facet | Marc Noguera-Julian Emma R. Lee Robert W. Shafer Rami Kantor Hezhao Ji |
| author_sort | Marc Noguera-Julian |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T19:01:44Z |
| format | Article |
| id | doaj.art-e4792d5c500545478ab8c96bdc273a94 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T19:01:44Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-e4792d5c500545478ab8c96bdc273a942023-11-20T04:27:01ZengMDPI AGViruses1999-49152020-06-0112666610.3390/v12060666Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance TestingMarc Noguera-Julian0Emma R. Lee1Robert W. Shafer2Rami Kantor3Hezhao Ji4IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, Catalonia, 08196 Badalona, SpainNational HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, CanadaStanford University Medical School, Stanford, CA 94305, USADivision of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02903, USANational HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, CanadaExternal 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.https://www.mdpi.com/1999-4915/12/6/666HIVdrug resistance testingnext generation sequencingexternal quality assessmentdry panel |
| spellingShingle | Marc Noguera-Julian Emma R. Lee Robert W. Shafer Rami Kantor Hezhao Ji Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing Viruses HIV drug resistance testing next generation sequencing external quality assessment dry panel |
| title | Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing |
| title_full | Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing |
| title_fullStr | Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing |
| title_full_unstemmed | Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing |
| title_short | Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing |
| title_sort | dry panels supporting external quality assessment programs for next generation sequencing based hiv drug resistance testing |
| topic | HIV drug resistance testing next generation sequencing external quality assessment dry panel |
| url | https://www.mdpi.com/1999-4915/12/6/666 |
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