scholarly journals Japanese External Quality Assessment Program to Standardize HIV-1 Drug-Resistance Testing (JEQS2010 Program) UsingIn VitroTranscribed RNA as Reference Material

2015 ◽  
Vol 31 (3) ◽  
pp. 318-325 ◽  
Author(s):  
Shigeru Yoshida ◽  
Junko Hattori ◽  
Masakazu Matsuda ◽  
Kiyomi Okada ◽  
Yukumasa Kazuyama ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Reference Material ◽  
Quality Assessment ◽  
External Quality Assessment ◽  
Resistance Testing ◽  
External Quality ◽  
Drug Resistance Testing ◽  
Assessment Program ◽  
Hiv 1

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

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 666 ◽  
Author(s):  
Marc Noguera-Julian ◽  
Emma R. Lee ◽  
Robert W. Shafer ◽  
Rami Kantor ◽  
Hezhao Ji
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Quality Assessment ◽  
External Quality Assessment ◽  
Resistance Testing ◽  
External Quality ◽  
Hiv Drug Resistance ◽  
Drug Resistance Testing ◽  
Ngs Data ◽  
Generation Sequencing

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.

External Quality Assessment Scheme for HIV-1 Drug-Resistance Genotyping in Thailand

2018 ◽  
Vol 34 (12) ◽  
pp. 1028-1035 ◽  
Author(s):  
Siriphan Saeng-aroon ◽  
Nonglak Saipradit ◽  
Ruangchai Loket ◽  
Nattapong Klamkhai ◽  
Ratrawee Boonmuang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Quality Assessment ◽  
External Quality Assessment ◽  
External Quality ◽  
External Quality Assessment Scheme ◽  
Drug Resistance Genotyping ◽  
Hiv 1

scholarly journals External Quality Assessment Program for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Logistical Considerations

Viruses ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 556 ◽  
Author(s):  
Hezhao Ji ◽  
Neil Parkin ◽  
Feng Gao ◽  
Thomas Denny ◽  
Cheryl Jennings ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Quality Assessment ◽  
External Quality Assessment ◽  
Resistance Testing ◽  
Next Generation ◽  
External Quality ◽  
Hiv Drug Resistance ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS) is likely to become the new standard method for HIV drug resistance (HIVDR) genotyping. Despite the significant advances in the development of wet-lab protocols and bioinformatic data processing pipelines, one often-missing critical component of an NGS HIVDR assay for clinical use is external quality assessment (EQA). EQA is essential for ensuring assay consistency and laboratory competency in performing routine biomedical assays, and the rollout of NGS HIVDR tests in clinical practice will require an EQA. In September 2019, the 2nd International Symposium on NGS HIVDR was held in Winnipeg, Canada. It convened a multidisciplinary panel of experts, including research scientists, clinicians, bioinformaticians, laboratory biologists, biostatisticians, and EQA experts. A themed discussion was conducted on EQA strategies towards such assays during the symposium. This article describes the logistical challenges identified and summarizes the opinions and recommendations derived from these discussions, which may inform the development of an inaugural EQA program for NGS HIVDR in the near future.

scholarly journals External Quality Assessment for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Unique Requirements and Challenges

Viruses ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 550 ◽  
Author(s):  
Emma R. Lee ◽  
Feng Gao ◽  
Paul Sandstrom ◽  
Hezhao Ji
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Quality Assessment ◽  
Sanger Sequencing ◽  
External Quality Assessment ◽  
Resistance Testing ◽  
Next Generation ◽  
External Quality ◽  
Hiv Drug Resistance ◽  
Generation Sequencing

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.

Automated quality assessment in HIV-1 drug resistance testing

2006 ◽  
Vol 36 ◽  
pp. S52
Author(s):  
A.A. Pandit ◽  
R. Schuurman ◽  
P. Wallace ◽  
T.E.J. Buultjens ◽  
H. Staines ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Quality Assessment ◽  
Resistance Testing ◽  
Drug Resistance Testing ◽  
Hiv 1

scholarly journals Antiretroviral Drug Resistance Testing in Adult HIV‐1 Infection: 2008 Recommendations of an International AIDS Society–USA Panel

2008 ◽  
Vol 47 (2) ◽  
pp. 266-285 ◽  
Author(s):  
Martin S. Hirsch ◽  
Huldrych F. Günthard ◽  
Jonathan M. Schapiro ◽  
Françoise Brun‐Vézinet ◽  
Bonaventura Clotet ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Resistance Testing ◽  
International Aids ◽  
Antiretroviral Drug Resistance ◽  
Drug Resistance Testing ◽  
Antiretroviral Drug ◽  
Hiv 1
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