scholarly journals Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus

2018 ◽  
Vol 21 (10) ◽  
pp. e25193 ◽  
Author(s):  
Hezhao Ji ◽  
Eric Enns ◽  
Chanson J. Brumme ◽  
Neil Parkin ◽  
Mark Howison ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Data Processing ◽  
Resistance Testing ◽  
Next Generation ◽  
Hiv Drug Resistance ◽  
Drug Resistance Testing ◽  
Generation Sequencing

scholarly journals Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 617 ◽  
Author(s):  
Santiago Ávila-Ríos ◽  
Neil Parkin ◽  
Ronald Swanstrom ◽  
Roger Paredes ◽  
Robert Shafer ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Clinical Care ◽  
Pcr Amplification ◽  
Resistance Testing ◽  
Sample Type ◽  
Next Generation ◽  
Hiv Drug Resistance ◽  
Drug Resistance Testing ◽  
Generation Sequencing

Higher accessibility and decreasing costs of next generation sequencing (NGS), availability of commercial kits, and development of dedicated analysis pipelines, have allowed an increasing number of laboratories to adopt this technology for HIV drug resistance (HIVDR) genotyping. Conventional HIVDR genotyping is traditionally carried out using population-based Sanger sequencing, which has a limited capacity for reliable detection of variants present at intra-host frequencies below a threshold of approximately 20%. NGS has the potential to improve sensitivity and quantitatively identify low-abundance variants, improving efficiency and lowering costs. However, some challenges exist for the standardization and quality assurance of NGS-based HIVDR genotyping. In this paper, we highlight considerations of these challenges as related to laboratory, clinical, and implementation of NGS for HIV drug resistance testing. Several sources of variation and bias occur in each step of the general NGS workflow, i.e., starting material, sample type, PCR amplification, library preparation method, instrument and sequencing chemistry-inherent errors, and data analysis options and limitations. Additionally, adoption of NGS-based HIVDR genotyping, especially for clinical care, poses pressing challenges, especially for resource-poor settings, including infrastructure and equipment requirements and cost, logistic and supply chains, instrument service availability, personnel training, validated laboratory protocols, and standardized analysis outputs. The establishment of external quality assessment programs may help to address some of these challenges and is needed to proceed with NGS-based HIVDR genotyping adoption.

Routine drug resistance testing in HIV-1 proviral DNA, using an automated next- generation sequencing assay

2019 ◽  
Vol 121 ◽  
pp. 104207 ◽  
Author(s):  
Enagnon Kazali Alidjinou ◽  
Pauline Coulon ◽  
Christophe Hallaert ◽  
Olivier Robineau ◽  
Agnès Meybeck ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Resistance Testing ◽  
Next Generation ◽  
Proviral Dna ◽  
Drug Resistance Testing ◽  
Generation Sequencing ◽  
Hiv 1

scholarly journals Next Generation Sequencing for HIV-1 Drug Resistance Testing—A Special Issue Walkthrough

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 340
Author(s):  
Rami Kantor
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Resistance Testing ◽  
Next Generation ◽  
Special Issue ◽  
Global Challenge ◽  
Drug Resistance Testing ◽  
Generation Sequencing ◽  
Hiv 1

Drug resistance remains a global challenge in the fight against the HIV pandemic [...]

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.

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.

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