ArticlePloS one2012
Analysis of HIV using a high resolution melting (HRM) diversity assay: automation of HRM data analysis enhances the utility of the assay for analysis of HIV incidence.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Association of pol diversity with antiretroviral treatment outcomes among HIV-infected African children.PloS one · 2013Trial
- Modeling methods for estimating HIV incidence: a mathematical review.Theoretical biology & medical modelling · 2020Review
- Diagnosis of Human Immunodeficiency Virus Infection.Clinical microbiology reviews · 2019Review
- Field-deployable, quantitative, rapid identification of active Ebola virus infection in unprocessed blood.Chemical science · 2017Article
- Moving towards a reliable HIV incidence test - current status, resources available, future directions and challenges ahead.Epidemiology and infection · 2017Review
- Article
- Analysis of HIV Diversity in HIV-Infected Black Men Who Have Sex with Men (HPTN 061).PloS one · 2016Article
- A Generalized Entropy Measure of Within-Host Viral Diversity for Identifying Recent HIV-1 Infections.Medicine · 2015Article
- Rapid and specific detection of porcine parvovirus using real-time PCR and high resolution melting (HRM) analysis.BMC veterinary research · 2015Article
- How can we better identify early HIV infections?Current opinion in HIV and AIDS · 2015Review
- In silico single strand melting curve: a new approach to identify nucleic acid polymorphisms in Totiviridae.BMC bioinformatics · 2014Article
- HIV diversity as a biomarker for HIV incidence estimation: including a high-resolution melting diversity assay in a multiassay algorithm.Journal of clinical microbiology · 2014Article
- Rapid detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini using real-time PCR and high resolution melting analysis.TheScientificWorldJournal · 2014Article
- A comparison of two measures of HIV diversity in multi-assay algorithms for HIV incidence estimation.PloS one · 2014Article
- Article
- Impact of mutation type and amplicon characteristics on genetic diversity measures generated using a high-resolution melting diversity assay.The Journal of molecular diagnostics : JMD · 2013Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundHIV diversity may be a useful biomarker for discriminating between recent and non-recent HIV infection. The high resolution melting (HRM) diversity assay was developed to quantify HIV diversity in viral populations without sequencing. In this assay, HIV diversity is expressed as a single numeric HRM score that represents the width of a melting peak. HRM scores are highly associated with diversity measures obtained with next generation sequencing. In this report, a software package, the HRM Diversity Assay Analysis Tool (DivMelt), was developed to automate calculation of HRM scores from melting curve data.
methodsDivMelt uses computational algorithms to calculate HRM scores by identifying the start (T1) and end (T2) melting temperatures for a DNA sample and subtracting them (T2 - T1 = HRM score). DivMelt contains many user-supplied analysis parameters to allow analyses to be tailored to different contexts. DivMelt analysis options were optimized to discriminate between recent and non-recent HIV infection and to maximize HRM score reproducibility. HRM scores calculated using DivMelt were compared to HRM scores obtained using a manual method that is based on visual inspection of DNA melting curves.
resultsHRM scores generated with DivMelt agreed with manually generated HRM scores obtained from the same DNA melting data. Optimal parameters for discriminating between recent and non-recent HIV infection were identified. DivMelt provided greater discrimination between recent and non-recent HIV infection than the manual method.
conclusionDivMelt provides a rapid, accurate method of determining HRM scores from melting curve data, facilitating use of the HRM diversity assay for large-scale studies.
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