ArticleJournal of clinical microbiology2012
Comparison of a high-resolution melting assay to next-generation sequencing for analysis of HIV diversity.
Article in Journal of clinical microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 48 citations in OpenAlex.
- The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards.Scientific reports · 2017Pooled it
- Association of HIV diversity and virologic outcomes in early antiretroviral treatment: HPTN 052.PloS one · 2017Trial
- Association of pol diversity with antiretroviral treatment outcomes among HIV-infected African children.PloS one · 2013Trial
- Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis.Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy · 2021Article
- Isolation and Genetic Characterization of Puumala Orthohantavirus Strains from France.Pathogens (Basel, Switzerland) · 2021Article
- Feasibility of melting fingerprint obtained from ISSR-HRM curves for marine mammal species identification.PeerJ · 2021Article
- How Bank Vole-PUUV Interactions Influence the Eco-Evolutionary Processes Driving Nephropathia Epidemica Epidemiology-An Experimental and Genomic Approach.Pathogens (Basel, Switzerland) · 2020Article
- Subclinical Cytomegalovirus and Epstein-Barr Virus Shedding Is Associated with Increasing HIV DNA Molecular Diversity in Peripheral Blood during Suppressive Antiretroviral Therapy.Journal of virology · 2020Article
- Rapid screening of MMACHC gene mutations by high-resolution melting curve analysis.Molecular genetics & genomic medicine · 2020Article
- HIITE: HIV-1 incidence and infection time estimator.Bioinformatics (Oxford, England) · 2018Article
- Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM) Curve Analysis for Authentication ofFrontiers in plant science · 2018Article
- LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature.Journal of the American Chemical Society · 2017Article
- Article
- Rapid Detection of Common HIV-1 Drug Resistance Mutations by Use of High-Resolution Melting Analysis and Unlabeled Probes.Journal of clinical microbiology · 2017Article
- Mutation analysis of 13 driver genes of colorectal cancer-related pathways in Taiwanese patients.World journal of gastroenterology · 2016Article
- Analysis of HIV Diversity in HIV-Infected Black Men Who Have Sex with Men (HPTN 061).PloS one · 2016Article
- Review
- A Generalized Entropy Measure of Within-Host Viral Diversity for Identifying Recent HIV-1 Infections.Medicine · 2015Article
- Developing high-throughput HIV incidence assay with pyrosequencing platform.Journal of virology · 2014Article
- A comparison of two measures of HIV diversity in multi-assay algorithms for HIV incidence estimation.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 6 institutions in 3 countries.
Funding
Abstract
Next-generation sequencing (NGS) has recently been used for analysis of HIV diversity, but this method is labor-intensive, costly, and requires complex protocols for data analysis. We compared diversity measures obtained using NGS data to those obtained using a diversity assay based on high-resolution melting (HRM) of DNA duplexes. The HRM diversity assay provides a single numeric score that reflects the level of diversity in the region analyzed. HIV gag and env from individuals in Rakai, Uganda, were analyzed in a previous study using NGS (n = 220 samples from 110 individuals). Three sequence-based diversity measures were calculated from the NGS sequence data (percent diversity, percent complexity, and Shannon entropy). The amplicon pools used for NGS were analyzed with the HRM diversity assay. HRM scores were significantly associated with sequence-based measures of HIV diversity for both gag and env (P < 0.001 for all measures). The level of diversity measured by the HRM diversity assay and NGS increased over time in both regions analyzed (P < 0.001 for all measures except for percent complexity in gag), and similar amounts of diversification were observed with both methods (P < 0.001 for all measures except for percent complexity in gag). Diversity measures obtained using the HRM diversity assay were significantly associated with those from NGS, and similar increases in diversity over time were detected by both methods. The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.