Trial reportPloS one2014
Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.
Trial report in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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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
13 citing papers in PubMed, 35 citations in OpenAlex.
- Article
- A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance.Scientific reports · 2019Article
- Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.Nature biotechnology · 2019Article
- Nanopore-based detection and characterization of yam viruses.Scientific reports · 2018Article
- Impact of Human Immunodeficiency Virus Type 1 Minority Variants on the Virus Response to a Rilpivirine-Based First-line Regimen.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2018Article
- Efficient In Vivo Liver-Directed Gene Editing Using CRISPR/Cas9.Molecular therapy : the journal of the American Society of Gene Therapy · 2018Article
- The Role of HIV-1 Drug-Resistant Minority Variants in Treatment Failure.The Journal of infectious diseases · 2017Review
- Large-scale SNP screenings identify markers linked with GCRV resistant traits through transcriptomes of individuals and cell lines in Ctenopharyngodon idella.Scientific reports · 2017Article
- Challenges in the analysis of viral metagenomes.Virus evolution · 2016Review
- QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles.BMC bioinformatics · 2015Article
- Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities.Frontiers in microbiology · 2015Review
- Review
- Short communication: HIV-1 gag genetic variation in a single acutely infected participant defined by high-resolution deep sequencing.AIDS research and human retroviruses · 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
31 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundThe impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs.
methodsA5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naïve patients. Pre-treatment plasma was obtained from 5 participants with raltegravir resistance at the time of virologic failure. A control library was created by pooling integrase clones at predefined proportions. Multiplexed sequencing was performed with Illumina and 454 platforms at comparable costs. Illumina sequence analysis was performed with the novel snp-assess tool and 454 sequencing was analyzed with V-Phaser.
resultsIllumina sequencing resulted in significantly higher sequence coverage and a 0.095% limit of detection. Illumina accurately detected all MVs in the control library at ≥0.5% and 7/10 MVs expected at 0.1%. 454 sequencing failed to detect any MVs at 0.1% with 5 false positive calls. For MVs detected in the patient samples by both 454 and Illumina, the correlation in the detected variant frequencies was high (R2 = 0.92, P<0.001). Illumina sequencing detected 2.4-fold greater nucleotide MVs and 2.9-fold greater amino acid MVs compared to 454. The only raltegravir-resistant MV detected was an E138K mutation in one participant by Illumina sequencing, but not by 454.
conclusionsIn participants of A5262 with raltegravir resistance at virologic failure, baseline raltegravir-resistant MVs were rarely detected. At comparable costs to 454 sequencing, Illumina demonstrated greater depth of coverage, increased sensitivity for detecting HIV MVs, and fewer false positive variant calls.
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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.