ArticleBriefings in bioinformatics2021
RNA2HLA: HLA-based quality control of RNA-seq datasets.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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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.
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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.
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Who cites it
12 citing papers in PubMed.
- Multi-omics analysis reveals COVID-19 vaccine induced attenuation of inflammatory responses during breakthrough disease.Nature communications · 2024Trial
- Molecular correlates of vaccine-induced protection against typhoid fever.The Journal of clinical investigation · 2023Trial
- Development and validation of a pipeline for the systematic search for new HLA alleles in WGS data.Frontiers in bioinformatics · 2026Article
- Prediction and characterisation of the human B cell response to a heterologous two-dose Ebola vaccine.Nature communications · 2025Article
- Article
- The relationship between extreme inter-individual variation in macrophage gene expression and genetic susceptibility to inflammatory bowel disease.Human genetics · 2024Article
- Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response.BMC medical genomics · 2024Article
- A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data.bioRxiv : the preprint server for biology · 2024Article
- Advances of mRNA vaccine in tumor: a maze of opportunities and challenges.Biomarker research · 2023Review
- A current and future perspective on T cell receptor repertoire profiling.Frontiers in genetics · 2023Review
- Hypomethylation-induced regulatory programs in T cells unveiled by transcriptomic analyses.Frontiers in immunology · 2023Article
- RNA2HLA: HLA-based quality control of RNA-seq datasets.Briefings in bioinformatics · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
RNA-sequencing (RNA-seq) is a widely used approach for accessing the transcriptome in biomedical research. Studies frequently include multiple samples taken from the same individual at various time points or under different conditions, correct assignment of those samples to each particular participant is evidently of great importance. Here, we propose taking advantage of typing the highly polymorphic genes from the human leukocyte antigen (HLA) complex in order to verify the correct allocation of RNA-seq samples to individuals. We introduce RNA2HLA, a novel quality control (QC) tool for performing study-wide HLA-typing for RNA-seq data and thereby identifying the samples from the common source. RNA2HLA allows precise allocation and grouping of RNA samples based on their HLA types. Strikingly, RNA2HLA revealed wrongly assigned samples from publicly available datasets and thereby demonstrated the importance of this tool for the quality control of RNA-seq studies. In addition, our tool successfully extracts HLA alleles in four-digital resolution and can be used to perform massive HLA-typing from RNA-seq based studies, which will serve multiple research purposes beyond sample QC.
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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.