ArticleGenome research2020
Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 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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Who cites it
32 citing papers in PubMed, 58 citations in OpenAlex.
- The circadian isoform landscape of mouse livers.NAR genomics and bioinformatics · 2026Article
- Beyond counting: how single-cell long-read sequencing turns transcriptome complexity into precision targets.Frontiers in oncology · 2026Review
- Primate retroelement exonization and sexually dimorphicScience immunology · 2025Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.Genome research · 2025Article
- Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain.Journal of molecular neuroscience : MN · 2025Article
- Sex-Specific HLA Alleles Contribute to the Modulation of COVID-19 Severity.International journal of molecular sciences · 2024Article
- Real-time and programmable transcriptome sequencing with PROFIT-seq.Nature cell biology · 2024Article
- Generation and analysis of a mouse multitissue genome annotation atlas.Genome research · 2024Article
- Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- Article
- Generation and analysis of a mouse multi-tissue genome annotation atlas.bioRxiv : the preprint server for biology · 2024Article
- Improving the RNA velocity approach with single-cell RNA lifecycle (nascent, mature and degrading RNAs) sequencing technologies.Nucleic acids research · 2023Article
- Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures.Nature methods · 2023Article
- The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells.Molecular cancer · 2023Review
- Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion.Genome biology · 2023Article
- isONform: reference-free transcriptome reconstruction from Oxford Nanopore data.Bioinformatics (Oxford, England) · 2023Article
- TEx-MST: tissue expression profiles of MANE select transcripts.Database : the journal of biological databases and curation · 2022Article
- Exploring differential exon usage via short- and long-read RNA sequencing strategies.Open biology · 2022Article
- Single-cell isoform analysis in human immune cells.Genome biology · 2022Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The human immune system relies on highly complex and diverse transcripts and the proteins they encode. These include transcripts encoding human leukocyte antigen (HLA) receptors as well as B cell and T cell receptors (BCR and TCR). Determining which alleles an individual possesses for each HLA gene (high-resolution HLA typing) is essential to establish donor-recipient compatibility in organ and bone marrow transplantations. In turn, the repertoires of millions of unique BCR and TCR transcripts in each individual carry a vast amount of health-relevant information. Both short-read RNA-seq-based HLA typing and BCR/TCR repertoire sequencing (AIRR-seq) currently rely on our incomplete knowledge of the genetic diversity at HLA and BCR/TCR loci. Here, we generated over 10,000,000 full-length cDNA sequences at a median accuracy of 97.9% using our nanopore sequencing-based Rolling Circle Amplification to Concatemeric Consensus (R2C2) protocol. We used this data set to (1) show that deep and accurate full-length cDNA sequencing can be used to provide isoform-level transcriptome analysis for more than 9000 loci, (2) generate accurate sequences of HLA alleles, and (3) extract detailed AIRR data for the analysis of the adaptive immune system. The HLA and AIRR analysis approaches we introduce here are untargeted and therefore do not require prior knowledge of the composition or genetic diversity of HLA and BCR/TCR loci.
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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.