ArticleBriefings in bioinformatics2017
Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations.
Article in Briefings in bioinformatics, 2017. 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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Who cites it
32 citing papers in PubMed.
- Sheep Genetic Resistance to Gastrointestinal Nematode Infections: Current Insights from Transcriptomics and Other OMICs Technologies-A Review.Pathogens (Basel, Switzerland) · 2026Review
- Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies.Human vaccines & immunotherapeutics · 2024Review
- NewmedRxiv : the preprint server for health sciences · 2024Article
- Article
- Detecting Somatic Insertions/Deletions (Indels) Using Tumor RNA-Seq Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA.Nature protocols · 2023Review
- LPS-Induced Liver Injury of Magang Geese through Toll-like Receptor and MAPK Signaling Pathway.Animals : an open access journal from MDPI · 2022Article
- Unified gene expression signature of novel NPM1 exon 5 mutations in acute myeloid leukemia.Blood advances · 2022Article
- scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq.Science advances · 2022Article
- Performance of an RNA-Based Next-Generation Sequencing Assay for Combined Detection of Clinically Actionable Fusions and Hotspot Mutations in NSCLC.JTO clinical and research reports · 2022Article
- Identifying gene variants underlying the pathogenesis of diabetic retinopathy based on integrated genomic and transcriptomic analysis of clinical extreme phenotypes.Frontiers in genetics · 2022Article
- Detecting Medium and Large Insertions and Deletions with transIndel.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Neoantigen prediction in human breast cancer using RNA sequencing data.Cancer science · 2021Article
- Finding a suitable library size to call variants in RNA-Seq.BMC bioinformatics · 2020Article
- Identification and Characterization of Hypothalamic Alternative Splicing Events and Variants in Ovine Fecundity-Related Genes.Animals : an open access journal from MDPI · 2020Article
- Article
- Temporal changes in the spinal cord transcriptome after peripheral nerve injury.Neural regeneration research · 2020Article
- RNAIndel: discovering somatic coding indels from tumor RNA-Seq data.Bioinformatics (Oxford, England) · 2020Article
- CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data.Nature communications · 2020Article
- Transcriptome Profiling of Acquired Gefitinib Resistant Lung Cancer Cells Reveals Dramatically Changed Transcription Programs and New Treatment Targets.Frontiers in oncology · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Driver somatic mutations are a hallmark of a tumor that can be used for diagnosis and targeted therapy. Mutations are primarily detected from tumor DNA. As dynamic molecules of gene activities, transcriptome profiling by RNA sequence (RNA-seq) is becoming increasingly popular, which not only measures gene expression but also structural variations such as mutations and fusion transcripts. Although single-nucleotide variants (SNVs) can be easily identified from RNA-seq, intermediate long insertions/deletions (indels > 2 bases and less than sequence reads) cause significant challenges and are ignored by most RNA-seq analysis tools. This study evaluates commonly used RNA-seq analysis programs along with variant and somatic mutation callers in a series of data sets with simulated and known indels. The aim is to develop strategies for accurate indel detection. Our results show that the RNA-seq alignment is the most important step for indel identification and the evaluated programs have a wide range of sensitivity to map sequence reads with indels, from not at all to decently sensitive. The sensitivity is impacted by sequence read lengths. Most variant calling programs rely on hard evidence indels marked in the alignment and the programs with realignment may use soft-clipped reads for indel inferencing. Based on the observations, we have provided practical recommendations for indel detection when different RNA-seq aligners are used and demonstrated the best option with highly reliable results. With careful customization of bioinformatics algorithms, RNA-seq can be reliably used for both SNV and indel mutation detection that can be used for clinical decision-making.
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