ArticlePeerJ2018
Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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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
40 citing papers in PubMed.
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Molecular origin, discovery, validation and application of neoantigens.Asian journal of pharmaceutical sciences · 2026Review
- Clinicopathologic and molecular characterization of a series of sporadic trichoblastic neoplasms.Virchows Archiv : an international journal of pathology · 2026Article
- Small Nucleotide Variant Analysis Using RNA Fusion Panel (SMURF): Making the Most of RNAseq Data in Solid Tumours.Journal of clinical laboratory analysis · 2026Article
- Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter.Nucleic acids research · 2026Article
- Efficient and effective identification of cancer neoantigens from tumor only RNA-seq.NAR genomics and bioinformatics · 2025Article
- Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations.NPJ precision oncology · 2025Article
- Refined variant calling pipeline on RNA-seq data of breast cancer cell lines without matched-normal samples.BMC research notes · 2025Article
- RNA sequencing enables neoantigen discovery and vaccine validation in breast and lung cancer.Frontiers in immunology · 2025Article
- Metabolic stress in space: ROS-induced mutations in mice hint at a new path to cancer.Redox biology · 2024Article
- Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci.Nature communications · 2024Article
- Digital RNA sequencing using unique molecular identifiers enables ultrasensitive RNA mutation analysis.Communications biology · 2024Article
- Article
- Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification.Nature communications · 2023Article
- Article
- RaScALL: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL).PLoS genetics · 2022Article
- FVC as an adaptive and accurate method for filtering variants from popular NGS analysis pipelines.Communications biology · 2022Article
- Widespread redundancy in -omics profiles of cancer mutation states.Genome biology · 2022Article
- Estimating tumor mutational burden from RNA-sequencing without a matched-normal sample.Nature communications · 2022Article
- Circulating Tumor Cell Transcriptomics as Biopsy Surrogates in Metastatic Breast Cancer.Annals of surgical oncology · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
To detect functional somatic mutations in tumor samples, whole-exome sequencing (WES) is often used for its reliability and relative low cost. RNA-seq, while generally used to measure gene expression, can potentially also be used for identification of somatic mutations. However there has been little systematic evaluation of the utility of RNA-seq for identifying somatic mutations. Here, we develop and evaluate a pipeline for processing RNA-seq data from glioblastoma multiforme (GBM) tumors in order to identify somatic mutations. The pipeline entails the use of the STAR aligner 2-pass procedure jointly with MuTect2 from genome analysis toolkit (GATK) to detect somatic variants. Variants identified from RNA-seq data were evaluated by comparison against the COSMIC and dbSNP databases, and also compared to somatic variants identified by exome sequencing. We also estimated the putative functional impact of coding variants in the most frequently mutated genes in GBM. Interestingly, variants identified by RNA-seq alone showed better representation of GBM-related mutations cataloged by COSMIC. RNA-seq-only data substantially outperformed the ability of WES to reveal potentially new somatic mutations in known GBM-related pathways, and allowed us to build a high-quality set of somatic mutations common to exome and RNA-seq calls. Using RNA-seq data in parallel with WES data to detect somatic mutations in cancer genomes can thus broaden the scope of discoveries and lend additional support to somatic variants identified by exome sequencing alone.
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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.