ArticleNature protocols2021
Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 17 citations in OpenAlex.
- MutAnt: mutation annotation tool predicts deleteriousness of missense mutations and improves mutation calling from transcriptomics.Human genetics · 2025Article
- Drivers and implications of lineage-specific cancer-related mutations in human pluripotent and adult stem cells.Stem cell reports · 2025Article
- Cool temperature inhibits binary fission and results in phenotypic and transcriptomic changes that suggest inducible aging in Diadumene lineata.BMC research notes · 2025Article
- Large-scale analysis of loss of chromosome Y in human pluripotent stem cells: Implications for Turner syndrome and ribosomopathies.Stem cell reports · 2025Article
- Depletion of TP53 in Human Pluripotent Stem Cells Triggers Malignant-Like Behavior.Advanced biology · 2025Article
- High prevalence of acquired cancer-related mutations in 146 human pluripotent stem cell lines and their differentiated derivatives.Nature biotechnology · 2024Article
- Multilayer Analysis of RNA Sequencing Data in Alzheimer's Disease to Unravel Molecular Mysteries.Advances in neurobiology · 2024Review
- EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq.Nature protocols · 2023Review
- Benchmark study for evaluating the quality of reference genomes and gene annotations in 114 species.Frontiers in veterinary science · 2023Article
- The Tumorigenic Potential of Human Pluripotent Stem Cells.Stem cells translational medicine · 2022Article
- Large-Scale Analysis of X Inactivation Variations between Primed and Naïve Human Embryonic Stem Cells.Cells · 2022Article
- Induced Pluripotent Stem Cells (iPSCs) and Gene Therapy: A New Era for the Treatment of Neurological Diseases.International journal of molecular sciences · 2021Review
- Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis.Nature protocols · 2021Article
- Targeting α-Synuclein in Parkinson's Disease by Induced Pluripotent Stem Cell Models.Frontiers in neurology · 2021Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human pluripotent stem cells (hPSCs) are known to acquire genetic aberrations during in vitro propagation. In addition to recurrent chromosomal aberrations, it has recently been shown that these cells also gain point mutations in cancer-related genes, predominantly in TP53. The need for routine quality control of hPSCs is critical for both basic research and clinical applications. Here we discuss the relevance of detecting mutations for various hPSCs applications, and present a detailed protocol to identify cancer-related point mutations using data from RNA sequencing, an assay commonly performed during the growth and differentiation of hPSCs. In this protocol, we describe how to process and align the sequencing data, analyze it and conservatively interpret the results in order to generate an accurate estimation of mutations in tumor-related genes. This pipeline is designed to work in high throughput and is available as a software container at https://github.com/elyadlezmi/RNA2CM . The protocol requires minimal command-line skills and can be carried out in 1-2 d.
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