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Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis


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 The protocol requires minimal command-line skills and can be carried out in 1–2 d.

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Fig. 1: Relevance of cancer-related point mutations in hPCSs.
Fig. 2: Schematic representation of the pipeline for identification of cancer-related mutations in hPSCs from RNA-seq data.

Data availability

The RNA-seq sample used as an example in this protocol can be retrieved from the Sequence Read Archive (SRA) database ( under the accession number SRR3090631.

Code availabilty

All the code used in this protocol is available at


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We thank S. Kinreich and A. Pagis for testing the pipeline and providing their constructive input and all members of The Azrieli Center for Stem Cells and Genetic Research for critical reading of the manuscript. This work was partially supported by the Israel Science Foundation (494/17), the Rosetrees Trust, and Azrieli Foundation. N.B. is the Herbert Cohn Chair in Cancer Research.

Author information




E.L. and N.B. designed the analysis. E.L. developed the bioinformatic pipeline and wrote the manuscript with input from N.B., who supervised the work.

Corresponding authors

Correspondence to Elyad Lezmi or Nissim Benvenisty.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Protocols thanks Anna Esteve-Codina and the other, anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Related links

Key references using this protocol

Merkle, F. et al. Nature 545, 229–233 (2017):

Avior, Y. et al. Cell Stem Cell 28, 10–11 (2021):

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Lezmi, E., Benvenisty, N. Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis. Nat Protoc 16, 4522–4537 (2021).

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