Population-scale iPSC Genomics

Collaborators: Stephen Montgomery & Oliver Stegle (with Kelly Fraser, UCSD)


Induced Pluripotent Stem Cells as models for health and disease research

Technological advances have enabled the generation of human induced pluripotent stem cells (iPSC) derived from hundreds of individuals. iPSCs have the potential be reprogrammed into any cell type in the human body, whilst still carrying the trademarks of the individual that the cells originally came from. Using iPSC technology, researchers have access to cell types that are difficult to access (e.g. neuronal cells), specific cell types that affected by disease, and cells from healthy patients to undertake comparative genomic studies. Large-scale iPSC resources enable novel insights and focused analyses to uncover the regulatory dependencies between genetic factors and molecular properties of stem cells.


Population-scale human iPSC genomics

Using data available in the Human Induced Pluripotent Stem Cell Initiative (HipSci initiative), the laboratories of Stephen Montgomery (Stanford), Oliver Stegle (EMBL), and Kelly Frazer (UCSD) have initiated a collaborative platform to collect genetic and genomic data from a diverse range of human iPSC. At present, this resource already spans over 1000 distinct iPSC lines, with detailed molecular data including genomic, proteomic and phenotypic data. This invaluable database provides a comprehensive source of information for the scientific community to advance iPSC research and drive further discoveries. The team seeks to use this platform to address genetic questions for which iPSC are particularly suited, including rare disease genomics and the genetic regulation of stem cells in general.


Bonder, M.J., Smail, C., [...] Montgomery, SB., Stegle, O. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nat Genet 53, 313–321 (2021). https://doi.org/10.1038/s41588-021-00800-7

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