To determine the mutational impact of the in vitro culture, clonal human adult and pluripotent stem cell lines were subjected to a second clonal step after 3 months of culture. These subclones were whole genome sequenced to identify all the mutations that accumulated during the 3 month culture period.

Study ID Alternative Stable ID Type
EGAS00001002955 Other

Study Description

Genetic changes acquired during culture pose a potential risk for the successful application of stem cells. To assess the risk of in vitro expansion on mutation accumulation we have performed whole genome sequencing of clonally expanded human induced pluripotent stem cells (iPS cells) and adult stem cells (ASCs) to identify all mutations that accumulated over a fixed culture period. We find that ASCs acquire more single nucleotide variants (SNVs) and indels per population doubling than the iPS cells. When compared with ASCs, iPS cells are more vulnerable to mutations in genes and promoters. Mutational analysis revealed a clear in vitro induced mutational signature that is irrespective of stem cell type. This in vitro signature is characterized by C to G transversions that are probably caused by oxidative stress. Additionally, we observed stem cell specific mutational signatures and differences in transcriptional strand bias, indicating differential activity of DNA repair mechanisms between stem cell types in culture. In conclusion, in vitro culture induces mutation accumulation in ... (Show More)

Study Datasets 1 dataset.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
Clonally expanded human pluripotent and adult (liver + intestine) stem cell clones were subjected to whole genome sequencing to determine the mutational impact of in vitro culture
HiSeq X Ten,NextSeq 500 11

Who archives the data?