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Project
The identification of copy number variations that impede differentiation of human pluripotent stem cells. (FWOKN300)
Recently, the existence of non-clonal low-grade mosaicism of copy number variations (CNVs) in human pluripotent stem cells (hPSC) was demonstrated. This means that a significant percentage of the cells within a culture display a chromosomal abnormality, but that each individual abnormality exists only at very low levels, too low to be identified if bulk DNA from the whole culture is analyzed.
If a CNV confers a culture advantage to the cells, cells carrying this mutation often take over the culture. Several of these recurrent chromosomal abnormalities have already been described. At the differentiated level, though, few data are available. In this project, we want to investigate whether after differentiation of hPSC the same mosaicism of CNVs is detected in the differentiated populations or whether there is a bias towards specific CNVs for cells that differentiated correctly or failed differentiation (rSC) at different stages during the protocol. For this, we will use hepatic differentiation as a paradigm. We will isolate correctly differentiated hepatocyte-like cells and cells that remained undifferentiated and will compare the genetic content of single cells of these two populations and the initial undifferentiated cells using high-throughput single cell shallow sequencing. This will allow us to evaluate whether rSC the result of a specific subset of CNVs found in hPSC and allow us to identify a panel of CNVs which may confer a safety risk to cells upon transplantation.
If a CNV confers a culture advantage to the cells, cells carrying this mutation often take over the culture. Several of these recurrent chromosomal abnormalities have already been described. At the differentiated level, though, few data are available. In this project, we want to investigate whether after differentiation of hPSC the same mosaicism of CNVs is detected in the differentiated populations or whether there is a bias towards specific CNVs for cells that differentiated correctly or failed differentiation (rSC) at different stages during the protocol. For this, we will use hepatic differentiation as a paradigm. We will isolate correctly differentiated hepatocyte-like cells and cells that remained undifferentiated and will compare the genetic content of single cells of these two populations and the initial undifferentiated cells using high-throughput single cell shallow sequencing. This will allow us to evaluate whether rSC the result of a specific subset of CNVs found in hPSC and allow us to identify a panel of CNVs which may confer a safety risk to cells upon transplantation.
Date:1 Jan 2018 → 31 Dec 2018
Keywords:genetics, reproduction, genome
Disciplines:Clinical genetics and molecular diagnostics