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Abstract

The human induced pluripotent stem cells (h-iPSCs) are valuable and promising tools for regenerative medicine and disease modelling because of their capacity to differentiate into multiple types of cells. For the application of female h-iPSCs, an important open question is whether they possess abnormal X chromosome inactivation (XCI) levels which might result in the alteration of gene expression and further downstream consequences. This thesis investigates a population-level set of 273 female h-iPSCs from the Human Induced Pluripotent Stem Cell Initiative (HipSci) and shows a clear line-to-line variety in XCI levels, with four lines (1%) showing complete XCI loss. XCI level is associated with the expression of 2,086 genes (q-value < 0.1), 85% of which are on autosomes. XCI level is inherited in cells differentiated from h-iPSCs. Therefore, the variance of XCI might have an impact on downstream phenotypes, such as immune response. To allow researchers to quality control their h-iPSCs and to maximize the utility of existing h-iPSC banks, methylation-based and expression-based XCI metrics are proposed. These XCI metrics show a clear association between each other and can be used as covariates in further analysis. To explore potential causal factors of XCI loss, variance component analyses are carried out with multiple potential sources, including donor information and technical or biological explanatory variables. These analyses reveal that culture time explains little of the XCI variation, that the expression of XIST is one of the most important explanatory factors, while still not a perfect marker, and that there is a significant donor effect. To identify potential genetic determinants of XCI level, a genome-wide association study (GWAS) and a linear analysis with a subset of expression-related genetic variants are carried out. With cross-check of two XCI metrics, a variant region, as well as a single variant rs3790598, which is associated with the putative RNA helicase MOV10, are found as promising genetic sources of XCI variation.