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BIRS Workshop Lecture Videos

eQTL mapping in iPSC lines Gilad, Yoav


Human induced pluripotent stem cells (iPSCs) provide unprecedented potential to study multiple human cell types from a single individual. This greatly impacts human genomics by allowing researchers to study cell type specific gene regulation and perform experiments on living samples. A necessary step in this process is the generation of a panel of iPSCs large enough to study the effects of genetic variation on gene regulation. To this end, we reprogrammed lyphoblastoid cell lines (LCLs) from 70 individuals into iPSCs. The individuals in this panel have been used extensively in previous studies, making them attractive for further studies on gene regulation. In this study, we characterized regulatory variation, by collecting gene expression data and identifying expression quantitative trait loci (eQTLs). In our hands, the number of eQTLs identified in iPSCs are comparable to those identified in somatic cell types with similar sample sizes. This result was at first surprising, given that we also observed a high degree of homogeneity in gene expression between individuals. Yet, we found that eQTL effect sizes are smaller on average in iPSCs compared to eQTLs in somatic cells. Standard errors of the estimates of effect size are also an order of magnitude lower in iPSCs. I will discuss these results in the context of statistical issues and the biology of eQTLs in iPSCs and across other tissues.

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