Extreme clonality in lymphoblastoid cell lines with implications for allele specific expression analyses

Abstract

Lymphoblastoid cell lines (LCL) are being actively and extensively used to examine the expression of specific genes and genome-wide expression profiles, including allele specific expression assays. However, it has recently been shown that approximately 10% of human genes exhibit random patterns of monoallelic expression within single clones of LCLs. Consequently allelic imbalance studies could be significantly compromised if bulk populations of donor cells are clonal, or near clonal. Here, using X chromosome inactivation as a readout, we confirm and quantify widespread near monoclonality in two independent sets of cell lines. Consequently, we recommend where possible the use of bulk, non cell line, ex vivo cells for allele specific expression assays.

Figure 1. Distribution of XCI in the British 1958 Birth Cohort samples, JDRF/WT T1D cases collection (both with DNA extracted from transformed cells lines) and the control Turkish population (DNA extracted from peripheral blood).

Figure 2. Likelihood curve for the fraction of cells f that underwent a bottleneck.

We considered three values for the standard error in the measurement of the skew in X inactivation (standard deviation of 0.03, 0.05 and 0.1). The horizontal line indicates the 95% confidence interval.

Figure 3. Confidence intervals for the probability of XCI>90% as a function of the time required for first growth (ie. between transformation and until the culture volume reaches 100 ml).

Figure 4. Simulation study comparing the XCI between our best fitting scenario and both sets of cell line (1958 British Birth Cohort and T1D samples).