The challenges of conducting eQTL studies are also widely appreciated. The eQTLs identified in array-based transcriptome studies in LCLs are likely to be a limited subset of the eQTLs that will ultimately be identified using more sensitive techniques in comprehensive collections of human tissues. Moreover, a variety of studies have highlighted the potential sensitivity of eQTL studies to cell and tissue subtypes [15],[19],[20]. Although several studies have suggested that eQTLs will be largely tissue specific [21],[22], others note that substantial numbers of eQTLs are shared across tissues [15],[23]. Similarly, some have found that LCLs are prone to such high levels of non-genetic variability (growth parameters, EBV levels, ATP levels, etc.) that they might be considered unreliable for genomic studies [24], while others highlight the reproducibility of results of transcriptome studies [25],[26] and find that LCLs show little variability as a consequence of non-genetic factors [27].
