Gene expression comparison between human embryonic stem cell lines with a normal karyotype and after acquiring a duplication of 20q11.21

Since the introduction of high-resolution molecular cytogenetic methods for the screening for chromosomal abnormalities in human embryonic stem cells (hESC), numerous laboratories worldwide have reported the gain of 20q11.21 as a recurrent mutation. Recently, in a large joint study, the International Stem Cell Initiative (ISCI) screened 125 hESC lines worldwide and found this aberration in over 20% of the lines. In our laboratory, we found an increased copy number of 20q11.21 in four hESC lines, VUB01, VUB02, VUB03 and VUB07. We first carried out Affymetrix HG-U133-Plus2 gene-expression microarray analysis of pairs of the mutant and wild type sublines. We identified a small group of very significantly deregulated genes, but none of them were located in the region of duplication. Validation of these results by qRT-PCR revealed that CHCHD2 and TRPC6 were most consistently deregulated. Gene expression was compared between four karyotypically normal hESC lines: VUB01, VUB02, VUB03 and VUB07 and their subline containing a duplication of 20q11.21.