Comparative genomic hybridization and karyotyping of human embryonic stem cells reveals the occurrence of an isodicentric X chromosome after long-term cultivation

Human embryonic stem (hES) cells are important research tools in studies of the physiology of early tissue differentiation. In addition, prospects are high regarding the use of these cells for successful cell transplantation. However, one concern has been that cultivation of these cells over many passages might induce chromosomal changes. It is thus important to investigate these cell lines, and check that a normal chromosomal content is retained even during long-term in vitro culture. Comparative genomic hybridization (CGH) was used to analyse three hES cell lines derived in our laboratory and cultured continuously for 30-42 weeks, comprising 35-39 cell passages. CGH could be successfully performed in 48 out of a total of 50 isolated single cells (96%). All three lines (HS181, HS235 and HS237) were shown to have a normal chromosomal content when analysed by both single cell CGH and by karyotyping up to passages 39, 39 and 35 respectively. No aneuploidies or larger deletions or amplifications were detected, and they were female (46,XX). However, HS237 was reanalysed at passage 61, and at that point an aberrant X chromosome was detected by karyotyping. The aberration was confirmed and characterized by single cell CGH and fluorescence in situ hybridization analysis, 46,X,idic(X)(q21). Thus, chromosomal aberrations may occur over time in stem cell lines, and continuous analysis of these cells during cultivation is crucial. Single cell CGH is a method that can be used for continuous analysis of the hES cell lines during cultivation, in order to detect chromosome imbalance.