Affymetrix SNP 6.0 array data for human embryonic stem cell lines

Pluripotent human embryonic stem cells are studied for potential applications in regenerative cell replacement therapies because of their untransformed nature and unique capacity to self-renew and differentiate. However it is known that adaptation of hESCs occurs on prolonged culture and may be associated with the acquisition of chromosome abnormalities. We report a high resolution DNA SNP 6.0 array analysis showing copy number variation in 17 different hESC lines maintained in different laboratories. Several of the changes were culture induced and changed the expression levels of affected genes. Loss of heterozygosity (LOH) of chromosome 16q was detected in one line, in addition to several smaller LOH regions. Importantly, hESCs were found to contain several CNVs less than 3 Mb in size which is below the detection limit of conventional karyotyping. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 29 hESC samples of various passages and laboratory origin. 40 reference HapMap samples from Affymetrix were hybridized at the same time to built a reference genome used in the analysis.