Figure 1.

Duplications and large deletions identified by CNVPartition mapped onto the genome, for all samples. The number and extent of regions of CNV regions are shown. Duplicated regions (3 or 4 copies) are shown in the dark bars, deleted regions (0 or 1 copy) are shown in the light bars, and copy neutral LOH regions are place on the ideograms of the chromosomes. Where 5 or more samples of the same cell type have aberrations at the same region, the number of samples affected is indicated (e.g. “×5). Regions for hESC samples are shown in red, regions for hiPSC samples are shown in blue, and regions for non-PSC samples are shown in green. Some aneuploidies had been identified prior to hESC derivation, and are indicated as “known from PGS”. Regions where the CNV is present in only a subpopulation of the cells in a sample are denoted “(sub).” The 3 regions of duplication on chromosome 20 that arose in a subpopulation of the cells during differentiation of the WA07P96CMD7 sample are indicated. CNVs that overlap with the common CNVs observed in 450 HapMap samples (Conrad et al., 2010) are indicated by an asterisk. See also Figure S1, and Tables S1, S2, S3, and S4).