Copy number analysis by SNP array. DNA from hESC was amplified by PCR and hybridized to Sentrix BeadArrays. Paired lines (low versus high passage or karyotypic normal versus variant sublines) were compared at 101,000 loci. The 25-SNP moving average of the difference in allele intensity ratios is shown above the axis (red). (A) hESC line H7 compared at 41 and 63 passages. (B) hESC line H9 compared at 33 and 78 passages. (C) hESC line SA02.5 compared with the karyotypic variant SA02 (+13). (D) hESC line BG01 compared with the karyotypic variant subline BG01V (+12, +17, +X).