Fig. 2

De novo mutations and structural variations caused by the reprogramming process. a Summary of the number of somatic mutations. SVs were detected by an aCGH analysis. Candidate SNVs were identified by whole genome analysis and confirmed by a direct nucleotide sequence analysis. Only the nonsynonymous variants in protein coding regions outside the immunoglobulin or T-cell receptor gene regions are shown. b A recurrent structural variation in the short arm of chromosome 19 in healthy donor KA detected by CGH analysis is shown. The deletion was detected in all the LiPSC clones examined, but was not detected in the LCLs. c The coverage data for each sample (LKA10, LKA29 and LKA36), as shown by the Integrative Genomic Viewer [44]. In the LiPSC clones, decreased coverages were observed and corresponded to the deletions detected by the CGH analysis. d The breakpoint sequences were identified in the short reads obtained from the LCLs. Identical breakpoint sequences were also identified in the short reads obtained from LKA10, LKA29 and LKA36. There is a 2 bp microhomology at the breakpoint. e The short read sequences indicating the breakpoint were identified in only 6.3 % of the total reads spanning this region in LCLs. Short read sequences indicating the same breakpoint were identified in all the LiPSC clones. These short read sequences were observed in 26, 43 and 55 % of the total reads obtained from LKA10, LKA29 and LKA36 clones, respectively