Figure 6.

Exome sequencing enables multiple cellular analyses. (A) Box- and scatterplots of the relative mitochondrial genome ratio for all samples. Average read coverage for the mitochondrial genome (chrM) was normalized to the targeted regions of chromosome 1 (chr1). The level of significance is annotated by asterisks or as not significant (NS) (two sided Wilcoxon signed-rank test). Fibroblast (FI) and RiPSC/SiPSC cultures show a higher mitochondrial genome dosage than PBLs (BL = blood samples from individuals in this study; BL-CNT = blood samples from 53 in-house control samples) and compared to NPC cultures. (B) Telomere content of all 16 RiPSC samples from the 4 individuals estimated from off-target telomeric reads by two different algorithms, telomerecat (upper panel) and telomerehunter (lower panel) plotted vs. the passage number. While both plots show a negative correlation of telomere content with higher passage number (telomerecat: Pearson’s r = −0.483, R² = 0.233, p-value = 0.058; telomerehunter: Pearson’s r = −0.251, R² = 0.062, p-value = 0.349) the results are not significant (see also Fig. S5). (C) Comparison of the read coverage profile at the KLF4 gene locus of different materials from individual “82A” (blood = brown, fibroblast = tan, SiPSC = green, RiPSC = blue). The sudden breaks at the exon-intron boundary indicate multiple integrations of a plasmid with a KLF4 transcription factor insert which has no introns (see also Fig. S6). (D) Example of a somatic deletion in the DLG2 gene called from the exome data of the NPC sample (“p82A-R1-002” = dark blue) and absent in the corresponding fibroblast culture (“f82A-X-001” = green). Dots represent target or anti-target coverage bins (y-axis = log2 ratio) and the orange line marks the copy number call by the CNVkit algorithm³² for each segment. Note that the deletion was only called in the NPC and not in the RiPSC (“i82A-R1-002” = light blue) although the deletion had been previously confirmed in both samples by CMA (see also Fig. S6). NS, not significant; “***”, 0.001; “**”, 0.01, “*”, 0.05.