Extended Data Figure 9: Indel quantification on the intended ‘on’ target and candidate ‘off’ target genomic sites of IL2RG ZFNs.

a, Indel quantification expressed as percentage of the total number of reads for each sample and target. The untreated (UT) sample F is shown in the rightmost column. 0 values underlie undetected events due to low sequencing read coverage (see Supplementary Information). b, Table of P-values obtained comparing the number of indels for each target and its untreated control sample (Fisher’s exact test for contingency data). P-values allowed distinguishing real accumulation of indels (labelled with a green arrow close to the P-value) from background noise (marked with a yellow horizontal bar). Only SCARB1 and SLC31A1 show indels in samples A, B and D at a frequency significantly higher than the untreated sample. c, Indel frequency distribution along the amplified genomic sequences of the positive control IL2RG and the two loci that showed a low but significant off target activity, SCARB1 and SLC31A1. The x axis represents the amplified sequence in base pairs while the y axis shows for each base the percentage of reads that reported indels for each sample after noise subtraction (see Supplementary Information). Note that indels mainly occur in the central region of the amplicon, corresponding to the spacer between the genomic sequences expected to be bound by the ZFNs. d, Representative sequence alignments of retrieved indels in IL2RG (sample A), SCARB1 (from samples A and B) and SLC31A1 (from samples A and D) focusing the analysis on the region bearing identity or homology to the intended ZFN target sequence. For each sequence type the relative frequency of retrieval in the sample is reported as a percentage. As shown in c indels mostly occur in the central spacer region between the 2 ZFN binding sites (underlined).