Table 3.

Analysis of NHEJ by sequencing of the remaining putative wild-type AAVS1 locus

Reference sequence	TGTCCCCTCCACCCCACAGTGGGGCCACTAGGGACAGGATTGGTGACAGA
iXC9-APC-gp91 c9	TGTCCCCTCCACCCCACAGTGGGGCCACTAGGGACAGGATTGGTGACAGA
iXC9-APC-gp91 c21	TGTCCCCTCCACCCCACAGTGGGGCCACTAGGGACAGGATTGGTGACAGA
iXC9-APC-gp91 c23	TGTCCCCTCCACCCCACAGTGGGGCCA––––––––AGGATTGGTGACAGA
iXC9-APC-gp91 c25	TGTCCCCTCCACCCCACAGTGGGGccagCCACTAGGGACAGGATTGGTGACAGA
iXC9-APC-gp91 c26	TGTCCCCTCCACCCCACAGTGGGGCCA–––-GGACAGGATTGGTGACAGA
iXC1-APC-gp91 c1	TGTCCCCTCCACCCCACAGTGGGGCCACTAGGGACAGGATTGGTGACAGA
iXC1-APC-gp91 c3	TGTCCCCTCCACCCCACAGTGGGGCCACTAGGGACAGGATTGGTGACAGA
iXC1-APC-gp91 c5	TGTCCCCTCCACCCCACAGTGGGGcaCCACTAGGGACAGGATTGGTGACAGA

Shown are the results from sequencing the AASV1 ZFN target site in 5 iXC9-APC-gp91 clones and 3 iXC1-APC-gp91 clones that contained one allele of targeted integration and no random integrations. The putative wild-type allele was PCR-amplified (as described in “Sequencing detection of NHEJ mutations”) and products were sequenced to look for NHEJ-mediated mutations. The upper case letters indicate matches to reference AAVS1 sequence, where the bolded underlined upper case letters indicate target sequences to which the ZFN pair was designed to bind. Bolded underlined lower case letters indicate base pair inserts, and bolded dashed lines indicate base pair deletions relative to the reference. Four of the 8 clones fully match the reference sequence with no inserts or deletions.