FIG. 5.
Patterns of palindrome (Pal.) center retention/deletion associated with rAAV integration. (A) Definition of center-deleted and center-retained rAAV integration. (B) Percentage of center-deleted rAAV integrations of total rAAV integrations is plotted as a function of palindrome arm length and compared to that for random integration. To increase the power of analysis, palindromes with different arm lengths are combined in the following manner: 9 to 10 bp (shown as 10 in the figure), 11 to 14 bp (14), 15 to 18 bp (18), 19 to 22 bp (22), 23 to 26 bp (26), 27 to 28 bp (28), 29 to 30 bp (30), and 31 bp or more (≥31). We compared the observed frequency to that of 20 independently generated random integration data sets (see Materials and Methods) by the χ2 test or Fisher's exact test. Solid triangles indicate statistical significance (P < 0.05; Fisher's exact test) for all 20 random data set comparisons. Three representative random integration data sets are included. (C and D) Positional relationship between center-deleted or center-retained rAAV integrations and the palindrome symmetry center. rAAV integration sites are shown as histograms, giving their locations in 50-bp increments across a 1-kb region centered on the palindrome symmetry center. An exception is the 51-bp center window from positions −50 to 0, which includes the palindrome symmetry center. Center-deleted or center-retained rAAV integrations are displayed in the left (clear background) or right (gray background) portion of the 1-kb window as labeled. (C) rAAV-labeled DNA palindromes with an arm length of ≥20 bp (134 palindromes in all). (D) rAAV-labeled DNA palindromes with an arm length between 6 and 19 bp (235 in all).