TABLE 1.

Summary of VIS sequence analysis

Sample and expt.Time (mos.)Amt of genomic DNA (μg)JunctiondNo. of sequencesNo. of sequence counts/per unique VISNo. of unique VIS ≤450 bp
TotalaUncertainbVIScUnique VISMaxfMedianAvGSD
In vivo repopulating PBC (95E132)
    Expt. 155.3L3,8735433,332192346617.3541.35109
R2,6495242,124174179512.2819.6399
502.8L4,1653583,814187300520.4041.3485
R3,8024613,341147367722.7347.6576
882.5L3,7472113,537192222818.4227.7784
R3,1571043,203196322816.3431.9777
10810.7L4,6922284,475225371519.8943.00125
R6,7563656,241258674524.1963.27106
    Expt. 255.3L3,6696483,025178183716.9928.44110
R2,8281,1921,63617017959.6217.2989
502.8L3,1931473,049121287725.2041.9967
R3,0034972,506224214311.1927.13112
882.5L3,9362163,725134265827.8046.7971
R2,5582932,265178258412.7227.9490
10810.7L3,3722203,161233169413.5724.60110
R5,9471,1124,8353065233.515.8041.52124
TotalL30,6472,57128,118559216
R30,7004,54826,151615205
Combined (L-R match)e61,3477,11954,2691,174 (212)422 (24)
In vitro acutely infected CD34+ cells
    Expt. 110L2,6701,2881,3308612211.541.39739
R1,541995493370711.330.84299
    Expt. 210L2,4781,2521,1657521511.551.39642
R5,4344,1751,1961,039811.150.55871
TotalL5,1482,5402,4951,5911,362
R6,9755,1701,6891,4051,167
Combined (L-R match)e12,1237,7104,1842,996 (3)2,529 (2)
  • a Total number of sequences that passed filtering after pyrosequencing.

  • b Uncertain sequences include low-quality sequences and vector sequences.

  • c Authenticated VIS sequences (vector DNA joined to cellular DNA).

  • d Analyzed vector-cellular DNA junctions L, left; R, right.

  • e Number of VIS pairs from the left and the right junctions originating from the same vector integrant. The number of matches is shown in parentheses.

  • f Max, maximum.