Table 2.
Analysis of lenti, gamma, and foamy RIS by MGS-PCR with MiSeq
| A. Triplicate data for lentiviral vector samples | ||||||
|---|---|---|---|---|---|---|
| Lenti viral vector | SET A | SET B | Set C | |||
| Total reads | 3,636,088 | 3,163,330 | 1,198,876 | |||
| Alignment filters | N | % | N | % | N | % |
| No LTR-Chr junction | 1,906,919 | 52.44 | 1,594,545 | 50.40 | 618,374 | 51.57 |
| Query less than 30 bp | 696,270 | 19.14 | 596,832 | 18.86 | 223,263 | 18.62 |
| No BLAT alignment | 653,463 | 17.97 | 757,407 | 18.73 | 201,551 | 16.81 |
| Repeat filter | 28,350 | 0.78 | 28,260 | 0.89 | 9,322 | 0.77 |
| Low identity alignments | 9,401 | 0.25 | 10,075 | 0.31 | 1,136 | 0.09 |
| Candidate RIS | 341,685 | 9.39 | 340,845 | 10.77 | 145,230 | 12.11 |
| Unique RIS filters | ||||||
| Total RIS | 341,685 | 340,845 | 145,230 | |||
| Unique RIS | 318 | 0.093 | 290 | 0.085 | 134 | 0.092 |
| B. Triplicate data for gammaretroviral vector samples | ||||||
|---|---|---|---|---|---|---|
| Gammaretroviral vector | SET A | SET B | SET C | |||
| Total reads | 2,705,335 | 3,841,112 | 3,558,352 | |||
| Alignment filters | N | % | N | % | N | % |
| No LTR-Chr junction | 1,443,168 | 53.34 | 1,982,913 | 51.62 | 1,853,803 | 52 |
| Query less than 30 bp | 334,576 | 12.37 | 464,337 | 12.08 | 429,431 | 12 |
| No BLAT alignment | 57,900 | 2.14 | 103,277 | 2.68 | 167,423 | 5 |
| Repeat filter | 46,336 | 0.88 | 794,665 | 20.68 | 668,024 | 19 |
| Low identity alignments | 11,722 | 0.43 | 24,885 | 0.64 | 28,183 | 1 |
| Candidate RIS | 287,545 | 10.63 | 472,764 | 12.30 | 411,488 | 12 |
| Unique RIS filters | ||||||
| Total RIS | 287,545 | 472,764 | 411,488 | |||
| Unique RIS | 337 | 0.117 | 483 | 0.10 | 667 | 0 |
| C. Triplicate data for foamy viral vector samples | ||||||
|---|---|---|---|---|---|---|
| Foamy viral vector | SET A | SET B | SET C | |||
| Total reads | 4,069,518 | 5,250,488 | 4,263,921 | |||
| Alignment filters | N | % | N | % | N | % |
| No LTR-Chr junction | 2,431,679 | 59.75 | 3,142,864 | 59.86 | 2,602,694 | 61.04 |
| Query less than 30 bp | 559,789 | 13.75 | 797,934 | 15.20 | 708,551 | 16.62 |
| No BLAT alignment | 701,473 | 17.23 | 829,096 | 15.80 | 640,730 | 15.03 |
| Repeat filter | 37,702 | 0.92 | 46,336 | 0.90 | 29,864 | 0.70 |
| Low identity alignments | 10,181 | 0.25 | 13,682 | 0.26 | 11589 | 0.27 |
| Candidate RIS | 328,694 | 8.07 | 420,576 | 8.01 | 270,493 | 6.34 |
| Unique RIS filters | ||||||
| Total RIS | 328,694 | 420,576 | 270,493 | |||
| Unique RIS | 10,616 | 3.23 | 11,257 | 2.677 | 13,119 | 4.85 |
Three independent shears were performed for each sample, and sequenced on three MiSeq paired-end runs. Merged paired-end sequences were analyzed. The table reports the total number of retroviral integration sites (RIS), the number and percentage of those potential RIS as they pass through alignment and inclusion filters, and the total number of aligned RIS and the total number of unique RIS.