Table 1.
Long-term eGSH distribution in SCID-X1 trial samples
| eGSHs located within ATAC-seq peaks or within 5 kb of ATAC-seq peak boundary∗ | ||||||
|---|---|---|---|---|---|---|
| Condition | T0 (165) |
Tl (1430) |
Fold change | P value | ||
| No. | % | No. | % | |||
| Activated | 14 | 8.50 | 423 | 29.60 | 3.48 | 5.14E-10 |
| Resting | 36 | 21.80 | 733 | 51.30 | 2.35 | 2.54E-13 |
| eGSHs with ATAC-seq peaks both upstream and downstream within specified distances from integration site† | ||||||
|---|---|---|---|---|---|---|
| Condition_distance | T0 (165) |
Tl (1430) |
Fold change | P value | ||
| No. | % | No. | % | |||
| ACT_50 kb | 16 | 9.7 | 244 | 17.1 | 1.76 | 1.41E-02 |
| ACT_100 kb | 26 | 15.8 | 452 | 31.6 | 2.01 | 1.39E-05 |
| ACT_200 kb | 32 | 19.4 | 522 | 36.5 | 1.88 | 6.30E-06 |
| REST_50 kb | 29 | 17.6 | 664 | 46.4 | 2.64 | 1.69E-13 |
| REST_100 kb | 41 | 24.8 | 752 | 52.6 | 2.12 | 6.99E-12 |
| REST_200kb | 60 | 36.4 | 843 | 59.0 | 1.62 | 4.81E-08 |
| eGSHs with ATAC-seq peaks only upstream within specified distances from integration site‡ | ||||||
|---|---|---|---|---|---|---|
| Condition_distance | T0 (165) |
Tl (1430) |
Fold change | P value | ||
| No. | % | No. | % | |||
| ACT_50 kb | 12 | 7.3 | 94 | 6.57 | 0.90 | 7.41E-01 |
| ACT_100 kb | 16 | 9.7 | 116 | 8.11 | 0.84 | 4.57E-01 |
| ACT_200 kb | 26 | 15.8 | 176 | 12.31 | 0.78 | 2.16E-01 |
| REST_50 kb | 13 | 7.9 | 91 | 6.36 | 0.81 | 4.09E-01 |
| REST_100 kb | 18 | 10.9 | 143 | 10.00 | 0.92 | 6.83E-01 |
| REST_200 kb | 25 | 15.2 | 188 | 13.15 | 0.87 | 4.69E-01 |
| eGSHs with ATAC-seq peaks only downstream within specified distances from integration site§ | ||||||
|---|---|---|---|---|---|---|
| Condition_distance | T0 (165) |
Tl (1430) |
Fold change | P value | ||
| No. | % | No. | % | |||
| ACT_50 kb | 8 | 4.85 | 241 | 16.85 | 3.48 | 1.23E-05 |
| ACT_100 kb | 12 | 7.27 | 74 | 5.17 | 0.71 | 2.72E-01 |
| ACT_200 kb | 20 | 12.12 | 148 | 10.35 | 0.85 | 5.02E-01 |
| REST_50 kb | 23 | 13.94 | 130 | 9.09 | 0.65 | 5.07E-02 |
| REST_100 kb | 23 | 13.94 | 73 | 5.10 | 0.37 | 7.33E-05 |
| REST_200 kb | 21 | 12.73 | 124 | 8.67 | 0.68 | 8.74E-02 |
Table shows the number of eGSH insertion sites that have ATAC-seq peaks within the distances and direction specified in the table headers. Upstream and downstream are determined in relation to the direction of the integrated transgene. A 2-tailed Fisher exact test is used to compute the P value for the enrichment between time zero (before infusion, T0) and later (Tl) time points.
ACT, ATAC-seq peaks in the activated T-cell data set; REST, ATAC-seq peaks in the resting T-cell data set within the specified distances.
Number of eGSH integration sites that are located in an ATAC-seq peak or within 5 kb from an ATAC-seq peak boundary.
Number of eGSH integration sites with at least 1 ATAC-seq peak upstream and at least 1 ATAC-seq peak downstream considering a distance of 50 kb, 100 kb, or 200 kb from integration site.
Number of eGSH integration sites with at least 1 ATAC-seq peak upstream and no peaks downstream direction considering a distance of 50 kb, 100 kb, or 200 kb from integration site.
Number of eGSH integration sites with at least 1 ATAC-seq peak downstream direction and no peaks upstream direction considering a distance of 50 kb, 100 kb, or 200 kb from integration site.