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 
ConditionT0 (165)Tl (1430)Fold changeP 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 located within ATAC-seq peaks or within 5 kb of ATAC-seq peak boundary 
ConditionT0 (165)Tl (1430)Fold changeP 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_distanceT0 (165)Tl (1430)Fold changeP 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 both upstream and downstream within specified distances from integration site 
Condition_distanceT0 (165)Tl (1430)Fold changeP 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_distanceT0 (165)Tl (1430)Fold changeP 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 upstream within specified distances from integration site 
Condition_distanceT0 (165)Tl (1430)Fold changeP 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_distanceT0 (165)Tl (1430)Fold changeP value
No.%No.%
ACT_50 kb 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 
eGSHs with ATAC-seq peaks only downstream within specified distances from integration site§ 
Condition_distanceT0 (165)Tl (1430)Fold changeP value
No.%No.%
ACT_50 kb 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.

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