Distribution and relative abundance of integration sites isolated from several cell types 6 and 12 months after therapy
Time point and cell type . | Total reads . | Inferred cells . | Unique sites . | S.chao1 . | Gini . | Shannon . | UC50 . |
---|---|---|---|---|---|---|---|
6 mo | |||||||
B cells | 1 036 782 | 4639 | 3891 | 19855 | 0.1204 | 8.2045 | 1647 |
Monocytes | 222 125 | 329 | 248 | 893 | 0.1950 | 5.4176 | 86 |
Neutrophils | 803 235 | 2018 | 1522 | 6981 | 0.1866 | 7.2162 | 552 |
NK cells | 1 111 841 | 3000 | 2128 | 7757 | 0.1751 | 7.5657 | 795 |
PBMC | 684 175 | 2115 | 1386 | 4844 | 0.2668 | 7.0254 | 381 |
T cells | 1 038 680 | 5685 | 3089 | 10 815 | 0.3937 | 7.4591 | 539 |
12 mo | |||||||
B cells | 925 356 | 2197 | 1745 | 7702 | 0.1438 | 7.3907 | 701 |
Monocytes | 347 061 | 351 | 242 | 1970 | 0.2517 | 5.3341 | 69 |
Neutrophils | 558 321 | 729 | 492 | 1866 | 0.2496 | 6.0383 | 139 |
NK cells | 507 007 | 697 | 469 | 1865 | 0.2413 | 6.0123 | 135 |
PBMC | 463 071 | 2076 | 1744 | 7513 | 0.1387 | 7.3578 | 720 |
T cells | 981 471 | 3142 | 2089 | 9696 | 0.2748 | 7.3678 | 574 |
Time point and cell type . | Total reads . | Inferred cells . | Unique sites . | S.chao1 . | Gini . | Shannon . | UC50 . |
---|---|---|---|---|---|---|---|
6 mo | |||||||
B cells | 1 036 782 | 4639 | 3891 | 19855 | 0.1204 | 8.2045 | 1647 |
Monocytes | 222 125 | 329 | 248 | 893 | 0.1950 | 5.4176 | 86 |
Neutrophils | 803 235 | 2018 | 1522 | 6981 | 0.1866 | 7.2162 | 552 |
NK cells | 1 111 841 | 3000 | 2128 | 7757 | 0.1751 | 7.5657 | 795 |
PBMC | 684 175 | 2115 | 1386 | 4844 | 0.2668 | 7.0254 | 381 |
T cells | 1 038 680 | 5685 | 3089 | 10 815 | 0.3937 | 7.4591 | 539 |
12 mo | |||||||
B cells | 925 356 | 2197 | 1745 | 7702 | 0.1438 | 7.3907 | 701 |
Monocytes | 347 061 | 351 | 242 | 1970 | 0.2517 | 5.3341 | 69 |
Neutrophils | 558 321 | 729 | 492 | 1866 | 0.2496 | 6.0383 | 139 |
NK cells | 507 007 | 697 | 469 | 1865 | 0.2413 | 6.0123 | 135 |
PBMC | 463 071 | 2076 | 1744 | 7513 | 0.1387 | 7.3578 | 720 |
T cells | 981 471 | 3142 | 2089 | 9696 | 0.2748 | 7.3678 | 574 |
The table summarizes the sample metadata and sequencing data and reports summary statistics for each sample. To summarize the data, the total number of sequence reads (total reads), the inferred number of cells with integrated vector identified (inferred cells), and the number of unique integration sites identified (unique sites) are shown. Statistics to summarize population structure are also presented. The Chao1 analysis (S.chao1) is an estimate of minimum population size.23 The Gini coefficient is a measure to represent distribution. Here, a value of 0 indicates even distribution of integration sites, while values increasing toward 1 demonstrate increasing inequality of integration site abundance within the population. The Shannon index summarizes diversity by accounting for both abundance and evenness among the integration sites in the cell population. Lastly, the UC50, a new metric, indicates the number of unique clones contributing the top 50% of the sample’s total abundance.16