Per-patient summary of malignant clones in B-ALL samples and sample sorts
| Patient ID . | No. of index clones . | Total frequency of index clones, % . | Individual index clone frequencies, % . | Total no. (%) evolved clones* . | Total frequency of index clones in sort for normal B cells, % . | Total frequency of index clone in gate for malignant cells, % . |
|---|---|---|---|---|---|---|
| 1 | 0 | No index | No index | No index | No index | No index |
| 2 | 0 | No index | No index | No index | No index | No index |
| 3 | 1 | 90.3 | 90† | 14 (0.3) | 0.5 | 98.0 |
| 4 | 0 | No index | No index | No index | No index‡ | No index‡ |
| 5 | 3 | 95.7 | 76†, 10†, 10† | 668 (33.3) | 3.3 | 98.3 |
| 6 | 5 | 80.8 | 33†, 18†, 11†, 9†, 9† | 883 (61.7) | 0.7 | 90.3 |
| 7 | 1 | 88.7 | 89† | 25 (3.4) | Not sorted | Not sorted |
| 8 | 2 | 96 | 79†, 17† | 301 (62.2) | Not sorted | Not sorted |
| 9 | 2 | 98.1 | 63†, 35 | 42 (8.8) | 7.3 | 98.8 |
| 10 | 3 | 99.3 | 47†, 31†, 22† | 18 (6.8) | 0.4 | 99.8 |
| 11 | 0 | No index | No index | No index | No index | No index |
| 12 | 2 | 99.5 | 53†, 46† | 12 (60.0) | NA | 99.5 |
| 13 | 0 | No index | No index | No index | No index | No index |
| 14 | 1 | 92.8 | 93† | 22 (0.3) | 0.2 | 98.0 |
| 15 | 5 | 78.4 | 23†, 21†, 17†, 13†, 5† | 4024 (85.5) | 14 | 79.6 |
| 16 | 2 | 98.4 | 63†, 35† | 4 (0.8) | 6.7 | 99.3 |
| 17 | 3 | 98.8 | 39†, 36, 24† | 13 (2.4) | 0 | 99.0 |
| 18 | 3 | 72 | 59†, 8†, 6† | 368 (43.0) | Not sorted | Not sorted |
| 19 | 1 | 75.2 | 75 | 0 (0.0) | Not sorted | Not sorted |
| 20 | 3 | 89 | 50†, 30†, 9† | 460 (29.9) | Not sorted | Not sorted |
| 21 | 1 | 97.3 | 97 | 0 (0.0) | 0.2 | 96.4 |
| 22 | 1 | 96.4 | 96† | 35 (18.1) | 41.5 | 96.2 |
| 23 | 3 | 64.9 | 30†, 21†, 13† | 2645 (34.6) | 0.03 | 57.2 |
| 24 | 0 | No index | No index | No index | No index | No index |
| 25 | 1 | 99.9 | 100† | 7 (12.7) | 8.4 | 99.9 |
| 26 | 2 | 97.3 | 59†, 38† | 196 (8.1) | 1.5 | 99.6 |
| 27 | 2 | 97.1 | 58, 39† | 22 (1.3) | 0 | 96.6 |
| 28 | 3 | 98.6 | 38†, 36, 25† | 9 (4.9) | NA | 98.5 |
| 29 | 3 | 71.6 | 51, 12†, 8† | 17 (0.2) | 0.5 | 79.7 |
| 30 | 1 | 93.1 | 93† | 18 (2.9) | 5 | 94.5 |
| 31 | 2 | 76.9 | 39, 38† | 4 (0.4) | 0 | NA§ |
| 32 | 2 | 99 | 50†, 49† | 11 (1.4) | 0.3 | 99.9 |
| 33 | 1 | 66.6 | 67† | 3 (0.3) | 0.4 | 99.4 |
| 34 | 2 | 99.5 | 85, 14 | 0 (0.0) | 7.5 | 99.9 |
| 35 | 2 | 63.4 | 49†, 15† | 1149 (27.5) | 1 | 65.8 |
| 36 | 1 | 22.4 | 22 | 0 (0.0) | 0 | 96.2 |
| 37 | 0 | No index | No index | No index | No index | No index |
| 38 | 2 | 97 | 66†, 32 | 154 (13.4) | 4.7 | 97.7 |
| 39 | 1 | 99 | 99 | 0 (0.0) | NA | 99.7 |
| 40 | 1 | 84.9 | 85† | 24 (0.3) | 1.8 | 89.4 |
| 41 | 0 | No index | No index | No index | No index | No index |
| 42 | 2 | 99.1 | 56†, 43† | 5 (4.2) | 2.1 | 99.3 |
| 43 | 2 | 98.9 | 58†, 41 | 2 (8.7) | NA | 98.6 |
| 44 | 2 | 99.1 | 74, 25† | 3 (0.8) | 1.4 | 99.9 |
| 45 | 2 | 79.9 | 72†, 8 | 5 (0.3) | 0.6 | 73.7 |
| 46 | 1 | 94.6 | 95 | 0 (0.0) | 2.1 | 97.8 |
| 47 | 1 | 98.5 | 99† | 60 (5.1) | 1.5 | 99.7 |
| 48 | 4 | 99.8 | 29, 24†, 24†, 23† | 30 (36.1) | 3.2 | 99.9 |
| 49 | 1 | 99 | 99† | 4 (0.6) | 0.7 | 99.5 |
| 50 | 2 | 81.5 | 75†, 7† | 2724 (41.7) | 0.9 | 86.4 |
| 51 | 1 | 5.8 | 6† | 4 (0.5) | 0 | 39.6 |
| Patient ID . | No. of index clones . | Total frequency of index clones, % . | Individual index clone frequencies, % . | Total no. (%) evolved clones* . | Total frequency of index clones in sort for normal B cells, % . | Total frequency of index clone in gate for malignant cells, % . |
|---|---|---|---|---|---|---|
| 1 | 0 | No index | No index | No index | No index | No index |
| 2 | 0 | No index | No index | No index | No index | No index |
| 3 | 1 | 90.3 | 90† | 14 (0.3) | 0.5 | 98.0 |
| 4 | 0 | No index | No index | No index | No index‡ | No index‡ |
| 5 | 3 | 95.7 | 76†, 10†, 10† | 668 (33.3) | 3.3 | 98.3 |
| 6 | 5 | 80.8 | 33†, 18†, 11†, 9†, 9† | 883 (61.7) | 0.7 | 90.3 |
| 7 | 1 | 88.7 | 89† | 25 (3.4) | Not sorted | Not sorted |
| 8 | 2 | 96 | 79†, 17† | 301 (62.2) | Not sorted | Not sorted |
| 9 | 2 | 98.1 | 63†, 35 | 42 (8.8) | 7.3 | 98.8 |
| 10 | 3 | 99.3 | 47†, 31†, 22† | 18 (6.8) | 0.4 | 99.8 |
| 11 | 0 | No index | No index | No index | No index | No index |
| 12 | 2 | 99.5 | 53†, 46† | 12 (60.0) | NA | 99.5 |
| 13 | 0 | No index | No index | No index | No index | No index |
| 14 | 1 | 92.8 | 93† | 22 (0.3) | 0.2 | 98.0 |
| 15 | 5 | 78.4 | 23†, 21†, 17†, 13†, 5† | 4024 (85.5) | 14 | 79.6 |
| 16 | 2 | 98.4 | 63†, 35† | 4 (0.8) | 6.7 | 99.3 |
| 17 | 3 | 98.8 | 39†, 36, 24† | 13 (2.4) | 0 | 99.0 |
| 18 | 3 | 72 | 59†, 8†, 6† | 368 (43.0) | Not sorted | Not sorted |
| 19 | 1 | 75.2 | 75 | 0 (0.0) | Not sorted | Not sorted |
| 20 | 3 | 89 | 50†, 30†, 9† | 460 (29.9) | Not sorted | Not sorted |
| 21 | 1 | 97.3 | 97 | 0 (0.0) | 0.2 | 96.4 |
| 22 | 1 | 96.4 | 96† | 35 (18.1) | 41.5 | 96.2 |
| 23 | 3 | 64.9 | 30†, 21†, 13† | 2645 (34.6) | 0.03 | 57.2 |
| 24 | 0 | No index | No index | No index | No index | No index |
| 25 | 1 | 99.9 | 100† | 7 (12.7) | 8.4 | 99.9 |
| 26 | 2 | 97.3 | 59†, 38† | 196 (8.1) | 1.5 | 99.6 |
| 27 | 2 | 97.1 | 58, 39† | 22 (1.3) | 0 | 96.6 |
| 28 | 3 | 98.6 | 38†, 36, 25† | 9 (4.9) | NA | 98.5 |
| 29 | 3 | 71.6 | 51, 12†, 8† | 17 (0.2) | 0.5 | 79.7 |
| 30 | 1 | 93.1 | 93† | 18 (2.9) | 5 | 94.5 |
| 31 | 2 | 76.9 | 39, 38† | 4 (0.4) | 0 | NA§ |
| 32 | 2 | 99 | 50†, 49† | 11 (1.4) | 0.3 | 99.9 |
| 33 | 1 | 66.6 | 67† | 3 (0.3) | 0.4 | 99.4 |
| 34 | 2 | 99.5 | 85, 14 | 0 (0.0) | 7.5 | 99.9 |
| 35 | 2 | 63.4 | 49†, 15† | 1149 (27.5) | 1 | 65.8 |
| 36 | 1 | 22.4 | 22 | 0 (0.0) | 0 | 96.2 |
| 37 | 0 | No index | No index | No index | No index | No index |
| 38 | 2 | 97 | 66†, 32 | 154 (13.4) | 4.7 | 97.7 |
| 39 | 1 | 99 | 99 | 0 (0.0) | NA | 99.7 |
| 40 | 1 | 84.9 | 85† | 24 (0.3) | 1.8 | 89.4 |
| 41 | 0 | No index | No index | No index | No index | No index |
| 42 | 2 | 99.1 | 56†, 43† | 5 (4.2) | 2.1 | 99.3 |
| 43 | 2 | 98.9 | 58†, 41 | 2 (8.7) | NA | 98.6 |
| 44 | 2 | 99.1 | 74, 25† | 3 (0.8) | 1.4 | 99.9 |
| 45 | 2 | 79.9 | 72†, 8 | 5 (0.3) | 0.6 | 73.7 |
| 46 | 1 | 94.6 | 95 | 0 (0.0) | 2.1 | 97.8 |
| 47 | 1 | 98.5 | 99† | 60 (5.1) | 1.5 | 99.7 |
| 48 | 4 | 99.8 | 29, 24†, 24†, 23† | 30 (36.1) | 3.2 | 99.9 |
| 49 | 1 | 99 | 99† | 4 (0.6) | 0.7 | 99.5 |
| 50 | 2 | 81.5 | 75†, 7† | 2724 (41.7) | 0.9 | 86.4 |
| 51 | 1 | 5.8 | 6† | 4 (0.5) | 0 | 39.6 |
No index indicates that no index clone was identified in the sample; therefore, index clone frequency data were not applicable; Not sorted, only DNA was available for these samples; therefore, no sorting was performed; and NA, no data are included because of the low number of cells in the flow cytometry gate.
Percent evolved clones of total clones in the sample.
Index clone shows evidence of evolution.
No sorting was performed because of the low number of total viable cells in the sample.
Given the flow cytometry marker used (see supplemental Table 2), no apparent malignant population was observed.