Table 1.
IG/TR rearrangements detected by DNA amplicon-based methods (DNAamp) and by RNAseq.
| Rearrangements/casea | RNAseq MRD markers according to DNAamp benchmarkb | |||||
|---|---|---|---|---|---|---|
| DNAamp | RNAseq (“damaged”) | RNAseq Productive | DNAamp | RNAseq | RNAseq (%) | |
| IGH complete VJ:Vh-(Dh)-Jh | 2241 | 643 (215) | 364 | 223 | 188 | 84.3 |
| IGH incomplete DJ:Dh-Jh | 1407 | 21 (9) | na | 89 | 69 | 77.5 |
| IGK complete VJ:Vk-Jk | 762 | 436 (61) | 323 | 63 | 23 | 36.5 |
| IGK other Vk-Kde | 285 | <1 | na | 57 | 2 | 3.5 |
| IGK other intron-Kde | 780 | <1 | na | 45 | 1 | 2.2 |
| IGL complete VJ:Vl-Jl | nac | 329 (53) | 233 | na | ||
| TRA complete VJ:Va-Ja | 11 | 62 (20) | 25 | 0 | ||
| TRA + D complete VJ:Va-Jd | 10 | <1 | <1 | 0 | ||
| TRA + D complete VJ:Vd-(Dd)-Ja | 133 | 2 (1) | <1 | 33 | 14 | 42.4 |
| TRA + D incomplete DJ:Dd-Ja | 71 | 37 (25) | na | 27 | 1 | 3.7 |
| TRA + D incomplete VD:Va-Dd3 | na | <1 | na | na | ||
| TRB complete VJ:Vb-(Db)-Jb | 1921 | 128 (34) | 72 | 101 | 53 | 52.5 |
| TRB incomplete DJ:Db-Jb | 1555 | 13 (6) | na | 71 | 19 | 26.8 |
| TRB incomplete VD:Vb-Db | na | 1 (<1) | na | na | ||
| TRB other DD:Db-Db | na | <1 | na | na | ||
| TRD complete VJ:Vd-(Dd)-Jd | 184 | 2 (<1) | 1 | 17 | 4 | 23.5 |
| TRD incomplete DJ:Dd2-Jd | 139 | 1 (1) | na | 11 | 1 | 9.1 |
| TRD incomplete DJ:Dd3-Jd | na | <1 | na | na | ||
| TRD incomplete VD:Vd-Dd3 | 188 | <1 | na | 82 | 1 | 1.2 |
| TRD other DD:Dd2-Dd3 | 74 | 0 | na | 36 | 0 | 0 |
| TRD other DD:Dd3-Dd2 | na | <1 | na | na | ||
| TRG complete VJ:Vg-Jg | 2163 | 12 (2) | 3 | 198 | 91 | 46 |
aAverage number of rearrangements per case as detected by DNAamp and RNAseq. The RNAseq data refer to total number of rearrangements (with in between brackets the number of “damaged” sequences) and to the number of productive rearrangements. A total of 165 ALL patients were evaluated.
bNumber of potential MRD markers identified by DNAamp (as per abundance thresholds), and number and percentage of those markers identified by RNAseq at any abundance. A total of 165 ALL patients were evaluated.
cna: not analyzed/not applicable.