Association of clinical and outcome features with gene expression cluster groups
| . | Method* . | 1 . | 2 . | 3 . | 4 . | 5 . | 6 . | 7 . | 8 . | Sum . | P† . |
|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of cases per cluster group | H | 20 | 23 | 8 | 11 | 9 | 19 | 95 | 22 | 207 | — |
| C | 20 | 23 | 10 | — | 11 | 21 | 102 | 20 | 207 | — | |
| R | 21 | 23 | 12 | 14 | 10 | 21 | 82 | 24 | 207 | — | |
| Median age, years | H | 6.9 | 13.1 | 13.8 | 14.2 | 14. 7 | 14.5 | 11.4 | 13.8 | 13.1 | .002 |
| C | 6.9 | 13.1 | 15.2 | — | 14.7 | 14.5 | 11.7 | 14.3 | 13.1 | <.001 | |
| R | 4.7 | 13.1 | 15.2 | 14.3 | 14.5 | 14.5 | 7.8 | 14.1 | 13.1 | <.001 | |
| Sex (male) | H | 11/20 | 11/23 | 4/8 | 10/11 | 7/9 | 15/19 | 64/95 | 15/22 | 137/207 | .165 |
| C | 11/20 | 11/23 | 5/10 | — | 8/11 | 17/21 | 71/102 | 14/20 | 137/207 | .196 | |
| R | 11/21 | 11/23 | 6/12 | 13/14 | 8/10 | 17/21 | 54/82 | 17/24 | 137/207 | .043 | |
| Hispanic ethnicity | H | 3/20 | 6/23 | 2/8 | 2/11 | 0/8 | 3/18 | 22/95 | 13/22 | 51/205 | .018 |
| C | 3/20 | 6/23 | 2/10 | — | 0/10 | 3/20 | 25/102 | 12/20 | 51/205 | .008 | |
| R | 4/21 | 6/23 | 2/12 | 3/14 | 0/9 | 3/20 | 18/82 | 15/24 | 51/205 | .004 | |
| MLL rearrangement | H | 20/20 | 0/23 | 0/8 | 0/11 | 0/9 | 0/19 | 1/95 | 0/22 | 21/207 | < .001 |
| C | 20/20 | 0/23 | 0/10 | — | 0/11 | 0/21 | 1/102 | 0/20 | 21/207 | <.001 | |
| R | 21/21 | 0/23 | 0/12 | 0/14 | 0/10 | 0/21 | 0/82 | 0/24 | 21/207 | <.001 | |
| TCF3-PBX1 | H | 0/20 | 23/23 | 0/8 | 0/11 | 0/9 | 0/19 | 0/95 | 0/22 | 23/207 | < .001 |
| C | 0/20 | 23/23 | 0/10 | — | 0/11 | 0/21 | 0/102 | 0/20 | 23/207 | <.001 | |
| R | 0/21 | 23/23 | 0/12 | 0/14 | 0/10 | 0/21 | 0/82 | 0/24 | 23/207 | <.001 | |
| Positive MRD (day 29) | H | 8/16 | 0/20 | 0/7 | 2/11 | 7/9 | 6/19 | 27/88 | 17/21 | 67/191 | < .001 |
| C | 9/17 | 0/20 | 1/9 | — | 8/11 | 6/21 | 26/94 | 17/19 | 67/191 | <.001 | |
| R | 9/17 | 0/20 | 1/11 | 3/14 | 8/10 | 6/21 | 21/75 | 19/23 | 67/191 | <.001 | |
| WBC, × 103/μL, median | H | 129.4 | 67.2 | 139.0 | 13.3 | 32.6 | 31.4 | 59.9 | 197.5 | 62.3 | <.001 |
| C | 129.4 | 67.2 | 33.5 | — | 32.6 | 26.0 | 52.5 | 158.3 | 62.3 | .028 | |
| R | 125.8 | 67.2 | 49.6 | 9.2 | 31.5 | 26.0 | 68.8 | 153.8 | 62.3 | <.001 | |
| 4-year RFS, ± SE | H | 65.0 ± 10.7 | 73.9 ± 9.2 | 75.0 ± 15.3 | 58.2 ± 16.9 | 88.9 ± 10.5 | 94.1 ± 5.7 | 67.4 ± 5.1 | 23.0 ± 10.3 | 66.3 ± 3.5 | — |
| C | 70.0 ± 10.3 | 73.9 ± 9.2 | 70.0 ± 14.5 | — | 78.7 ± 13.4 | 94.7 ± 5.1 | 66.4 ± 5.0 | 15.1 ± 9.3 | 66.3 ± 3.5 | — | |
| R | 66.7 ± 10.3 | 73.9 ± 9.2 | 72.7 ± 13.4 | 75.0 ± 12.9 | 78.7 ± 13.4 | 94.7 ± 5.1 | 66.2 ± 5.5 | 21.0 ± 9.5 | 66.3 ± 3.5 | — | |
| Log-rank P for RFS‡ | H | .722 | .409 | .582 | .930 | .185 | .018 | .993 | <.001 | — | — |
| C | .808 | .409 | .788 | — | .364 | .010 | .944 | <.001 | — | — | |
| R | .881 | .409 | .615 | .259 | .366 | .010 | .680 | <.001 | — | — | |
| Hazard ratio for RFS‡ | H | 1.152 | 0.704 | 0.675 | 1.046 | 0.286 | 0.133 | 0.998 | 3.491 | — | — |
| C | 0.901 | 0.704 | 0.853 | — | 0.527 | 0.117 | 1.017 | 4.382 | — | — | |
| R | 1.060 | 0.704 | 0.744 | 0.520 | 0.528 | 0.117 | 1.110 | 3.878 | — | — |
| . | Method* . | 1 . | 2 . | 3 . | 4 . | 5 . | 6 . | 7 . | 8 . | Sum . | P† . |
|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of cases per cluster group | H | 20 | 23 | 8 | 11 | 9 | 19 | 95 | 22 | 207 | — |
| C | 20 | 23 | 10 | — | 11 | 21 | 102 | 20 | 207 | — | |
| R | 21 | 23 | 12 | 14 | 10 | 21 | 82 | 24 | 207 | — | |
| Median age, years | H | 6.9 | 13.1 | 13.8 | 14.2 | 14. 7 | 14.5 | 11.4 | 13.8 | 13.1 | .002 |
| C | 6.9 | 13.1 | 15.2 | — | 14.7 | 14.5 | 11.7 | 14.3 | 13.1 | <.001 | |
| R | 4.7 | 13.1 | 15.2 | 14.3 | 14.5 | 14.5 | 7.8 | 14.1 | 13.1 | <.001 | |
| Sex (male) | H | 11/20 | 11/23 | 4/8 | 10/11 | 7/9 | 15/19 | 64/95 | 15/22 | 137/207 | .165 |
| C | 11/20 | 11/23 | 5/10 | — | 8/11 | 17/21 | 71/102 | 14/20 | 137/207 | .196 | |
| R | 11/21 | 11/23 | 6/12 | 13/14 | 8/10 | 17/21 | 54/82 | 17/24 | 137/207 | .043 | |
| Hispanic ethnicity | H | 3/20 | 6/23 | 2/8 | 2/11 | 0/8 | 3/18 | 22/95 | 13/22 | 51/205 | .018 |
| C | 3/20 | 6/23 | 2/10 | — | 0/10 | 3/20 | 25/102 | 12/20 | 51/205 | .008 | |
| R | 4/21 | 6/23 | 2/12 | 3/14 | 0/9 | 3/20 | 18/82 | 15/24 | 51/205 | .004 | |
| MLL rearrangement | H | 20/20 | 0/23 | 0/8 | 0/11 | 0/9 | 0/19 | 1/95 | 0/22 | 21/207 | < .001 |
| C | 20/20 | 0/23 | 0/10 | — | 0/11 | 0/21 | 1/102 | 0/20 | 21/207 | <.001 | |
| R | 21/21 | 0/23 | 0/12 | 0/14 | 0/10 | 0/21 | 0/82 | 0/24 | 21/207 | <.001 | |
| TCF3-PBX1 | H | 0/20 | 23/23 | 0/8 | 0/11 | 0/9 | 0/19 | 0/95 | 0/22 | 23/207 | < .001 |
| C | 0/20 | 23/23 | 0/10 | — | 0/11 | 0/21 | 0/102 | 0/20 | 23/207 | <.001 | |
| R | 0/21 | 23/23 | 0/12 | 0/14 | 0/10 | 0/21 | 0/82 | 0/24 | 23/207 | <.001 | |
| Positive MRD (day 29) | H | 8/16 | 0/20 | 0/7 | 2/11 | 7/9 | 6/19 | 27/88 | 17/21 | 67/191 | < .001 |
| C | 9/17 | 0/20 | 1/9 | — | 8/11 | 6/21 | 26/94 | 17/19 | 67/191 | <.001 | |
| R | 9/17 | 0/20 | 1/11 | 3/14 | 8/10 | 6/21 | 21/75 | 19/23 | 67/191 | <.001 | |
| WBC, × 103/μL, median | H | 129.4 | 67.2 | 139.0 | 13.3 | 32.6 | 31.4 | 59.9 | 197.5 | 62.3 | <.001 |
| C | 129.4 | 67.2 | 33.5 | — | 32.6 | 26.0 | 52.5 | 158.3 | 62.3 | .028 | |
| R | 125.8 | 67.2 | 49.6 | 9.2 | 31.5 | 26.0 | 68.8 | 153.8 | 62.3 | <.001 | |
| 4-year RFS, ± SE | H | 65.0 ± 10.7 | 73.9 ± 9.2 | 75.0 ± 15.3 | 58.2 ± 16.9 | 88.9 ± 10.5 | 94.1 ± 5.7 | 67.4 ± 5.1 | 23.0 ± 10.3 | 66.3 ± 3.5 | — |
| C | 70.0 ± 10.3 | 73.9 ± 9.2 | 70.0 ± 14.5 | — | 78.7 ± 13.4 | 94.7 ± 5.1 | 66.4 ± 5.0 | 15.1 ± 9.3 | 66.3 ± 3.5 | — | |
| R | 66.7 ± 10.3 | 73.9 ± 9.2 | 72.7 ± 13.4 | 75.0 ± 12.9 | 78.7 ± 13.4 | 94.7 ± 5.1 | 66.2 ± 5.5 | 21.0 ± 9.5 | 66.3 ± 3.5 | — | |
| Log-rank P for RFS‡ | H | .722 | .409 | .582 | .930 | .185 | .018 | .993 | <.001 | — | — |
| C | .808 | .409 | .788 | — | .364 | .010 | .944 | <.001 | — | — | |
| R | .881 | .409 | .615 | .259 | .366 | .010 | .680 | <.001 | — | — | |
| Hazard ratio for RFS‡ | H | 1.152 | 0.704 | 0.675 | 1.046 | 0.286 | 0.133 | 0.998 | 3.491 | — | — |
| C | 0.901 | 0.704 | 0.853 | — | 0.527 | 0.117 | 1.017 | 4.382 | — | — | |
| R | 1.060 | 0.704 | 0.744 | 0.520 | 0.528 | 0.117 | 1.110 | 3.878 | — | — |
— indicates not applicable.
H indicates gene expression cluster groups determined by selection of genes using high CV and standard hierarchical clustering (HC); C, COPA; and R, ROSE.
All P values are calculated for Fisher exact test (all variables except age and WBC) or Kruskal-Wallis rank-sum test (age and WBC) using R (Version 2.9.1, survival and stats packages).
Log-rank P values and HRs calculated separately for each cluster using R (Version 2.9.1, stats package).