| Literature DB >> 31305031 |
Kyoko Fuse1, Shun Uemura1, Suguru Tamura1, Tatsuya Suwabe1, Takayuki Katagiri1, Tomoyuki Tanaka1, Takashi Ushiki1, Yasuhiko Shibasaki2, Naoko Sato3, Toshio Yano3, Takashi Kuroha3, Shigeo Hashimoto3, Tatsuo Furukawa3, Miwako Narita4, Hirohito Sone1, Masayoshi Masuko2.
Abstract
Although allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative therapy for high-risk acute leukemia (AL), some patients still relapse. Since patients simultaneously have many prognostic factors, difficulties are associated with the construction of a patient-based prediction algorithm of relapse. The alternating decision tree (ADTree) is a successful classification method that combines decision trees with the predictive accuracy of boosting. It is a component of machine learning (ML) and has the capacity to simultaneously analyze multiple factors. Using ADTree, we attempted to construct a prediction model of leukemia relapse within 1 year of transplantation. With the model of training data (n = 148), prediction accuracy, the AUC of ROC, and the κ-statistic value were 78.4%, 0.746, and 0.508, respectively. The false positive rate (FPR) of the relapse prediction was as low as 0.134. In an evaluation of the model with validation data (n = 69), prediction accuracy, AUC, and FPR of the relapse prediction were similar at 71.0%, 0.667, and 0.216, respectively. These results suggest that the model is generalized and highly accurate. Furthermore, the output of ADTree may visualize the branch point of treatment. For example, the selection of donor types resulted in different relapse predictions. Therefore, clinicians may change treatment options by referring to the model, thereby improving outcomes. The present results indicate that ML, such as ADTree, will contribute to the decision-making process in the diversified allo-HSCT field and be useful for preventing the relapse of leukemia.Entities:
Keywords: acute leukemia; allogeneic hematopoietic stem cell transplantation; machine learning; patient-based prediction; relapse posttransplantation
Mesh:
Year: 2019 PMID: 31305031 PMCID: PMC6718546 DOI: 10.1002/cam4.2401
Source DB: PubMed Journal: Cancer Med ISSN: 2045-7634 Impact factor: 4.452
Patient characteristics
| Hospital | |||||
|---|---|---|---|---|---|
| Factor | All | Niigata (training set) | Nagaoka (validation set) | ||
| Number of patients | N = 217 | N = 148 | N = 69 |
| |
| Age (range) | 38 y (10‐67) | 38 y (10‐66) | 39 y (14‐67) | 0.196 | |
| Age (%) | <40 y | 119 (54.8) | 83 (56.1) | 36 (52.2) | |
| ≤40 y | 98 (45.2) | 65 (43.9) | 33 (47.8) | 0.661 | |
| Sex (%) | Male | 111 (51.2) | 74 (50.0) | 37 (53.6) | 0.663 |
| Female | 106 (48.8) | 74 (50.0) | 32 (46.4) | ||
| Diagnosis (%) | AML | 135 (62.2) | 97 (65.5) | 38 (55.1) | 0.176 |
| ALL | 82 (37.8) | 51 (34.5) | 31 (44.9) | ||
| with (9;22) | 31 (37.8) | 18 (35.3) | 13 (41.9) | 0.64 | |
| Hospital (%) | Niigata | 148 (68.2) | |||
| Nagaoka | 69 (31.8) | ||||
| rDRI (%) | LOW | 14 (6.5) | 10 (6.8) | 4 (5.8) | 0.574 |
| INT | 121 (55.8) | 78 (52.7) | 43 (62.3) | ||
| HI | 51 (23.5) | 36 (24.3) | 15 (21.7) | ||
| VH | 31 (14.3) | 24 (16.2) | 7 (10.1) | ||
| Graft source (%) | BM | 123 (56.7) | 85 (57.4) | 38 (55.1) | 0.115 |
| PBSC | 25 (11.5) | 19 (12.8) | 6 (8.7) | ||
| HAPLO‐PBSC | 22 (10.1) | 18 (12.2) | 4 (5.8) | ||
| CB | 47 (21.7) | 26 (17.6) | 21 (30.4) | ||
| Donor type (%) | Unrelated | 120 (55.3) | 77 (52.0) | 43 (62.3) | 0.187 |
| Related | 97 (44.7) | 71 (48.0) | 26 (37.7) | ||
| Conditioning (%) including | MAC | 169 (77.9) | 110 (74.3) | 59 (85.5) | 0.079 |
| RIC | 48 (22.1) | 38 (25.7) | 10 (14.5) | ||
| Thymoglobulin | 14 (6.5) | 13 (8.8) | 1 (1.4) | ||
| Post cyclophosphamide | 8 (3.7) | 5 (3.4) | 3 (4.3) | ||
| HCT_CI score (%) | ≤2 | 183 (84.3) | 126 (85.1) | 57 (82.6) | 0.69 |
| ≤3 | 34 (15.7) | 22 (14.9) | 12 (17.4) | ||
| NRM (%) | Yes | 42 (19.4) | 29 (19.6) | 13 (18.8) | 1 |
| Using TBI (%) | No | 19 (8.8) | 17 (11.5) | 2 (2.9) | 0.041 |
| Yes | 197 (91.2) | 131 (88.5) | 66 (97.1) | ||
| Relapse within 1 y (%) | Yes | 69 (31.8) | 51 (34.5) | 18 (26.1) | 0.273 |
| OS | Months (range) | 28.9 (1.2‐223.2) | 31.4 (1.2‐223.2) | 27.3 (1.2‐127.1) | 0.382 |
| RFS | Months (range) | 20.6 (1.0‐223.2) | 20.4 (1.0‐223.2) | 20.7 (1.0‐124.8) | 0.816 |
No significant differences were observed between the training and validation sets.
Abbreviations: ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; BM, bone marrow; CB, cord blood; HAPLO‐PBSC, PBSC from haploidentical donors; HCT‐CI, Hematopoietic Cell Transplantation‐Comorbidity Index; HI, high risk; INT, intermediate risk; LOW, low risk; MAC, myeloablative conditioning; NRM, nonrelapse mortality; OS, overall survival; PBSC, peripheral blood stem cells; rDRI, the Refined Disease Risk Index; RFS, relapse‐free survival; RIC, reduced intensity conditioning; TBI, total body irradiation; VH, very high risk.
Figure 1OS and CIR of all patients. (A) and (D); OS and CIR of all patients. One‐ and 3‐year OS rates were 75.1% (95% CI: 68.8%‐80.3%) and 59.1% (95% CI: 52.0%‐65.6%), respectively. (B) and (E); No significant differences were observed in OS (P = 0.82) or CIR (P = 0.097) between Niigata Hospital (training set) and Nagaoka Hospital (validation set). (C) and (F) When stratified based on rDRI, OS (P < 0.0001) and CIR (P < 0.0001) showed significant differences among the categories
Patient outcomes for OS and CIR
| OS (%) (95% CI) | CIR (%) (95% CI) | |||||||
|---|---|---|---|---|---|---|---|---|
| 1 y | 3 y |
| 1 y | 3 y |
| |||
| All | N = 217 | 75.1 (68.8‐80.3) | 59.1 (52.0‐65.6) | 33.8 (26.9‐40.0) | 42.1 (34.7‐48.6) | |||
| Age | <40 y | N = 119 | 75.6 (66.9‐82.4) | 59.9 (50.3‐68.3) |
| 34.3 (24.9‐42.5) | 39.9 (28.5‐49.4) |
|
| ≤40 y | N = 98 | 74.5 (64.6‐82.0) | 58.2 (47.3‐67.6) | 33.2 (22.7‐42.3) | 39.9 (28.5‐52.5) | |||
| Sex | Male | N = 111 | 72.1 (62.7‐79.5) | 54.7 (44.7‐63.5) |
| 36.9 (26.8‐45.6) | 43.9 (33.1‐52.9) |
|
| Female | N = 106 | 78.3 (69.2‐85.0) | 63.8 (53.3‐72.5) | 30.7 (21.0‐39.1) | 40.4 (29.8‐49.3) | |||
| Diagnosis | AML | N = 135 | 73.3 (65.0‐80.0) | 57.4 (48.3‐65.5) |
| 36.1 (27.2‐44.0) | 43.1 (33.6‐51.2) |
|
| ALL | N = 82 | 78.0 (67.4‐85.6) | 61.9 (67.4‐85.6) | 29.9 (18.8‐39.4) | 40.4 (27.9‐50.7) | |||
| Hospital | Niigata (training data) | N = 148 | 77.7 (70.1‐83.6) | 59.3 (50.6‐66.9) |
| 36.0 (22.7‐27.6) | 46.9 (37.8‐54.7) |
|
| Nagaoka (validation data) | N = 69 | 69.6 (57.2‐79.0) | 59.1 (46.0‐70.0) | 28.5 (16.4‐38.9) | 30.3 (17.8‐40.9) | |||
| rDRI | LOW | N = 14 | 78.6 (47.2‐92.5) | 78.6 (47.2‐92.5) |
| 23.1 (0.0‐42.9) | NA |
|
| INT | N = 121 | 88.4 (81.2‐93.0) | 76.3 (67.2‐83.1) | 15.8 (0.6‐8.8) | 26.3 (1.5‐17.5) | |||
| HI | N = 51 | 56.9 (42.2‐69.1) | 40.0 (26.8‐53.6) | 54.9 (9.0‐37.6) | 62.8 (12.5‐45.0) | |||
| VH | N = 31 | 51.6 (33.0‐67.4) | 12.6 (3.3‐28.3) | 76.5 (25.2‐55.1) | 81.2 (32.4‐58.9) | |||
| Graft | BMT | N = 123 | 78.9 (70.5‐85.1) | 67.0 (57.8‐74.6) |
| 29.9 (21.0‐37.7) | 37.3 (27.7‐45.6) |
|
| PB | N = 25 | 64.0 (42.2‐79.4) | 44.3 (23.4‐63.4) | 51.6 (26.2‐68.2) | 61.5 (34.5‐77.3) | |||
| HAPLO‐PB | N = 22 | 63.6 (40.3‐79.9) | 33.5 (14.6‐53.7) | 56.1 (28.9‐73.0) | 69.3 (38.0‐84.8) | |||
| CBT | N = 47 | 76.6 (61.7‐86.3) | 56.3 (38.9‐70.5) | 23.6 (9.6‐35.4) | 31.7 (15.7‐44.7) | |||
| Graft | Related | N = 97 | 73.2 (63.2‐80.9) | 56.4 (45.6‐65.8) |
| 40.9 (30.0‐50.2) | 51.9 (40.2‐61.2) |
|
| Unrelated | N = 120 | 76.7 (68.‐83.3) | 61.4 (51.6‐69.7) | 27.8 (18.9‐35.7) | 33.8 (24.3‐42.2) | |||
| Conditioning | MAC | N = 169 | 74.6 (67.3‐80.5) | 60.8 (52.8‐67.9) |
| 32.8 (25.1‐39.8) | 40.6 (32.3‐47.9) |
|
| RIC | N = 48 | 77.1 (62.5‐85.6) | 52.9 (36.8‐66.6) | 37.1 (21.3‐49.7) | 47.1 (29.9‐60.1) | |||
| Using TBI | No | N = 19 | 68.4 (42.8‐84.4) | 45.6 (22.3‐66.3) |
| 47.4 (19.4‐65.6) | 32.6 (28.0‐80.5) |
|
| Yes | N = 197 | 75.6 (69.0‐81.0) | 60.5 (53.0‐72.5) | 32.6 (25.5‐39.1) | 40.5 (32.8‐47.3) | |||
| HCT_CI score | ≤2 | N = 183 | 76.0 (69.1‐81.5) | 59.2 (51.4‐66.2) |
| 35.0 (27.5‐41.7) | 42.8 (34.8‐49.8) |
|
| ≤3 | N = 34 | 70.6 (52.2‐83.0) | 58.4 (40.1‐72.9) | 27.3 (9.2‐41.8) | 38.6 (17.6‐54.2) | |||
Abbreviations: ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; BM, bone marrow; CB, cord blood; CIR, cumulative incidence of relapse; HAPLO‐PBSC, PBSC from haploidentical donors; HCT‐CI, Hematopoietic Cell Transplantation‐Comorbidity Index; HI, high risk; INT, intermediate risk; LOW, low risk; MAC, myeloablative conditioning; OS, overall survival; PBSC, peripheral blood stem cells; rDRI, the Refined Disease Risk Index; RIC, reduced intensity conditioning; TBI, total body irradiation; VH, very high risk.
Multivariate analysis of CIR
| Factor | Hazard ratio | (95% CI) |
|
|---|---|---|---|
| Age < 40 y | 0.783 | 0.453‐1.353 | 0.380 |
| Conditioning; RIC | 0.680 | 0.336‐1.376 | 0.280 |
| rDRI |
| ||
| Compared to LOW | |||
| DRI—INT | 0.877 | 0.255‐3.026 | 0.840 |
| DRI—HI | 2.953 | 0.854‐10.210 | 0.087 |
| DRI—VH | 6.236 | 1.696‐22.930 |
|
| ALL | 1.045 | 0.628‐1.740 | 0.860 |
| Graft source | 0.993 | ||
| Compared to BMT | |||
| graft—CBT | 0.913 | 0.435‐1.918 | 0.810 |
| graft—HAPLO‐PBSC | 1.051 | 0.419‐2.635 | 0.920 |
| graft—PBSC | 0.960 | 0.413‐2.227 | 0.920 |
| Donor type: Related | 1.401 | 0.781‐2.514 | 0.260 |
| Female | 1.175 | 0.714‐1.936 | 0.530 |
| Using TBI | 0.555 | 0.230‐1.339 | 0.190 |
In a multivariate analysis, rDRI was identified as a risk factor for CIR alone (P < 0.0001), particularly rDRI; VH (HR 6.236, 95% CI: 1.696‐22.93, P = 0.006).
Abbreviations: ALL, acute lymphoblastic leukemia; BM, bone marrow; CB, cord blood; HAPLO‐PBSC, PBSC from haploidentical donors; HI, high risk; INT, intermediate risk; LOW, low risk; PBSC, peripheral blood stem cells; rDRI, the Refined Disease Risk Index; RIC, reduced intensity conditioning; TBI, total body irradiation; VH, very high risk.
Figure 2Relapse prediction model; Graphical output. Each score beside nodes showed a prediction node weight (NW); NW < 0 means a lower relapse risk and NW > 0 a higher relapse risk. The final judgment of the AL relapse prediction was achieved by summing all the nodes through which it passed (NW sum). The NW sum > 0 predicted relapse and <0 predicted no relapse in this model
The actual number of patients and the prediction number of relapse
| Training set (n = 148) | Prediction | Total | ||
|---|---|---|---|---|
| No relapse | Relapse | |||
| Actual number | No relapse | 84 | 13 | 97 |
| Relapse | 19 | 32 | 51 | |
| Total | 103 | 45 | 148 | |
Comparison of predictability
| In relapse | |||||||
|---|---|---|---|---|---|---|---|
| Accuracy | AUC | κ‐statistic | TPR | TNR | FPR | FNR | |
| Niigata group (Training set) | 78.4% | 0.746 | 0.508 | 0.627 | 0.866 | 0.134 | 0.373 |
| Nagaoka group (Validation set) | 71.0% | 0.667 | 0.274 | 0.500 | 0.784 | 0.216 | 0.500 |
In this prediction model, true‐positive rate (TPR, also called the sensitivity) and false‐positive rate (FNR, it shows miss rate) in relapse were not sufficiently. However, true–negative rate (TNR, also called specificity) was high‐ and false‐positive rate (FPR, it means probability of false alarm) in relapse was very low. Therefore, clinicians may consider changes in treatment options if relapse is predicted.
AUC; area under the curve, Accuracy = (true positive + true negative)/ all, TPR = true positive/ (true positive + false negative) = 1‐FNR, FNR = false negative/ (false negative + true positive) = 1‐TPR, TNR = true negative/ (true negative + false positive) = 1‐ FPR, FPR = false positive/ (false positive + true negative) = 1‐TNR.
Figure 3Example of a simulation. In high‐risk AML, the branch point of therapeutic options was the donor type from our simulation