Table 1. Patient demographics and results of bone marrow analysis and clonality tests.
| Patient | Sample | Blasts in BM (%) | Leukemic cells in flow cytometry (%) | Cytogenetics | Abnormal cells by FISH§ (%) | Molecular analysis | Fragment analysis | N of reads and type of clone detected by NGS | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID | Sex | Age (yr) | ID | Time‡ | Clone 1 (%, type) | Clone 2 (%, type) | Clone 3 (%, type) | % of total clones | Total N of reads | ||||||
| 1 | M | 4 | 1-1* | Diagnosis | 92.5 | 56.9 | Not interpretable | 53.6 | Negative∥ | Positive | 44,001 (27.3, VH1-J4) | 9,877 (6.0, VH1-J4) | 9,765 (6.0, VH3-J4) | 39.3 | 160,971 |
| 1-2* | 10 days | 4.0 | Negative | ND | 4.0 | ND | Positive | 27,547 (11.6) | 9,019 (3.8) | 4,846 (2.1) | 17.5 | 236,250 | |||
| 1-3* | 30 days | 1.5 | Negative | 46,XY [20] | Negative | ND | Negative | 0 | 0 | 0 | 0 | 78,806 | |||
| 2 | M | 3 | 2-1* | Diagnosis | 87.0 | 88.2 | Not interpretable | 70.1 | Negative∥ | Positive | 119,153 (23.0, VH3-J4) | 114,278 (22.0, VH2-J4) | - | 45.0 | 518,728 |
| 2-2* | 2 weeks | NA | Negative | ND | ND | ND | Negative | 3,212 (0.7) | 12,524 (2.6) | 3.2 | 489,937 | ||||
| 2-3* | 30 days | 0.7 | Negative | 46,XY [20] | Negative | ND | Negative | 0 | 0 | 0 | 298,570 | ||||
| 3 | F | 2 | 3-1* | Diagnosis | 91.4 | 77.0 | Not interpretable | 62.8 | Negative∥ | Positive | 8,350 (23.7, VH6-J5) | 3,741 (10.6, VH6-J5) | - | 34.3 | 35,182 |
| 3-2* | 2 weeks | 6.8 | 1.0 | ND | 11.3 | ND | Positive | 7,585 (10.5) | 3,569 (4.9) | 15.4 | 72,494 | ||||
| 3-3* | 30 days | 1.0 | Negative | 46,XX [20] | Negative | ND | Negative | 515 (0.5) | 247 (0.2) | 0.7 | 100,618 | ||||
| 4 | F | 4 | 4-1* | Diagnosis | 87.8 | 75.3 | Not interpretable | 75.3 | Negative∥ | ∥Positive | 232,951 (54.8, VH1-J5) | 41,075 (9.7, VH1-J5) | - | 64.5 | 425,184 |
| 4-2* | 10 days | NA | Negative | ND | Negative | ND | Positive | 51,167 (11.8) | 8,317 (1.9) | 13.7 | 434,643 | ||||
| 4-3* | 30 days | 0.9 | Negative | 46,XX [20] | Negative | ND | Negative | 0 | 0 | 0 | 214,809 | ||||
| 5 | M | 8 | 5-1* | Diagnosis | 96.8 | 53.5 | Not interpretable | 65.9 | Negative∥ | Positive | 207,993 (53.8, VH3-J6) | 39,502 (10.2, VH3-J6) | - | 64.0 | 386,903 |
| 5-2* | 2 weeks | 0 | Negative | 46,XY[20] | Negative | ND | Negative | 468 (0.1) | 0 | 0.1 | 339,695 | ||||
| 6 | M | 3 | 6-1* | Diagnosis | 87.0 | 95.6 | Not interpretable | 76.8 | Negative∥ | Positive | 172,072 (54.3, VH3-J4) | 23,264 (7.3, VH3-J4) | - | 61.6 | 316,654 |
| 6-2* | 2 weeks | 0 | Negative | ND | Negative | ND | Negative | 9,290 (2.0) | 1,208 (0.3) | 2.3 | 462,911 | ||||
| 7 | M | 7 | 7-1* | Diagnosis | 92.0 | 90.8 | 45,XY,der(7;9)(q10;q10)[20] | 96.3 | Negative∥ | Positive | 2,429 (25.5, VH4-J6) | - | - | 25.5 | 9,513 |
| 7-2* | 30 days | 1.0 | Negative | ND | Negative | ND | Negative | 0 | 0 | 7,422 | |||||
| 8 | M | 15 | 8-1* | Diagnosis | 93.0 | 88.2 | 52,XY,+8,t(9;22)(q34;q11.2),+der(22)t(9;22),+mar1,+mar2,+mar3,+mar4[1]/46,XY[17] | 80.8 | 3.25¶ | Positive | 8,555 (57.7, VH3-J4) | - | - | 57.7 | 14,825 |
| 8-2* | 30 days | 0 | Negative | ND | ND | 3.94×10-4¶ | Negative | 3,501 (14.3) | 14.3 | 24,427 | |||||
| 8-3* | 10 months | 0.2 | Negative | ND | Negative | Negative¶ | Negative | 400 (2.8) | 2.8 | 14,099 | |||||
| 8-4* | Relapse** | 87.0 | 71.8 | 52,XY,+8,t(9;22)(q34;q11.2),+der(22)t(9;22),+mar1,+mar2,+mar3,+mar4[25]/46,XY[1] | 83.1 | 4.36¶ | Positive | 35,456 (65.8) | 65.8 | 53,881 | |||||
*Eighteen samples from Patients 1–7 were tested by using the Ion Torrent PGM (Thermo Fisher Scientific); †Four samples from Patient 8 were tested by using MiSeq (Illumina); ‡Days, weeks, or months after induction chemotherapy; §Five probe sets were tested by using the IGH/MYC/CEP8 tri-color dual fusion probe, BCR/ABL dual color dual fusion translocation probe, CDKN2A spectrum orange/CEP9 spectrum green probe, TEL/AML1 dual color extra signal probe, and MLL break-apart arrangement probe (Vysis, Downers Grove, IL, USA) at initial diagnosis. Follow-up tests were done by using the probe with abnormal results at initial diagnosis; ∥Molecular analysis was done by using HemaVision kit (DNA technology, Aarhus, Denmark); ¶BCR-ABL1 transcript frequency (relative ratio of BCR-ABL1 to G6PDH) was quantified by using the LightCycler t(9;22) Quantification (Roche Molecular Systems, Branchburg, NJ, USA) kit; **Patient 8 relapsed at one year after diagnosis.
Abbreviations: NGS, next-generation sequencing; BM, bone marrow; ND, not done; NA, not available due to dry-tap.