Frequency of recurrent CNAs in 14 E/R-positive relapse patients at diagnosis and relapse with paired analysis compared with those observed at diagnosis in 47 nonrelapse patients
| Cytoband . | Gene . | 47 without relapse . | 14 with relapse . | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Diagnosis . | Diagnosis . | Relapse . | Shared . | ||||||
| N . | % . | N . | % . | N . | % . | N . | % . | ||
| Losses | |||||||||
| 12p13.2 | ETV6 | 33 | 70 | 8 | 57 | 8 | 57 | 7 | 88 |
| 22q11.22 | VPREB1 | 32 | 68 | 8 (3) | 57 (38) | 10 (5) | 71 (50) | 8 (2) | 100 (20) |
| 9p21.3 | CDKN2A | 12 | 26 | 3 (1) | 21 (33) | 4 (1) | 29 (25) | 3 (0) | 100 (0) |
| 3q13.2 | CD200, BTLA | 7 | 15 | 5 | 36 | 4 | 29 | 3 | 60 |
| 9p21.3 | CDKN2B | NA | NA | 3 (1) | 21 (33) | 3 (1) | 21 (33) | 2 (0) | 67 (0) |
| 3q26.32 | TBL1XR1 | 6 | 13 | 4 | 29 | 3 | 21 | 3 | 75 |
| 9p13.2 | PAX5 | 13 | 28 | 3 | 21 | 3 | 21 | 2 | 67 |
| 12p13.1 | ATF7IP | NA | NA | 5 | 36 | 6 | 43 | 4 | 80 |
| 12p13.3 | VWF | NA | NA | 4 | 29 | 1 | 7 | 1 | 25 |
| 12p13.2 | BCL2L14, CDKN1B | NA | NA | 5 | 36 | 5 | 36 | 3 | 60 |
| 9p21.3 | MTAP | NA | NA | 2 (0) | 14 (0) | 3 (1) | 21 (33) | 2 (0) | 100 (100) |
| 12q21.33 | BTG1 | 6* | 13* | 3 | 21 | 0 | 0 | 0 | 0 |
| 15q15.1 | BMF | 0 | 0 | 2† | 14 | 2† | 14 | 2† | 100 |
| 6q21 | ARMC2, SESN1 | 7 | 15 | 1 | 7 | 1 | 7 | 0 | 0 |
| 5q31.3 | NR3C1 | 6 | 13 | 0 | 0 | 3‡ (1) | 21 (33) | 0 | 0 |
| 21q22.12 | RUNX1 | 3§ | 6§ | 2 | 14 | 2 | 14 | 2 | 100 |
| 9p21.3 | IFN cluster | 0‖ | 0‖ | 1 | 7 | 1 | 7 | 1 | 100 |
| 12p13.2 | GABARAPL1 | NA | NA | 4 | 29 | 4 | 29 | 3 | 75 |
| 5q33.3 | EBF1 | 5 | 11 | 0 | 0 | 2 | 14 | 0 | 0 |
| 7p12.2 | IKZF1 | 0 | 0 | 0 | 0 | 1 | 7 | 0 | 0 |
| 4q31.22 | NR3C2 | 5¶ | 11¶ | 0 | 0 | 2 | 14 | 1 | 50 |
| 2p21 | MSH2 | 0 | 0 | 0 | 0 | 1 | 7 | 0 | 0 |
| 3p21.3 | MLH1 | 0 | 0 | 0 | 0 | 0# | 0 | 0 | 0 |
| Gains | |||||||||
| 21q | Includes RUNX1 | 4 | 9 | 5 | 36 | 4 | 29 | 3 | 60 |
| Cytoband . | Gene . | 47 without relapse . | 14 with relapse . | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Diagnosis . | Diagnosis . | Relapse . | Shared . | ||||||
| N . | % . | N . | % . | N . | % . | N . | % . | ||
| Losses | |||||||||
| 12p13.2 | ETV6 | 33 | 70 | 8 | 57 | 8 | 57 | 7 | 88 |
| 22q11.22 | VPREB1 | 32 | 68 | 8 (3) | 57 (38) | 10 (5) | 71 (50) | 8 (2) | 100 (20) |
| 9p21.3 | CDKN2A | 12 | 26 | 3 (1) | 21 (33) | 4 (1) | 29 (25) | 3 (0) | 100 (0) |
| 3q13.2 | CD200, BTLA | 7 | 15 | 5 | 36 | 4 | 29 | 3 | 60 |
| 9p21.3 | CDKN2B | NA | NA | 3 (1) | 21 (33) | 3 (1) | 21 (33) | 2 (0) | 67 (0) |
| 3q26.32 | TBL1XR1 | 6 | 13 | 4 | 29 | 3 | 21 | 3 | 75 |
| 9p13.2 | PAX5 | 13 | 28 | 3 | 21 | 3 | 21 | 2 | 67 |
| 12p13.1 | ATF7IP | NA | NA | 5 | 36 | 6 | 43 | 4 | 80 |
| 12p13.3 | VWF | NA | NA | 4 | 29 | 1 | 7 | 1 | 25 |
| 12p13.2 | BCL2L14, CDKN1B | NA | NA | 5 | 36 | 5 | 36 | 3 | 60 |
| 9p21.3 | MTAP | NA | NA | 2 (0) | 14 (0) | 3 (1) | 21 (33) | 2 (0) | 100 (100) |
| 12q21.33 | BTG1 | 6* | 13* | 3 | 21 | 0 | 0 | 0 | 0 |
| 15q15.1 | BMF | 0 | 0 | 2† | 14 | 2† | 14 | 2† | 100 |
| 6q21 | ARMC2, SESN1 | 7 | 15 | 1 | 7 | 1 | 7 | 0 | 0 |
| 5q31.3 | NR3C1 | 6 | 13 | 0 | 0 | 3‡ (1) | 21 (33) | 0 | 0 |
| 21q22.12 | RUNX1 | 3§ | 6§ | 2 | 14 | 2 | 14 | 2 | 100 |
| 9p21.3 | IFN cluster | 0‖ | 0‖ | 1 | 7 | 1 | 7 | 1 | 100 |
| 12p13.2 | GABARAPL1 | NA | NA | 4 | 29 | 4 | 29 | 3 | 75 |
| 5q33.3 | EBF1 | 5 | 11 | 0 | 0 | 2 | 14 | 0 | 0 |
| 7p12.2 | IKZF1 | 0 | 0 | 0 | 0 | 1 | 7 | 0 | 0 |
| 4q31.22 | NR3C2 | 5¶ | 11¶ | 0 | 0 | 2 | 14 | 1 | 50 |
| 2p21 | MSH2 | 0 | 0 | 0 | 0 | 1 | 7 | 0 | 0 |
| 3p21.3 | MLH1 | 0 | 0 | 0 | 0 | 0# | 0 | 0 | 0 |
| Gains | |||||||||
| 21q | Includes RUNX1 | 4 | 9 | 5 | 36 | 4 | 29 | 3 | 60 |
Numbers represent cases/percentages with genomic aberrations; number of cases with biallelic deletions in parentheses.
NA indicates not applicable.
3′ of BTG1.
One additional case with a conserved BMF deletion in the group with unpaired analysis.
One additional case with a relapse-specific deletion among the cases with unpaired analysis.
Immediately distal to RUNX1.
Analyzed in only 13 patients.
Telomeric to NR3C2.
Two cases with a relapse-specific deletion among the cases with unpaired analysis (supplemental Tables 1 and 2).