Common (>5% frequency) secondary genetic abnormalities observed in ETV6-RUNX1–positive leukemia using various methods, including conventional cytogenetics, microarray, and FISH
| Secondary abnormality . | Frequency (%) . | Possible candidate genes . |
|---|---|---|
| 12p abnormalities* | 39 | ETV6, CDKN1B |
| 9p deletion (9p13-24) including aUPD | 9-25 | CDKN2A, CDKN2B, PAX5, JAK2, MTAP |
| 12q21.33 deletion† | 13-25 | BTG1 |
| Trisomy 21‡ | 17-25 | RUNX1 |
| 5q31.3-33.3 deletion† | 23 | NR3C1, EBF1 |
| 14q32.33 deletion† | 21 | IGH |
| 3p21 deletion† | 21 | LIMD1 |
| 6q abnormalities including deletion | 13-18 | AIM1, PRDM1, FOXO3, CCNC |
| 7p14.1 deletion† | 18 | IKZF1 |
| 4q31.23 deletion† | 17 | NR3C1, ARHGAP10 |
| Trisomy 10 | 5-15 | — |
| 3q26.32 deletion† | 3-15 | TBL1XR1 |
| 3q13.2 deletion† | 15 | CD200, BTLA |
| 19q13.11 deletion† | 13 | CEBPA |
| 22q11.2 deletion† | 13 | — |
| Xq duplication (in males)† | 11 | SPANXB, HMGB3, FAM50A, HTATSF1 |
| 1q31.3 deletion† | 10 | TROVE2, GLRX2, CDC73, B3GALT2 |
| 15q15.1 abnormalities including deletion | 10 | LTK, MIRN626 |
| 13q14-34 abnormalities including deletion | 6-10 | RB1, SERP2, DLEU2, ST13P4, TRIM13, KCNRG, MIRN16-1, MIRN15A, DLEU1, DLEU7 |
| 2p25.3 deletion† | 9 | — |
| 3p14.2 deletion† | 9 | FHIT |
| X chromosome loss (in females) | 8 | — |
| 11q abnormalities including deletion | 6 | ATM, KMT2A |
| 8p11.23 deletion† | 6 | — |
| Trisomy 16 | 6 | — |
| Xp duplication† | 5 | — |
| 14q11.2 deletion† | 8 | — |
| 7q34 deletion† | 6 | NAMPT |
| Secondary abnormality . | Frequency (%) . | Possible candidate genes . |
|---|---|---|
| 12p abnormalities* | 39 | ETV6, CDKN1B |
| 9p deletion (9p13-24) including aUPD | 9-25 | CDKN2A, CDKN2B, PAX5, JAK2, MTAP |
| 12q21.33 deletion† | 13-25 | BTG1 |
| Trisomy 21‡ | 17-25 | RUNX1 |
| 5q31.3-33.3 deletion† | 23 | NR3C1, EBF1 |
| 14q32.33 deletion† | 21 | IGH |
| 3p21 deletion† | 21 | LIMD1 |
| 6q abnormalities including deletion | 13-18 | AIM1, PRDM1, FOXO3, CCNC |
| 7p14.1 deletion† | 18 | IKZF1 |
| 4q31.23 deletion† | 17 | NR3C1, ARHGAP10 |
| Trisomy 10 | 5-15 | — |
| 3q26.32 deletion† | 3-15 | TBL1XR1 |
| 3q13.2 deletion† | 15 | CD200, BTLA |
| 19q13.11 deletion† | 13 | CEBPA |
| 22q11.2 deletion† | 13 | — |
| Xq duplication (in males)† | 11 | SPANXB, HMGB3, FAM50A, HTATSF1 |
| 1q31.3 deletion† | 10 | TROVE2, GLRX2, CDC73, B3GALT2 |
| 15q15.1 abnormalities including deletion | 10 | LTK, MIRN626 |
| 13q14-34 abnormalities including deletion | 6-10 | RB1, SERP2, DLEU2, ST13P4, TRIM13, KCNRG, MIRN16-1, MIRN15A, DLEU1, DLEU7 |
| 2p25.3 deletion† | 9 | — |
| 3p14.2 deletion† | 9 | FHIT |
| X chromosome loss (in females) | 8 | — |
| 11q abnormalities including deletion | 6 | ATM, KMT2A |
| 8p11.23 deletion† | 6 | — |
| Trisomy 16 | 6 | — |
| Xp duplication† | 5 | — |
| 14q11.2 deletion† | 8 | — |
| 7q34 deletion† | 6 | NAMPT |
aUPD, acquired uniparental disomy.
12p abnormalities include deletions and translocations [not including the t(12;21)] visible, using conventional cytogenetics and deletions detected using FISH or microarray technologies.
Deletions and duplications only detected using microarray techniques, and hence not visible via conventional cytogenetics.
The additional copy of chromosome 21 may be either a normal chromosome 21 or an additional copy of the der(21)t(12;21)(p13q22).