B-ALL Tables: Prognostic Genomic Abnormalities and Recurrent Gene Fusions
Table 1 - Gene fusions reported in Ph-like B-ALL and other new B-ALL molecular subtypes (Literature Review). Table derived from Akkari et al., 2020 [PMID 32302940] with permission from Cancer Genetics.
| Subtype | 3’ Partner | 5’ Partner | Chromosome rearrangement | Gene fusion | Visible by G-banding | PMID | Comment |
| Ph-like
B-ALL |
ABL1 (9q34) | CENPC1 | t(4;9)(q13;q34) | CENPC1-ABL1 | YES | 28408464 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms |
| ETV6 | t(9;12)(q34;p13) | ETV6-ABL1 | NO | 27229714 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | ||
| FOXP1 | t(3;9)(p13;q34) | FOXP1-ABL1 on der(3) | YES | 21391972 | |||
| LSM14A | t(9;19)(q34;q13.1) | LSM14A-ABL1 on der(19) | YES | 28408464 | |||
| NUP153 | t(6;9)(p22.3;q34) | NUP153-ABL1 on der(6) | YES | 28408464 | |||
| NUP214 | dup(9)(q34.1q34.1) | NUP214-ABL1 | NO | 26681761 | Tandem duplication (~370 kb) detectable by CMA | ||
| RANBP2 | t(2;9)(q12.3;q34) | RANBP-ABL1 on der(2) | YES | 25207766 | |||
| RCSD1 | t(1;9)(q24.2;q34) | RCSD1-ABL1 on der(1) | YES | 25768406 | |||
| SFPQ | t(1;9)(p34.3;q34) | SFPQ-ABL1 on der(1) | YES | 27894117 | |||
| SNX1 | t(9;15)(q34;q22.3) | SNX1-ABL1 on der(15) | YES | 28972016 | |||
| SNX2 | t(5;9)(q23.2;q34) | SNX2-ABL1 on der(5) | YES | 24367893 | |||
| ZMIZ1 | t(9;10)(q34;q22.3) | ZMIZ1-ABL1 on der(10) | YES | 18007576 | |||
| ABL2 (1q25.2) | PAG1 | t(1;8)(q25.2;q21.1) | PAG1-ABL2 on der(1) | YES | 25207766 | ||
| RCSD1 | 1q24.2q25.2 rearrangement | RCSD1-ABL2 | NO | 25098428 | On the same chromosome arm; however, a simple deletion cannot cause the fusion due to the orientation of genes | ||
| ZC3HAV1 | t(1;7)(q25.2;q34) | ZC3HAV1-ABL2 on der(1) | YES | 29507076 | |||
| CRLF2
(Xp22.3 & Yp11.3) |
IGH | t(X;14)(p22.3;q32) or
t(Y;14)(p11.3;q32) |
IGH/CRLF2 | NO | 27919910 25207766 | ||
| P2RY8 | del(X)(p22.3p22.3) or del(Y)(p11.3p11.3) | P2RY8-CRLF2 | NO | 27919910 25207766 | |||
| CSF1R (5q32) | MEF2D | t(1;5)(q22;q32) | MEF2D-CSF1R on der(5) | YES | 27824051 | ||
| SSBP2 | 5q14.1q32 rearrangement | SSBP2-CSF1R | YES | 28408464 | On the same chromosome arm; however, a simple deletion cannot cause the fusion due to the orientation of genes | ||
| TBL1XR1 | t(3;5)(q26.3;q32) | TBL1XR1-CSF1R on der(5) | YES | 28408464 | |||
| DGKH (13q14.1) | ZFAND3 | t(6;13)(p21.2;q14.1) | ZFAND3-DGKH | YES | 25207766 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | |
| EPOR (19p13.2) | IGH | ins(14;19)(q32;p13.2p13.2) | IGH/EPOR | Cryptic insertion | 26859458 | ||
| IGK | ins(2;19)(p11.2;p13.2p13.2) | IGK/EPOR | Cryptic insertion | 26859458 | |||
| LAIR1 | inv(19)(p13.2q13.42) | LAIR1-EPOR | NO | 26859458 | Inversion of chromosome 19 juxtaposes EPOR to the upstream region of LAIR1 | ||
| THADA | t(2;19)(p21;p13.2) | THADA-EPOR | YES | 28972016 | |||
| IL2RB (22q12.3) | MYH9 | 22q12.3 rearrangement | MYH9-IL2RB | NO | 25207766 | On the same chromosome arm; however, a simple deletion cannot cause the fusion due to the orientation of genes | |
| JAK2 (9p24.1)
|
ATF7IP | t(9;12)(p24.1;p13.1) | ATF7IP-JAK2 on der(9) | NO | 25207766 29487712 | ||
| BCR | t(9;22)(p24.1;q11.2) | BCR-JAK2 | ? YES | 16001431 | Seen also in myeloproliferative neoplasms. Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | ||
| EBF1 | t(5;9)(q33.3;p24.1) | EBF1-JAK2 on der(9) | NO (SUBTLE) | 29296813 | |||
| ETV6 | t(9;12)(p24.1;p13.2) | ETV6-JAK2 on der(9) | NO (SUBTLE) | 22373549
23204479 |
|||
| GOLGA5 | t(9;14)(p24.1;q32.1) | GOLGA5-JAK2 | NO (SUBTLE) | 29773603 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | ||
| HMBOX1 | t(8;9)(p21.1;p24.1) | HMBOX1-JAK2 on der(9) | YES | 27870571 | |||
| OFD1 | t(X;9)(p22.2;p24.1) | OFD1-JAK2 on der(9) | NO (SUBTLE) | 26404892 | |||
| PAX5 | inv(9)(p13.2p24.1) | PAX5-JAK2 | YES | 25515960 | An inversion is required as genes are oriented in opposite directions | ||
| PCM1 | t(8;9)(p22;p24.1) | PCM1-JAK2 on der(9) | YES (SUBTLE) | 28972016 | Seen also in myeloid/lymphoid neoplasms with eosinophilia | ||
| PPFIBP1 | t(9;12)(p24.1;p11.2) | PPFIBP1-JAK2 on der(9) | YES | 28972016 | |||
| RFX3 | inv(9)(p24.1p24.2) | RFX3-JAK2 | NO | 28408464 | An inversion is required as genes are oriented in opposite directions | ||
| SMU1 | inv(9)(p21.1p24.1) | SMU1-JAK2 | NO | 27870571 | An inversion is required as genes are oriented in opposite directions | ||
| SNX29 | t(9;16)(p24.1;p13.1) | SNX29-JAK2 on der(9) | YES | 27870571 | |||
| SPAG9 | t(9;17)(p24.1;q21.3) | SPAG9-JAK2 on der(9) | YES | 25951811 | |||
| SSBP2 | t(5;9)(q14.1;p24.1) | SSBP2-JAK2 on der(9) | YES | 18618714 | |||
| STRN3 | t(9;14)(p24.1;q12) | STRN3-JAK2 on der(9) | YES | 22897847 | |||
| TERF2 | t(9;16)(p24.1;q22.1) | TERF2-JAK2 on der(9) | YES | 29163799 | |||
| TPR | t(1;9)(q31.1;p24.1) | TPR-JAK2 on der(9) | YES | 25207766 | |||
| USP25 | t(9;21)(p24.1;q21.1) | USP25-JAK2 | ? YES | 28408464 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | ||
| ZBTB46 | t(9;20)(p24.1;q13.3) | ZBTB46-JAK2 on der(9) | NO | 28972016 | |||
| ZNF274 | t(9;19)(p24.1;q13.4) | ZNF274-JAK2 | NO | 28408464 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | ||
| ZNF340 | t(9;20)(p24.1;q13.3) | ZNF340-JAK2 on der(9) | NO | 28972016 | |||
| PDGFRA
(4q12) |
FIP1L1 | del(4)(q12q12) | FIP1L1-PDGFRA | NO | 27870571 | Interstitial deletion. Seen also in myeloid/lymphoid neoplasms with eosinophilia | |
| PDGFRB (5q32) | ATF7IP | t(5;12)(q32;p13.1) | ATF7IP-PDGFRB on der(5) | YES | 24628626
26703895 29133777 |
||
| EBF1 | del(5)(q32q33.3) | EBF1-PDGFRB | NO | 26872634 | Interstitial deletion | ||
| ETV6 | t(5;12)(q32;p13.2) | ETV6-PDGFRB on der(5) | YES | 28972016 | |||
| SNX29 | t(5;16)(q32;p13.1) | SNX29-PDGFRB on der(5) | YES | 28972016 | |||
| SSBP2 | t(5;5)(q14.1;q32) | SSBP2-PDGFRB | ? YES | 28972016 | On the same chromosome arm; however, a simple deletion cannot cause the fusion due to the orientation of genes | ||
| TNIP1 | del(5)(q32q33.1) | TNIP1-PDGFRB | NO | 28972016 | Interstitial deletion. Seen also in myeloid/lymphoid neoplasms with eosinophilia | ||
| ZEB2 | t(2;5)(q22.3;q32) | ZEB2-PDGFRB on der(5) | YES | 25207766 | |||
| ZMYND8 | t(5;20)(q32;q13.1) | ZMYND8-PDGFRB on der(5) | YES | 28408464 | |||
| PTK2B (8p21.2) | KDM6A | t(X;8)(p11.3;p21.2) | KDM6A-PTK2B on der(8) | YES | 25207766 | ||
| STAG2 | t(X;8)(q25;p21.2) | STAG2-PTK2B | YES | 25207766 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | ||
| TMEM2 | t(8;9)(p21.2;q21.1) | TMEM2-PTK2B on der(8) | YES | 28972016 | |||
| TYK2 (19p13.2) | MYB | t(6;19)(q23.3;p13.2) | MYB-TYK2 on der(6) | YES | 29296813 | ||
| SMARCA4 | inv(19)(p13.2p13.2) | SMARCA4-TYK2 | NO | 28972016 | |||
| ZNF340 | t(19;20)(p13.2;q13.3) | ZNF340-TYK2 | NO | 28972016 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | ||
| ZNF384-rearranged B-ALL | ZNF384 (12p13.3) | ARID1B | t(6;12)(q25.3;p13.3) | ARID1B-ZNF384 on der(6) | YES (subtle) | 27392123 | |
| BMP2K | t(4;12)(q21.2;p13.3) | BMP2K-ZNF384 on der(4) | YES | 27634205 | |||
| CREBBP | t(12;16)(p13.3;p13.3) | CREBBP-ZNF384 on der(16) | NO | 27428428 27634205 | |||
| EP300 | t(12;22)(p13.3;q13.2) | EP300-ZNF384 on der(22) | NO | 25943178 | |||
| EWSR1 | t(12;22)(p13.3;q12.2) | EWSR1-ZNF384 on der(22) | YES (subtle) | 12359745 | |||
| SMARCA2 | t(9;12)(p24.3;p13.3) | SMARCA2-ZNF384 | No | 27824051 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | ||
| SYNRG | t(12;17)(p13.3;q12) | SYNGR-ZNF384 | YES | 27634205 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | ||
| TAF15 | t(12;17)(p13.3;q12) | TAF15-ZNF384 on der(17) | YES | 21504714 | |||
| TCF3 | t(12;19)(p13.3;p13.3) | TCF3-ZNF384 on der(19) | NO | 27634205 | |||
| MEF2D-rearranged B-ALL | BCL9 | MEF2D (1q22) | inv(1)(q21.2q22) | MEF2D-BCL9 | No | 27507882 27824051 27428428 | |
| CSF1R | t(1;5)(q22;q32) | MEF2D-CSF1R on der(5) | YES | 27824051 | |||
| FOXJ2 | t(1;12)(q22;p13.3) | MEF2D-FOXJ2 on der(12) | YES | 27824051 | |||
| HNRNPH1 | t(1;5)(q22;q35.3) | MEF2D-HNRNPH1 on der(5) | YES | 27824051 | |||
| HNRNPUL1 | t(1;19)(q22;q13.2) | MEF2D-HNRNPUL1 | ? YES | 30171027 | Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms | ||
| SS18 | t(1;18)(q22;q11.2) | MEF2D-SS18 on der(18) | YES | 27824051 27824051 |
Reference
1. Xu X, Bryke C, Sukhanova M, Huxley E, Dash DP, Dixon-Mciver A, Fang M, Griepp PT, Hodge JC, Iqbal A, Jeffries S, Kanagal-Shamanna R, Quintero-Rivera F, Shetty S, Slovak ML, Yenamandra A, Lennon PA, Raca G. (2018). Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group. Cancer Genet [Epub ahead of print], PMID 30344013.