B-ALL Tables: Prognostic Genomic Abnormalities and Recurrent Gene Fusions

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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.