Compendium of Cancer Genome Aberrations

HAEM5:B-lymphoblastic leukaemia/lymphoma with BCR::ABL1-like features: Difference between revisions

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{{DISPLAYTITLE:B-lymphoblastic leukaemia/lymphoma with BCR::ABL1-like features}}
{{DISPLAYTITLE:B-lymphoblastic leukaemia/lymphoma with BCR::ABL1-like features}}
[[HAEM5:Table_of_Contents|Haematolymphoid Tumours (WHO Classification, 5th ed.)]]
[[HAEM5:Table_of_Contents|Haematolymphoid Tumours (WHO Classification, 5th ed.)]]


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==Primary Author(s)*==
==Primary Author(s)*==
Mark G. Evans, MD, University of California, Irvine
Mark G. Evans, MD, Caris Life Sciences


Fabiola Quintero-Rivera, MD, University of California, Irvine
Kilannin Krysiak, PhD, WashU Medicine
 
Sumire K. Kitahara, MD, Cedars-Sinai Medical Center
==WHO Classification of Disease==
==WHO Classification of Disease==


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==Gene Rearrangements==
==Gene Rearrangements==
Table derived from Akkari et al., 2020 <ref>{{Cite journal|last=Akkari|first=Yassmine M. N.|last2=Bruyere|first2=Helene|last3=Hagelstrom|first3=R. Tanner|last4=Kanagal-Shamanna|first4=Rashmi|last5=Liu|first5=Jie|last6=Luo|first6=Minjie|last7=Mikhail|first7=Fady M.|last8=Pitel|first8=Beth A.|last9=Raca|first9=Gordana|date=2020-05|title=Evidence-based review of genomic aberrations in B-lymphoblastic leukemia/lymphoma: Report from the cancer genomics consortium working group for lymphoblastic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/32302940|journal=Cancer Genetics|volume=243|pages=52–72|doi=10.1016/j.cancergen.2020.03.001|issn=2210-7762|pmid=32302940}}</ref> with permission from Cancer Genetics.
{| class="wikitable"
|'''3’ Partner'''
|'''5’ Partner'''
|'''Chromosome rearrangement'''
|'''Gene fusion'''
|'''Visible by G-banding'''
|'''References'''
|'''Comment'''
|-
| rowspan="12" |'''''[[ABL1]]'''''
(9q34)
|''CENPC1''
|t(4;9)(q13;q34)
|''CENPC1-ABL1''
|YES
|<ref name=":2">{{Cite journal|last=Reshmi|first=Shalini C.|last2=Harvey|first2=Richard C.|last3=Roberts|first3=Kathryn G.|last4=Stonerock|first4=Eileen|last5=Smith|first5=Amy|last6=Jenkins|first6=Heather|last7=Chen|first7=I.-Ming|last8=Valentine|first8=Marc|last9=Liu|first9=Yu|date=2017-06-22|title=Targetable kinase gene fusions in high-risk B-ALL: a study from the Children's Oncology Group|url=https://pubmed.ncbi.nlm.nih.gov/28408464|journal=Blood|volume=129|issue=25|pages=3352–3361|doi=10.1182/blood-2016-12-758979|issn=1528-0020|pmc=5482101|pmid=28408464}}</ref>
|Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms
|-
|''[[ETV6]]''
|t(9;12)(q34;p13)
|''ETV6-ABL1''
|NO
|<ref>{{Cite journal|last=Zaliova|first=Marketa|last2=Moorman|first2=Anthony V.|last3=Cazzaniga|first3=Giovanni|last4=Stanulla|first4=Martin|last5=Harvey|first5=Richard C.|last6=Roberts|first6=Kathryn G.|last7=Heatley|first7=Sue L.|last8=Loh|first8=Mignon L.|last9=Konopleva|first9=Marina|date=2016-09|title=Characterization of leukemias with ETV6-ABL1 fusion|url=https://pubmed.ncbi.nlm.nih.gov/27229714|journal=Haematologica|volume=101|issue=9|pages=1082–1093|doi=10.3324/haematol.2016.144345|issn=1592-8721|pmc=5060025|pmid=27229714}}</ref>
|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
|<ref>{{Cite journal|last=Ernst|first=Thomas|last2=Score|first2=Joannah|last3=Deininger|first3=Michael|last4=Hidalgo-Curtis|first4=Claire|last5=Lackie|first5=Peter|last6=Ershler|first6=William B.|last7=Goldman|first7=John M.|last8=Cross|first8=Nicholas C. P.|last9=Grand|first9=Francish|date=2011-04|title=Identification of FOXP1 and SNX2 as novel ABL1 fusion partners in acute lymphoblastic leukaemia|url=https://pubmed.ncbi.nlm.nih.gov/21391972|journal=British Journal of Haematology|volume=153|issue=1|pages=43–46|doi=10.1111/j.1365-2141.2010.08457.x|issn=1365-2141|pmid=21391972}}</ref>
|
|-
|''LSM14A''
|t(9;19)(q34;q13.1)
|''LSM14A-ABL1'' on der(19)
|YES
|<ref name=":2" />
|
|-
|''NUP153''
|t(6;9)(p22.3;q34)
|''NUP153-ABL1'' on der(6)
|YES
|<ref name=":2" />
|
|-
|''[[NUP214]]''
|dup(9)(q34.1q34.1)
|''NUP214-ABL1''
|NO
|<ref>{{Cite journal|last=Duployez|first=Nicolas|last2=Grzych|first2=Guillaume|last3=Ducourneau|first3=Benoît|last4=Alarcon Fuentes|first4=Martin|last5=Grardel|first5=Nathalie|last6=Boyer|first6=Thomas|last7=Abou Chahla|first7=Wadih|last8=Bruno|first8=Bénédicte|last9=Nelken|first9=Brigitte|date=2016-04|title=NUP214-ABL1 fusion defines a rare subtype of B-cell precursor acute lymphoblastic leukemia that could benefit from tyrosine kinase inhibitors|url=https://pubmed.ncbi.nlm.nih.gov/26681761|journal=Haematologica|volume=101|issue=4|pages=e133–134|doi=10.3324/haematol.2015.136499|issn=1592-8721|pmc=5004396|pmid=26681761}}</ref>
|Tandem duplication (~370 kb) detectable by CMA
|-
|''RANBP2''
|t(2;9)(q12.3;q34)
|''RANBP-ABL1'' on der(2)
|YES
|<ref>{{Cite journal|last=Roberts|first=Kathryn G.|last2=Li|first2=Yongjin|last3=Payne-Turner|first3=Debbie|last4=Harvey|first4=Richard C.|last5=Yang|first5=Yung-Li|last6=Pei|first6=Deqing|last7=McCastlain|first7=Kelly|last8=Ding|first8=Li|last9=Lu|first9=Charles|date=2014-09-11|title=Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/25207766|journal=The New England Journal of Medicine|volume=371|issue=11|pages=1005–1015|doi=10.1056/NEJMoa1403088|issn=1533-4406|pmc=4191900|pmid=25207766}}</ref>
|
|-
|''RCSD1''
|t(1;9)(q24.2;q34)
|''RCSD1-ABL1'' on der(1)
|YES
|
|
|-
|''SFPQ''
|t(1;9)(p34.3;q34)
|''SFPQ-ABL1'' on der(1)
|YES
|
|
|-
|''SNX1''
|t(9;15)(q34;q22.3)
|''SNX1-ABL1'' on der(15)
|YES
|
|
|-
|''SNX2''
|t(5;9)(q23.2;q34)
|''SNX2-ABL1'' on der(5)
|YES
|
|
|-
|''ZMIZ1''
|t(9;10)(q34;q22.3)
|''ZMIZ1-ABL1'' on der(10)
|YES
|
|
|-
| rowspan="3" |'''''[[ABL2]]'''''
(1q25.2)
|''PAG1''
|t(1;8)(q25.2;q21.1)
|''PAG1-ABL2'' on der(1)
|YES
|
|
|-
|''RCSD1''
|1q24.2q25.2 rearrangement
|''RCSD1-ABL2''
|NO
|
|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
|
|
|-
| rowspan="2" |'''''[[CRLF2]]'''''
(Xp22.3 & Yp11.3)
|''[[IGH]]''
|t(X;14)(p22.3;q32) or
t(Y;14)(p11.3;q32)
|''IGH/CRLF2''
|NO
|
|
|-
|''P2RY8''
|del(X)(p22.3p22.3) or del(Y)(p11.3p11.3)
|''P2RY8-CRLF2''
|NO
|
|
|-
| rowspan="3" |'''''CSF1R'''''
(5q32)
|''MEF2D''
|t(1;5)(q22;q32)
|''MEF2D-CSF1R'' on der(5)
|YES
|
|
|-
|''SSBP2''
|5q14.1q32 rearrangement
|''SSBP2-CSF1R''
|YES
|
|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
|
|
|-
|'''''DGKH''''' (13q14.1)
|''ZFAND3''
|t(6;13)(p21.2;q14.1)
|''ZFAND3-DGKH''
|YES
|
|Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms
|-
| rowspan="4" |'''''EPOR''''' (19p13.2)
|''[[IGH]]''
|ins(14;19)(q32;p13.2p13.2)
|''IGH/EPOR''
|Cryptic insertion
|
|
|-
|''IGK''
|ins(2;19)(p11.2;p13.2p13.2)
|''IGK/EPOR''
|Cryptic insertion
|
|
|-
|''LAIR1''
|inv(19)(p13.2q13.42)
|''LAIR1-EPOR''
|NO
|
|Inversion of chromosome 19 juxtaposes ''EPOR'' to the upstream region of ''LAIR1''
|-
|''THADA''
|t(2;19)(p21;p13.2)
|''THADA-EPOR''
|YES
|
|
|-
|'''''IL2RB''''' (22q12.3)
|''MYH9''
|22q12.3 rearrangement
|''MYH9-IL2RB''
|NO
|
|On the same chromosome arm; however, a simple deletion cannot cause the fusion due to the orientation of genes
|-
| rowspan="22" |'''''[[JAK2]]'''''
(9p24.1)
|''ATF7IP''
|t(9;12)(p24.1;p13.1)
|''ATF7IP-JAK2'' on der(9)
|NO
|
|
|-
|''[[BCR]]''
|t(9;22)(p24.1;q11.2)
|''BCR-JAK2''
|? YES
|
|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)
|
|
|-
|''[[ETV6]]''
|t(9;12)(p24.1;p13.2)
|''ETV6-JAK2'' on der(9)
|NO (SUBTLE)
|
|
|-
|''GOLGA5''
|t(9;14)(p24.1;q32.1)
|''GOLGA5-JAK2''
|NO (SUBTLE)
|
|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
|
|
|-
|''OFD1''
|t(X;9)(p22.2;p24.1)
|''OFD1-JAK2'' on der(9)
|NO (SUBTLE)
|
|
|-
|''PAX5''
|inv(9)(p13.2p24.1)
|''PAX5-JAK2''
|YES
|
|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)
|
|Seen also in myeloid/lymphoid neoplasms with eosinophilia
|-
|''PPFIBP1''
|t(9;12)(p24.1;p11.2)
|''PPFIBP1-JAK2'' on der(9)
|YES
|
|
|-
|''RFX3''
|inv(9)(p24.1p24.2)
|''RFX3-JAK2''
|NO
|
|An inversion is required as genes are oriented in opposite directions
|-
|''SMU1''
|inv(9)(p21.1p24.1)
|''SMU1-JAK2''
|NO
|
|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
|
|
|-
|''SPAG9''
|t(9;17)(p24.1;q21.3)
|''SPAG9-JAK2'' on der(9)
|YES
|
|
|-
|''SSBP2''
|t(5;9)(q14.1;p24.1)
|''SSBP2-JAK2'' on der(9)
|YES
|
|
|-
|''STRN3''
|t(9;14)(p24.1;q12)
|''STRN3-JAK2'' on der(9)
|YES
|
|
|-
|''TERF2''
|t(9;16)(p24.1;q22.1)
|''TERF2-JAK2'' on der(9)
|YES
|
|
|-
|''TPR''
|t(1;9)(q31.1;p24.1)
|''TPR-JAK2'' on der(9)
|YES
|
|
|-
|''USP25''
|t(9;21)(p24.1;q21.1)
|''USP25-JAK2''
|? YES
|
|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
|
|
|-
|''ZNF274''
|t(9;19)(p24.1;q13.4)
|''ZNF274-JAK2''
|NO
|
|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
|
|
|-
|'''''[[PDGFRA]]'''''
(4q12)
|''FIP1L1''
|del(4)(q12q12)
|''FIP1L1-PDGFRA''
|NO
|
|Interstitial deletion. Seen also in myeloid/lymphoid neoplasms with eosinophilia
|-
| rowspan="8" |'''''[[PDGFRB]]''''' (5q32)
|''ATF7IP''
|t(5;12)(q32;p13.1)
|''ATF7IP-PDGFRB'' on der(5)
|YES
|
|
|-
|''EBF1''
|del(5)(q32q33.3)
|''EBF1-PDGFRB''
|NO
|
|Interstitial deletion
|-
|''[[ETV6]]''
|t(5;12)(q32;p13.2)
|''ETV6-PDGFRB'' on der(5)
|YES
|
|
|-
|''SNX29''
|t(5;16)(q32;p13.1)
|''SNX29-PDGFRB'' on der(5)
|YES
|
|
|-
|''SSBP2''
|t(5;5)(q14.1;q32)
|''SSBP2-PDGFRB''
|? YES
|
|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
|
|Interstitial deletion. Seen also in myeloid/lymphoid neoplasms with eosinophilia
|-
|''ZEB2''
|t(2;5)(q22.3;q32)
|''ZEB2-PDGFRB'' on der(5)
|YES
|
|
|-
|''ZMYND8''
|t(5;20)(q32;q13.1)
|''ZMYND8-PDGFRB'' on der(5)
|YES
|
|
|-
| rowspan="3" |'''''PTK2B''''' (8p21.2)
|''[[KDM6A]]''
|t(X;8)(p11.3;p21.2)
|''KDM6A-PTK2B'' on der(8)
|YES
|
|
|-
|''[[STAG2]]''
|t(X;8)(q25;p21.2)
|''STAG2-PTK2B''
|YES
|
|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
|
|
|-
| rowspan="3" |'''''TYK2''''' (19p13.2)
|''MYB''
|t(6;19)(q23.3;p13.2)
|''MYB-TYK2'' on der(6)
|YES
|
|
|-
|''SMARCA4''
|inv(19)(p13.2p13.2)
|''SMARCA4-TYK2''
|NO
|
|
|-
|''ZNF340''
|t(19;20)(p13.2;q13.3)
|''ZNF340-TYK2''
|NO
|
|Requires complex rearrangement due to incompatible orientation of genes with respect to chromosome arms
|}




Line 112: Line 586:
Tyrosine kinase-type translocations are common and involve ''ABL1'' and other kinases (such as ''ABL2'', ''EPOR'', ''JAK2'', ''PDGFRB'', and ''CSF1R''); more than 30 gene partners have been described. Frequently reported examples include ''IGH''–''EPOR'' of the t(14;19)(q32;p13)/ins(14;19)(q32;p13), ''EBF1''–''PDGFRB'' of the del(5)(q32q33.3), ''NUP214''–''ABL1'' of the t(9;9)(q34;q34)/del(9)(q34q34), and ''ETV6''–''ABL1'' of the t(9;12)(q34;p13). Other notable fusions are ''BCR''–''JAK2'', ''PAX5''–''JAK2'', ''STRN3''–''JAK2'', ''RANBP2''–''ABL1'', ''RCSD1''–''ABL1'', and ''MEF2D''–''CSF1R''<ref>Heim S & Mitelman F. Cancer Cytogenetics: Chromosomal and Molecular Genetic Aberrations of Tumor Cells. John Wiley & Sons, Incorporated: Chichester, United Kingdom. 2015.</ref>.
Tyrosine kinase-type translocations are common and involve ''ABL1'' and other kinases (such as ''ABL2'', ''EPOR'', ''JAK2'', ''PDGFRB'', and ''CSF1R''); more than 30 gene partners have been described. Frequently reported examples include ''IGH''–''EPOR'' of the t(14;19)(q32;p13)/ins(14;19)(q32;p13), ''EBF1''–''PDGFRB'' of the del(5)(q32q33.3), ''NUP214''–''ABL1'' of the t(9;9)(q34;q34)/del(9)(q34q34), and ''ETV6''–''ABL1'' of the t(9;12)(q34;p13). Other notable fusions are ''BCR''–''JAK2'', ''PAX5''–''JAK2'', ''STRN3''–''JAK2'', ''RANBP2''–''ABL1'', ''RCSD1''–''ABL1'', and ''MEF2D''–''CSF1R''<ref>Heim S & Mitelman F. Cancer Cytogenetics: Chromosomal and Molecular Genetic Aberrations of Tumor Cells. John Wiley & Sons, Incorporated: Chichester, United Kingdom. 2015.</ref>.


<blockquote class="blockedit">
<blockquote class="blockedit"><center><span style="color:Maroon">'''End of V4 Section'''</span>
<center><span style="color:Maroon">'''End of V4 Section'''</span>
----
----
</blockquote>
</blockquote>
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[[File:FISH 1.jpg|thumb|none]]
[[File:FISH 1.jpg|thumb|none]]


[[File:FISH 2.jpg|thumb|none]]
[[File:FISH 2.jpg|thumb|none|link=Special:FilePath/FISH_2.jpg]]


[Abnormal FISH results in interphase nuclei from a bone marrow sample using the ''CRLF2'' dual-color, break-apart (Cytocell) and ''IGH'' dual-color, break-apart probes, reflective of ''IGH''-''CRLF2'' fusion]
[Abnormal FISH results in interphase nuclei from a bone marrow sample using the ''CRLF2'' dual-color, break-apart (Cytocell) and ''IGH'' dual-color, break-apart probes, reflective of ''IGH''-''CRLF2'' fusion]
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