Compendium of Cancer Genome Aberrations

HAEM5:Extranodal NK/T-cell lymphoma: Difference between revisions

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Amanda Xu, MD/MSc, Queen's University  
Amanda Xu, MD/MSc, Queen's University  
Put your text here<span style="color:#0070C0"> (''Name and affiliation; example:'' Jane Smith, PhD, Institute of Genomics) </span>


__TOC__
__TOC__
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==Chromosomal Rearrangements (Gene Fusions)==
==Chromosomal Rearrangements (Gene Fusions)==


Put your text here and fill in the table
No specific chromosomal translocation has been identified in ENKTL.


{| class="wikitable sortable"
{| class="wikitable sortable"
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!Notes
!Notes
|-
|-
|EXAMPLE t(9;22)(q34;q11.2)||EXAMPLE 3'ABL1 / 5'BCR||EXAMPLE der(22)||EXAMPLE 20% (COSMIC)
|N/A||N/A||N/A||N/A
EXAMPLE 30% (add reference)
|N/A
|Yes
|N/A
|No
|N/A
|Yes
|N/A
|EXAMPLE
 
The t(9;22) is diagnostic of CML in the appropriate morphology and clinical context (add reference). This fusion is responsive to targeted therapy such as Imatinib (Gleevec) (add reference).
|}
|}
==Individual Region Genomic Gain / Loss / LOH==
==Individual Region Genomic Gain / Loss / LOH==
ENKTL shows recurring deletion at 6q21-25<ref>{{Cite journal|last=Wong|first=K. F.|last2=Chan|first2=J. K.|last3=Kwong|first3=Y. L.|date=1997-09|title=Identification of del(6)(q21q25) as a recurring chromosomal abnormality in putative NK cell lymphoma/leukaemia|url=https://pubmed.ncbi.nlm.nih.gov/9326190|journal=British Journal of Haematology|volume=98|issue=4|pages=922–926|doi=10.1046/j.1365-2141.1997.3223139.x|issn=0007-1048|pmid=9326190}}</ref><ref>{{Cite journal|last=Ohshima|first=Koichi|last2=Haraokaa|first2=Seiji|last3=Ishihara|first3=Shigehiko|last4=Ohgami|first4=Akiko|last5=Yoshioka|first5=Shingo|last6=Suzumiya|first6=Junji|last7=Kikuchi|first7=Masahiro|date=2002-02|title=Analysis of chromosome 6q deletion in EBV-associated NK cell leukaemia/lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/11999560|journal=Leukemia & Lymphoma|volume=43|issue=2|pages=293–300|doi=10.1080/10428190290006062|issn=1042-8194|pmid=11999560}}</ref>.
Other less common chromosomal alterations include gain of 1p, 2q, 6p, 10q, 11q, 12q, 13q, 17q, 19p, 20q, and Xp; and loss of 1p36, 2p16, 4q12, 4q31-32, 5p14, 5q34-35, 6q13-14, 6q16-27, 11q22-23, 12q, 13q12-14, 13q14-34, 17p13, and entire chromosome X<ref>{{Cite journal|last=Nakashima|first=Yasuhiro|last2=Tagawa|first2=Hiroyuki|last3=Suzuki|first3=Ritsuro|last4=Karnan|first4=Sivasundaram|last5=Karube|first5=Kennosuke|last6=Ohshima|first6=Koichi|last7=Muta|first7=Koichiro|last8=Nawata|first8=Hajime|last9=Morishima|first9=Yasuo|date=2005-11|title=Genome-wide array-based comparative genomic hybridization of natural killer cell lymphoma/leukemia: different genomic alteration patterns of aggressive NK-cell leukemia and extranodal Nk/T-cell lymphoma, nasal type|url=https://pubmed.ncbi.nlm.nih.gov/16049916|journal=Genes, Chromosomes & Cancer|volume=44|issue=3|pages=247–255|doi=10.1002/gcc.20245|issn=1045-2257|pmid=16049916}}</ref><ref>{{Cite journal|last=Siu|first=L. L.|last2=Chan|first2=V.|last3=Chan|first3=J. K.|last4=Wong|first4=K. F.|last5=Liang|first5=R.|last6=Kwong|first6=Y. L.|date=2000-12|title=Consistent patterns of allelic loss in natural killer cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/11106552|journal=The American Journal of Pathology|volume=157|issue=6|pages=1803–1809|doi=10.1016/S0002-9440(10)64818-3|issn=0002-9440|pmc=1885756|pmid=11106552}}</ref><ref>{{Cite journal|last=Siu|first=L. L.|last2=Wong|first2=K. F.|last3=Chan|first3=J. K.|last4=Kwong|first4=Y. L.|date=1999-11|title=Comparative genomic hybridization analysis of natural killer cell lymphoma/leukemia. Recognition of consistent patterns of genetic alterations|url=https://pubmed.ncbi.nlm.nih.gov/10550295|journal=The American Journal of Pathology|volume=155|issue=5|pages=1419–1425|doi=10.1016/S0002-9440(10)65454-5|issn=0002-9440|pmc=1866965|pmid=10550295}}</ref><ref>{{Cite journal|last=Wong|first=K. F.|last2=Zhang|first2=Y. M.|last3=Chan|first3=J. K.|date=1999-07|title=Cytogenetic abnormalities in natural killer cell lymphoma/leukaemia--is there a consistent pattern?|url=https://pubmed.ncbi.nlm.nih.gov/10439361|journal=Leukemia & Lymphoma|volume=34|issue=3-4|pages=241–250|doi=10.3109/10428199909050949|issn=1042-8194|pmid=10439361}}</ref><ref>{{Cite journal|last=Ko|first=Y. H.|last2=Choi|first2=K. E.|last3=Han|first3=J. H.|last4=Kim|first4=J. M.|last5=Ree|first5=H. J.|date=2001-04-15|title=Comparative genomic hybridization study of nasal-type NK/T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/11309817|journal=Cytometry|volume=46|issue=2|pages=85–91|doi=10.1002/cyto.1069|issn=0196-4763|pmid=11309817}}</ref>.


Put your text here and fill in the table <span style="color:#0070C0">(''Instructions: Includes aberrations not involving gene fusions. Can include references in the table. Can refer to CGC workgroup tables as linked on the homepage if applicable.'') </span>
Put your text here and fill in the table <span style="color:#0070C0">(''Instructions: Includes aberrations not involving gene fusions. Can include references in the table. Can refer to CGC workgroup tables as linked on the homepage if applicable.'') </span>
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!Notes
!Notes
|-
|-
|EXAMPLE
|6
 
|Loss
7
|
|EXAMPLE Loss
|6q21-25
|EXAMPLE
|Unknown
 
|Unknown
chr7:1- 159,335,973 [hg38]
|Unknown
|EXAMPLE
|This locus harbours multiple candidate tumour suppressor genes including ''ATG5'', ''AIM1'', ''PRDM1'', ''PTPRK'', ''HACE1'', and ''FOXO3''<ref>{{Cite journal|last=Iqbal|first=J.|last2=Kucuk|first2=C.|last3=Deleeuw|first3=R. J.|last4=Srivastava|first4=G.|last5=Tam|first5=W.|last6=Geng|first6=H.|last7=Klinkebiel|first7=D.|last8=Christman|first8=J. K.|last9=Patel|first9=K.|date=2009-06|title=Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies|url=https://pubmed.ncbi.nlm.nih.gov/19194464|journal=Leukemia|volume=23|issue=6|pages=1139–1151|doi=10.1038/leu.2009.3|issn=1476-5551|pmid=19194464}}</ref><ref>{{Cite journal|last=Karube|first=Kennosuke|last2=Nakagawa|first2=Masao|last3=Tsuzuki|first3=Shinobu|last4=Takeuchi|first4=Ichiro|last5=Honma|first5=Keiichiro|last6=Nakashima|first6=Yasuhiro|last7=Shimizu|first7=Norio|last8=Ko|first8=Young-Hyeh|last9=Morishima|first9=Yasuo|date=2011-09-22|title=Identification of FOXO3 and PRDM1 as tumor-suppressor gene candidates in NK-cell neoplasms by genomic and functional analyses|url=https://pubmed.ncbi.nlm.nih.gov/21690554|journal=Blood|volume=118|issue=12|pages=3195–3204|doi=10.1182/blood-2011-04-346890|issn=1528-0020|pmid=21690554}}</ref><ref>{{Cite journal|last=Chen|first=Yun-Wen|last2=Guo|first2=Tianhuan|last3=Shen|first3=Lijun|last4=Wong|first4=Kai-Yau|last5=Tao|first5=Qian|last6=Choi|first6=William W. L.|last7=Au-Yeung|first7=Rex K. H.|last8=Chan|first8=Yuen-Piu|last9=Wong|first9=Michelle L. Y.|date=2015-03-05|title=Receptor-type tyrosine-protein phosphatase κ directly targets STAT3 activation for tumor suppression in nasal NK/T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/25612622|journal=Blood|volume=125|issue=10|pages=1589–1600|doi=10.1182/blood-2014-07-588970|issn=1528-0020|pmid=25612622}}</ref>.
 
chr7
|Yes
|Yes
|No
|EXAMPLE
 
Presence of monosomy 7 (or 7q deletion) is sufficient for a diagnosis of AML with MDS-related changes when there is ≥20% blasts and no prior therapy (add reference).  Monosomy 7/7q deletion is associated with a poor prognosis in AML (add reference).
|-
|-
|EXAMPLE
|EXAMPLE
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==Characteristic Chromosomal Patterns==
==Characteristic Chromosomal Patterns==


Put your text here <span style="color:#0070C0">(''EXAMPLE PATTERNS: hyperdiploid; gain of odd number chromosomes including typically chromosome 1, 3, 5, 7, 11, and 17; co-deletion of 1p and 19q; complex karyotypes without characteristic genetic findings; chromothripsis'')</span>
No characteristic chromosomal patterns have been identified in ENKTL.


{| class="wikitable sortable"
{| class="wikitable sortable"
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!Notes
!Notes
|-
|-
|EXAMPLE
|N/A
 
|N/A
Co-deletion of 1p and 18q
|N/A
|Yes
|N/A
|No
|N/A
|No
|EXAMPLE:
 
See chromosomal rearrangements table as this pattern is due to an unbalanced derivative translocation associated with oligodendroglioma (add reference).
|}
|}
==Gene Mutations (SNV / INDEL)==
==Gene Mutations (SNV / INDEL)==
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!Therapeutic Significance (Yes, No or Unknown)
!Therapeutic Significance (Yes, No or Unknown)
!Notes
!Notes
|-
|''JAK3''<ref>{{Cite journal|last=Koo|first=Ghee Chong|last2=Tan|first2=Soo Yong|last3=Tang|first3=Tiffany|last4=Poon|first4=Song Ling|last5=Allen|first5=George E.|last6=Tan|first6=Leonard|last7=Chong|first7=Soo Ching|last8=Ong|first8=Whee Sze|last9=Tay|first9=Kevin|date=2012-07|title=Janus kinase 3-activating mutations identified in natural killer/T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/22705984|journal=Cancer Discovery|volume=2|issue=7|pages=591–597|doi=10.1158/2159-8290.CD-12-0028|issn=2159-8290|pmid=22705984}}</ref>
|
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|EXAMPLE: TP53; Variable LOF mutations
|EXAMPLE: TP53; Variable LOF mutations
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