Compendium of Cancer Genome Aberrations

HAEM5:Subcutaneous panniculitis-like T-cell lymphoma: Difference between revisions

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!Established Clinical Significance Per Guidelines - Yes or No (Source)
!Established Clinical Significance Per Guidelines - Yes or No (Source)
!Clinical Relevance Details/Other Notes
!Clinical Relevance Details/Other Notes
|-
|<span class="blue-text">EXAMPLE:</span> ''ABL1''
|<span class="blue-text">EXAMPLE:</span> N/A
|<span class="blue-text">EXAMPLE:</span> Intragenic deletion of exons 2–7 in ''EGFR'' removes the ligand-binding domain, resulting in a constitutively active tyrosine kinase with downstream activation of multiple oncogenic pathways.
|<span class="blue-text">EXAMPLE:</span> N/A
|<span class="blue-text">EXAMPLE:</span> Recurrent (IDH-wildtype Glioblastoma)
|<span class="blue-text">EXAMPLE:</span> D, P, T
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!Established Clinical Significance Per Guidelines - Yes or No (Source)
!Established Clinical Significance Per Guidelines - Yes or No (Source)
!Clinical Relevance Details/Other Notes
!Clinical Relevance Details/Other Notes
|-
|<span class="blue-text">EXAMPLE:</span>
17
|<span class="blue-text">EXAMPLE:</span> Amp
|<span class="blue-text">EXAMPLE:</span>
17q12; chr17:39,700,064-39,728,658 [hg38; 28.6 kb]
|<span class="blue-text">EXAMPLE:</span>
''ERBB2''
|<span class="blue-text">EXAMPLE:</span> D, P, T
|
|<span class="blue-text">EXAMPLE:</span>
Amplification of ''ERBB2'' is associated with HER2 overexpression in HER2 positive breast cancer (add references). Add criteria for how amplification is defined.
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|Tumor suppressor
|Tumor suppressor
|Common >20%, <ref name=":0">{{Cite journal|last=Polprasert|first=Chantana|last2=Takeuchi|first2=Yasuhide|last3=Kakiuchi|first3=Nobuyuki|last4=Yoshida|first4=Kenichi|last5=Assanasen|first5=Thamathorn|last6=Sitthi|first6=Wimonmas|last7=Bunworasate|first7=Udomsak|last8=Pirunsarn|first8=Arunrat|last9=Wudhikarn|first9=Kitsada|date=2019-02-26|title=Frequent germline mutations of HAVCR2 in sporadic subcutaneous panniculitis-like T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/30792187|journal=Blood Advances|volume=3|issue=4|pages=588–595|doi=10.1182/bloodadvances.2018028340|issn=2473-9537|pmc=6391671|pmid=30792187}}</ref><ref name=":1" />
|Common >20%, <ref name=":0">{{Cite journal|last=Polprasert|first=Chantana|last2=Takeuchi|first2=Yasuhide|last3=Kakiuchi|first3=Nobuyuki|last4=Yoshida|first4=Kenichi|last5=Assanasen|first5=Thamathorn|last6=Sitthi|first6=Wimonmas|last7=Bunworasate|first7=Udomsak|last8=Pirunsarn|first8=Arunrat|last9=Wudhikarn|first9=Kitsada|date=2019-02-26|title=Frequent germline mutations of HAVCR2 in sporadic subcutaneous panniculitis-like T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/30792187|journal=Blood Advances|volume=3|issue=4|pages=588–595|doi=10.1182/bloodadvances.2018028340|issn=2473-9537|pmc=6391671|pmid=30792187}}</ref><ref name=":1" />
|None
|May have prognostic and therapeutic significance in patients presenting with hemophagocytic syndromes.<ref>{{Cite journal|last=Sonigo|first=Gabrielle|last2=Battistella|first2=Maxime|last3=Beylot-Barry|first3=Marie|last4=Ingen-Housz-Oro|first4=Saskia|last5=Franck|first5=Nathalie|last6=Barete|first6=Stéphane|last7=Boulinguez|first7=Serge|last8=Dereure|first8=Olivier|last9=Bonnet|first9=Nathalie|date=2020-03-26|title=HAVCR2 mutations are associated with severe hemophagocytic syndrome in subcutaneous panniculitis-like T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/32005988|journal=Blood|volume=135|issue=13|pages=1058–1061|doi=10.1182/blood.2019003811|issn=1528-0020|pmid=32005988}}</ref>
|No
|No
|More common in East Asian populations, with more than 85% of cases are associated with a homozygous or compound heterozygous germline pathogenic variants. In particular, p.Y82C, p.I97M, p.T101I.<ref name=":1" /><ref name=":0" />
|Homozygous p.Y82C pathogenic variant is more common in East Asian populations<ref name=":1" /><ref name=":0" />, with p.T101I being a variant in South Asian (Thai) populations<ref name=":0" />, and  p.I97M being more common in European and North African populations.<ref name=":1" /><ref name=":0" />
|}Note: A more extensive list of mutations can be found in [https://www.cbioportal.org/ <u>cBioportal</u>], [https://cancer.sanger.ac.uk/cosmic <u>COSMIC</u>], and/or other databases. When applicable, gene-specific pages within the CCGA site directly link to pertinent external content.
|}Note: A more extensive list of mutations can be found in [https://www.cbioportal.org/ <u>cBioportal</u>], [https://cancer.sanger.ac.uk/cosmic <u>COSMIC</u>], and/or other databases. When applicable, gene-specific pages within the CCGA site directly link to pertinent external content.
==Epigenomic Alterations==
==Epigenomic Alterations==
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!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome
!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome
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|-
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|ARID1B, SMARCA4, NCOR1, KMT2C, KMT2D, DOTIL, CHD3, CHD4, PBRM1, CREBBP, ASXL1, MBD1, KMT2B, HIST1H3J
|Epigenetic modifiers
|Epigenetic modifiers<ref name=":2" />
|
|Unregulated cell division
|-
|-
|<span class="blue-text">EXAMPLE:</span> ''BRAF'' and ''MAP2K1''; Activating mutations
|TSC1, MTOR, PIK3CB, PIK3CA, PIK3CD, TSC2, AKT2
|PI3K/AKT/mTOR pathway<ref>{{Cite journal|last=Li|first=Zhaoming|last2=Lu|first2=Lisha|last3=Zhou|first3=Zhiyuan|last4=Xue|first4=Weili|last5=Wang|first5=Yingjun|last6=Jin|first6=Mengyuan|last7=Qiu|first7=Yajuan|last8=Sun|first8=Wei|last9=Fu|first9=Xuefei|date=2018-05|title=Recurrent mutations in epigenetic modifiers and the PI3K/AKT/mTOR pathway in subcutaneous panniculitis-like T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/28294301|journal=British Journal of Haematology|volume=181|issue=3|pages=406–410|doi=10.1111/bjh.14611|issn=1365-2141|pmid=28294301}}</ref>
|PI3K/AKT/mTOR pathway<ref name=":2">{{Cite journal|last=Li|first=Zhaoming|last2=Lu|first2=Lisha|last3=Zhou|first3=Zhiyuan|last4=Xue|first4=Weili|last5=Wang|first5=Yingjun|last6=Jin|first6=Mengyuan|last7=Qiu|first7=Yajuan|last8=Sun|first8=Wei|last9=Fu|first9=Xuefei|date=2018-05|title=Recurrent mutations in epigenetic modifiers and the PI3K/AKT/mTOR pathway in subcutaneous panniculitis-like T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/28294301|journal=British Journal of Haematology|volume=181|issue=3|pages=406–410|doi=10.1111/bjh.14611|issn=1365-2141|pmid=28294301}}</ref>
|<span class="blue-text">EXAMPLE:</span> Increased cell growth and proliferation
|Increased cell growth and proliferation
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|-
|<span class="blue-text">EXAMPLE:</span> ''CDKN2A''; Inactivating mutations
|''IL7R, JAK3, STAT3''
|JAK3/STAT pathway
|JAK3/STAT pathway<ref name=":2" />
|<span class="blue-text">EXAMPLE:</span> Unregulated cell division
|Unregulated cell division
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|TP53 and NAV3; loss of tumor suppression
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|TP53
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|Increased cell growth and proliferation
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