Compendium of Cancer Genome Aberrations

HAEM5:B-lymphoblastic leukaemia/lymphoma with high hyperdiploidy: Difference between revisions

(View all pending changes)
[pending revision][pending revision]
← Older editNewer edit →
VisualWikitext
Line 48: Line 48:
==Gene Rearrangements==
==Gene Rearrangements==


Although no recurrent gene fusions or rearrangements a typically found, a study found reciprocal translocations involving the ''IGK'' locus in 2 cases <ref>{{Cite journal|last=Paulsson|first=Kajsa|last2=Lilljebjörn|first2=Henrik|last3=Biloglav|first3=Andrea|last4=Olsson|first4=Linda|last5=Rissler|first5=Marianne|last6=Castor|first6=Anders|last7=Barbany|first7=Gisela|last8=Fogelstrand|first8=Linda|last9=Nordgren|first9=Ann|date=2015-06|title=The genomic landscape of high hyperdiploid childhood acute lymphoblastic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/25961940|journal=Nature Genetics|volume=47|issue=6|pages=672–676|doi=10.1038/ng.3301|issn=1546-1718|pmid=25961940}}</ref>.
Although no recurrent gene fusions or rearrangements a typically found, a study found reciprocal translocations involving the ''IGK'' locus in 2 cases <ref name=":2">{{Cite journal|last=Paulsson|first=Kajsa|last2=Lilljebjörn|first2=Henrik|last3=Biloglav|first3=Andrea|last4=Olsson|first4=Linda|last5=Rissler|first5=Marianne|last6=Castor|first6=Anders|last7=Barbany|first7=Gisela|last8=Fogelstrand|first8=Linda|last9=Nordgren|first9=Ann|date=2015-06|title=The genomic landscape of high hyperdiploid childhood acute lymphoblastic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/25961940|journal=Nature Genetics|volume=47|issue=6|pages=672–676|doi=10.1038/ng.3301|issn=1546-1718|pmid=25961940}}</ref>.


Put your text here and fill in the table <span style="color:#0070C0">(''Instructions: Details on clinical significance such as prognosis and other important information can be provided in the notes section. Please include references throughout the table. Do not delete the table.'')</span>
Put your text here and fill in the table <span style="color:#0070C0">(''Instructions: Details on clinical significance such as prognosis and other important information can be provided in the notes section. Please include references throughout the table. Do not delete the table.'')</span>
Line 117: Line 117:
|No established significance.
|No established significance.
|No
|No
|
|N/A
|-
|-
|6
|6
Line 125: Line 125:
|No established significance.
|No established significance.
|No
|No
|
|N/A
|-
|-
|14
|14
Line 133: Line 133:
|No established significance.
|No established significance.
|No
|No
|
|N/A
|-
|-
|18
|18
Line 141: Line 141:
|Prognostic significance: has been correlated with a lower risk of relapse<ref name=":1">{{Cite journal|last=Moorman|first=Anthony V.|last2=Ensor|first2=Hannah M.|last3=Richards|first3=Sue M.|last4=Chilton|first4=Lucy|last5=Schwab|first5=Claire|last6=Kinsey|first6=Sally E.|last7=Vora|first7=Ajay|last8=Mitchell|first8=Chris D.|last9=Harrison|first9=Christine J.|date=2010-05|title=Prognostic effect of chromosomal abnormalities in childhood B-cell precursor acute lymphoblastic leukaemia: results from the UK Medical Research Council ALL97/99 randomised trial|url=https://pubmed.ncbi.nlm.nih.gov/20409752|journal=The Lancet. Oncology|volume=11|issue=5|pages=429–438|doi=10.1016/S1470-2045(10)70066-8|issn=1474-5488|pmid=20409752}}</ref>.
|Prognostic significance: has been correlated with a lower risk of relapse<ref name=":1">{{Cite journal|last=Moorman|first=Anthony V.|last2=Ensor|first2=Hannah M.|last3=Richards|first3=Sue M.|last4=Chilton|first4=Lucy|last5=Schwab|first5=Claire|last6=Kinsey|first6=Sally E.|last7=Vora|first7=Ajay|last8=Mitchell|first8=Chris D.|last9=Harrison|first9=Christine J.|date=2010-05|title=Prognostic effect of chromosomal abnormalities in childhood B-cell precursor acute lymphoblastic leukaemia: results from the UK Medical Research Council ALL97/99 randomised trial|url=https://pubmed.ncbi.nlm.nih.gov/20409752|journal=The Lancet. Oncology|volume=11|issue=5|pages=429–438|doi=10.1016/S1470-2045(10)70066-8|issn=1474-5488|pmid=20409752}}</ref>.
|No
|No
|
|N/A
|-
|-
|4
|4
Line 149: Line 149:
|The prognostic impact of the “triple trisomies”, i.e., concurrent rent +4, +10, and +17, is debated; they have been reported to be associated with low risk by the Children’s Oncology Group (COG) but not in UK trials<ref name=":1" /><ref>{{Cite journal|last=Schultz|first=Kirk R.|last2=Pullen|first2=D. Jeanette|last3=Sather|first3=Harland N.|last4=Shuster|first4=Jonathan J.|last5=Devidas|first5=Meenakshi|last6=Borowitz|first6=Michael J.|last7=Carroll|first7=Andrew J.|last8=Heerema|first8=Nyla A.|last9=Rubnitz|first9=Jeffrey E.|date=2007-02-01|title=Risk- and response-based classification of childhood B-precursor acute lymphoblastic leukemia: a combined analysis of prognostic markers from the Pediatric Oncology Group (POG) and Children's Cancer Group (CCG)|url=https://pubmed.ncbi.nlm.nih.gov/17003380|journal=Blood|volume=109|issue=3|pages=926–935|doi=10.1182/blood-2006-01-024729|issn=0006-4971|pmc=1785141|pmid=17003380}}</ref>.
|The prognostic impact of the “triple trisomies”, i.e., concurrent rent +4, +10, and +17, is debated; they have been reported to be associated with low risk by the Children’s Oncology Group (COG) but not in UK trials<ref name=":1" /><ref>{{Cite journal|last=Schultz|first=Kirk R.|last2=Pullen|first2=D. Jeanette|last3=Sather|first3=Harland N.|last4=Shuster|first4=Jonathan J.|last5=Devidas|first5=Meenakshi|last6=Borowitz|first6=Michael J.|last7=Carroll|first7=Andrew J.|last8=Heerema|first8=Nyla A.|last9=Rubnitz|first9=Jeffrey E.|date=2007-02-01|title=Risk- and response-based classification of childhood B-precursor acute lymphoblastic leukemia: a combined analysis of prognostic markers from the Pediatric Oncology Group (POG) and Children's Cancer Group (CCG)|url=https://pubmed.ncbi.nlm.nih.gov/17003380|journal=Blood|volume=109|issue=3|pages=926–935|doi=10.1182/blood-2006-01-024729|issn=0006-4971|pmc=1785141|pmid=17003380}}</ref>.
|No
|No
|
|N/A
|-
|-
|17
|17
Line 157: Line 157:
|''See prognosis section for +4 above.''
|''See prognosis section for +4 above.''
|No
|No
|
|N/A
|-
|-
|10
|10
Line 165: Line 165:
|''See prognosis section for +4 above.''
|''See prognosis section for +4 above.''
|No
|No
|
|N/A
|-
|-
|8
|8
Line 173: Line 173:
|No established significance.
|No established significance.
|No
|No
|
|N/A
|}
|}


Line 216: Line 216:
!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>
Co-deletion of 1p and 18q
|<span class="blue-text">EXAMPLE:</span> See chromosomal rearrangements table as this pattern is due to an unbalanced derivative translocation associated with oligodendroglioma (add reference).
|<span class="blue-text">EXAMPLE:</span> Common (Oligodendroglioma)
|<span class="blue-text">EXAMPLE:</span> D, P
|
|
|-
|<span class="blue-text">EXAMPLE:</span>
Microsatellite instability - hypermutated
|
|<span class="blue-text">EXAMPLE:</span> Common (Endometrial carcinoma)
|<span class="blue-text">EXAMPLE:</span> P, T
|
|
|-
|-
|Hyperdiploid
|Hyperdiploid
|
|Although pathogenetic mechanisms are poorly understood, chromosomal gains are early events in the pathogenesis of B-ALL/LBL with high hyperdiploidy and are the main driver<ref>WHO Classification of Tumours: Haematolymphoid Tumours [Internet; Beta Version Ahead of Print]
|
 
|
(5th ed.), International Agency for Research on Cancer (2022)
|
 
<nowiki>https://tumourclassification.iarc.who.int/chapters/63</nowiki></ref>.
|Common
|B-ALL/LBL with high-hyperdiploidy has a very favorable prognosis, with long-term overall survival in > 90% of children
|No
|
|
|}
|}
Line 266: Line 254:


<br />
<br />
|<span class="blue-text">EXAMPLE:</span> Exon 18-21 activating mutations
|Nonsynonymous single nucleotide variant (SNV)
|Oncogene
|Oncogene
|Common
|Common
|No
|No
|<span class="blue-text">EXAMPLE:</span> Yes (NCCN)
|No
|<span class="blue-text">EXAMPLE:</span> Exons 18, 19, and 21 mutations are targetable for therapy. Exon 20 T790M variants cause resistance to first generation TKI therapy and are targetable by second and third generation TKIs (add references).
|<span class="blue-text">EXAMPLE:</span> Exons 18, 19, and 21 mutations are targetable for therapy. Exon 20 T790M variants cause resistance to first generation TKI therapy and are targetable by second and third generation TKIs (add references).
|-
|-
|''NRAS''
|''NRAS''
<br />
<br />
|<span class="blue-text">EXAMPLE:</span> Variable LOF mutations
|Nonsynonymous SNV
|Oncogene
|Oncogene
|<span class="blue-text">EXAMPLE:</span> Common (breast cancer)
|Recurrent
|No
|No
|No
|
|<span class="blue-text">EXAMPLE:</span> >90% are somatic; rare germline alterations associated with Li-Fraumeni syndrome (add reference). Denotes a poor prognosis in breast cancer.
|<span class="blue-text">EXAMPLE:</span> >90% are somatic; rare germline alterations associated with Li-Fraumeni syndrome (add reference). Denotes a poor prognosis in breast cancer.
|-
|-
|''FLT3''
|''FLT3''
|<span class="blue-text">EXAMPLE:</span> Activating mutations
|Nonsynonymous SNV, nonframeshift insertion, nonframeshift deletion, nonframeshift substitution
|Tyrosine kinase receptor
|Tyrosine kinase receptor
|<span class="blue-text">EXAMPLE:</span> Common (melanoma)
|Recurrent
|No
|No
|No
|
|
|
|-
|-
|''PTPN11''
|''PTPN11''
|
|Nonsynonymous SNV
|Protein tyrosine phosphatase
|Protein tyrosine phosphatase
|
|Recurrent
|No
|No
|No
|
|
|
|-
|-
|''CREBBP''
|''CREBBP''
|
|Nonsynonymous SNV, frameshift insertion, splice site
|Histone acetyltransferase
|Histone acetyltransferase
|
|Recurrent
|No
|No
|No
|
|
|
|-
|-
|''WHSC1''
|''WHSC1''
|
|Nonsynonymous SNV
|Histone methyltransferase
|Histone methyltransferase
|
|Recurrent
|No
|No
|No
|
|
|
|-
|-
|''SUV420H1''
|''SUV420H1''
|
|Nonsynonymous SNV
|Histone methyltransferase
|Histone methyltransferase
|
|Rare
|No
|No
|No
|
|
|
|-
|-
|''SETD2''
|''SETD2''
|
|Frameshift insertion
|Histone methyltransferase
|Histone methyltransferase
|
|Rare
|No
|No
|No
|
|
|
|-
|-
|''EZH2''
|''EZH2''
|
|Nonsynonymous SNV
|Histone methyltransferase
|Histone methyltransferase
|
|Rarre
|No
|No
|No
|
|
|
|}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.
Line 350: Line 338:
!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome
!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome
|-
|-
|<span class="blue-text">EXAMPLE:</span> ''BRAF'' and ''MAP2K1''; Activating mutations
|''FLT3, NRAS, KRAS'' and ''PTPN11''<ref name=":2" />; Activating mutations
|<span class="blue-text">EXAMPLE:</span> MAPK signaling
|Receptor tyrosine kinase (RTK)-RAS signaling
|<span class="blue-text">EXAMPLE:</span> Increased cell growth and proliferation
|Increased proliferation, differentiation, and survival
|-
|<span class="blue-text">EXAMPLE:</span> ''CDKN2A''; Inactivating mutations
|<span class="blue-text">EXAMPLE:</span> Cell cycle regulation
|<span class="blue-text">EXAMPLE:</span> Unregulated cell division
|-
|<span class="blue-text">EXAMPLE:</span> ''KMT2C'' and ''ARID1A''; Inactivating mutations
|<span class="blue-text">EXAMPLE:</span> Histone modification, chromatin remodeling
|<span class="blue-text">EXAMPLE:</span> Abnormal gene expression program
|-
|
|
|
|}
|}
==Genetic Diagnostic Testing Methods==
==Genetic Diagnostic Testing Methods==
Retrieved from "https://test.ccga.io/index.php/HAEM5:B-lymphoblastic_leukaemia/lymphoma_with_high_hyperdiploidy"