Compendium of Cancer Genome Aberrations

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BRST5:Secretory Carcinoma (view source)

Revision as of 20:31, 12 October 2022

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{{Under Construction}}
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==Primary Author(s)*==
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==Primary Author(s)*==
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Put your text here
    
__TOC__
 
__TOC__
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==Cancer Category/Type==
 
==Cancer Category/Type==
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Breast cancer
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Put your text here
    
==Cancer Sub-Classification / Subtype==
 
==Cancer Sub-Classification / Subtype==
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==Clinical Features==
 
==Clinical Features==
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Put your text here
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Put your text here and fill in the table
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{| class="wikitable"
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|'''Signs and Symptoms'''
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|EXAMPLE Asymptomatic (incidental finding on complete blood counts)
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EXAMPLE B-symptoms (weight loss, fever, night sweats)
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EXAMPLE Fatigue
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EXAMPLE Lymphadenopathy (uncommon)
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|-
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|'''Laboratory Findings'''
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|EXAMPLE Cytopenias
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EXAMPLE Lymphocytosis (low level)
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|}
    
==Sites of Involvement==
 
==Sites of Involvement==
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==Immunophenotype==
 
==Immunophenotype==
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Put your text here and/or fill in the table
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Put your text here and fill in the table
    
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
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! Finding   !! Marker
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!Finding!!Marker
 
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|-
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|Positive (universal) || EXAMPLE CD1
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|Positive (universal)||EXAMPLE CD1
 
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|-
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|Positive (subset) || EXAMPLE CD2
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|Positive (subset)||EXAMPLE CD2
 
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|-
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|Negative (universal) || EXAMPLE CD3
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|Negative (universal)||EXAMPLE CD3
 
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|-
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|Negative (subset) || EXAMPLE CD4
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|Negative (subset)||EXAMPLE CD4
 
|}
 
|}
    
==Chromosomal Rearrangements (Gene Fusions)==
 
==Chromosomal Rearrangements (Gene Fusions)==
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Put your text here and/or fill in the table
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Put your text here and fill in the table
    
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
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! Chromosomal Rearrangement !! Genes in Fusion (5’ or 3’ Segments) !! Pathogenic Derivative !! Prevalence
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!Chromosomal Rearrangement!!Genes in Fusion (5’ or 3’ Segments)!!Pathogenic Derivative!!Prevalence
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!Diagnostic Significance (Yes, No or Unknown)
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!Prognostic Significance (Yes, No or Unknown)
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!Therapeutic Significance (Yes, No or Unknown)
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!Notes
 
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|-
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|EXAMPLE t(9;22)(q34;q11.2) || EXAMPLE 3'ABL1 / 5'BCR || EXAMPLE der(22) || EXAMPLE 5%
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|EXAMPLE t(9;22)(q34;q11.2)||EXAMPLE 3'ABL1 / 5'BCR||EXAMPLE der(22)||EXAMPLE 20% (COSMIC)
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|-
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EXAMPLE 30% (add reference)
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|EXAMPLE t(8;21)(q22;q22) || EXAMPLE 5'RUNX1 / 3'RUNXT1 || EXAMPLE der(8) || EXAMPLE 5%
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|Yes
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|No
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|Yes
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|EXAMPLE
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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).
 
|}
 
|}
 
 
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==Characteristic Chromosomal Aberrations / Patterns==
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==Individual Region Genomic Gain/Loss/LOH==
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Put your text here
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Put your text here and fill in the table
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==Genomic Gain/Loss/LOH==
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Put your text here and/or fill in the table
      
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
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! Chromosome Number !! Gain/Loss/Amp/LOH !! Region
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!Chr #!!Gain / Loss / Amp / LOH!!Minimal Region Genomic Coordinates [Genome Build]!!Minimal Region Cytoband
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!Diagnostic Significance (Yes, No or Unknown)
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!Prognostic Significance (Yes, No or Unknown)
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!Therapeutic Significance (Yes, No or Unknown)
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!Notes
 
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|-
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|EXAMPLE 8 || EXAMPLE Gain || EXAMPLE chr8:0-1000000
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|EXAMPLE
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7
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|EXAMPLE Loss
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|EXAMPLE
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chr7:1- 159,335,973 [hg38]
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|EXAMPLE
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chr7
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|Yes
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|Yes
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|No
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|EXAMPLE
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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).
 
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|EXAMPLE 7 || EXAMPLE Loss || EXAMPLE chr7:0-1000000
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|EXAMPLE
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|}
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8
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==Gene Mutations (SNV/INDEL)==
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|EXAMPLE Gain
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|EXAMPLE
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chr8:1-145,138,636 [hg38]
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|EXAMPLE
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chr8
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|No
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|No
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|No
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|EXAMPLE
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Common recurrent secondary finding for t(8;21) (add reference).
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|}
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==Characteristic Chromosomal Patterns==
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Put your text here and/or fill in the tables
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Put your text here
    
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
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! Gene !! Mutation !! Oncogene/Tumor Suppressor/Other !! Presumed Mechanism (LOF/GOF/Other; Driver/Passenger) !! Prevalence (COSMIC/TCGA/Other)
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!Chromosomal Pattern
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!Diagnostic Significance (Yes, No or Unknown)
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!Prognostic Significance (Yes, No or Unknown)
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!Therapeutic Significance (Yes, No or Unknown)
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!Notes
 
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|-
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| EXAMPLE TP53 || EXAMPLE R273H || EXAMPLE Tumor Suppressor || EXAMPLE LOF || EXAMPLE 20%
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|EXAMPLE
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|}
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Co-deletion of 1p and 18q
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===Other Mutations===
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|Yes
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|No
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|No
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|EXAMPLE:
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See chromosomal rearrangements table as this pattern is due to an unbalanced derivative translocation associated with oligodendroglioma (add reference).
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|}
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==Gene Mutations (SNV/INDEL)==
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Put your text here and fill in the table
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{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
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! Type !! Gene/Region/Other
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!Gene; Genetic Alteration!!'''Presumed Mechanism (Tumor Suppressor Gene [TSG] / Oncogene / Other)'''!!'''Prevalence (COSMIC / TCGA / Other)'''!!'''Concomitant Mutations'''!!'''Mutually Exclusive Mutations'''
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|-
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!'''Diagnostic Significance (Yes, No or Unknown)'''
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| Concomitant Mutations || EXAMPLE IDH1 R123H
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!Prognostic Significance (Yes, No or Unknown)
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|-
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!Therapeutic Significance (Yes, No or Unknown)
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| Secondary Mutations || EXAMPLE Trisomy 7
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!Notes
 
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|-
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|Mutually Exclusive || EXAMPLE EGFR Amplification
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|EXAMPLE: TP53; Variable LOF mutations
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|}
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==Epigenomics (Methylation)==
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EXAMPLE:
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Put your text here
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EGFR; Exon 20 mutations
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==Genes and Main Pathways Involved==
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EXAMPLE: BRAF; Activating mutations
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|EXAMPLE: TSG
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|EXAMPLE: 20% (COSMIC)
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Put your text here
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EXAMPLE: 30% (add Reference)
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|EXAMPLE: IDH1 R123H
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|EXAMPLE: EGFR amplification
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|
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|
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|
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|EXAMPLE:  Excludes hairy cell leukemia (HCL) (add reference).
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<br />
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|}
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Note: A more extensive list of mutations can be found in cBioportal (https://www.cbioportal.org/), COSMIC (https://cancer.sanger.ac.uk/cosmic), ICGC (https://dcc.icgc.org/) and/or other databases. When applicable, gene-specific pages within the CCGA site directly link to pertinent external content.
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==Diagnostic Testing Methods==
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==Epigenomic Alterations==
    
Put your text here
 
Put your text here
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==Clinical Significance (Diagnosis, Prognosis and Therapeutic Implications)==
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==Genes and Main Pathways Involved==
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Put your text here and fill in the table
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{| class="wikitable sortable"
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|-
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!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome
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|-
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|EXAMPLE: BRAF and MAP2K1; Activating mutations
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|EXAMPLE: MAPK signaling
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|EXAMPLE: Increased cell growth and proliferation
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|-
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|EXAMPLE: CDKN2A; Inactivating mutations
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|EXAMPLE: Cell cycle regulation
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|EXAMPLE: Unregulated cell division
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|-
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|EXAMPLE:  KMT2C and ARID1A; Inactivating mutations
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|EXAMPLE:  Histone modification, chromatin remodeling
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|EXAMPLE:  Abnormal gene expression program
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|}
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==Genetic Diagnostic Testing Methods==
    
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==Other Information==
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==Additional Information==
    
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==Links==
 
==Links==
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Put your links here
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Put your text placeholder here (use "Link" icon at top of page)
    
==References==
 
==References==
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<references />
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(use "Cite" icon at top of page)
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===EXAMPLE Book===
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=== EXAMPLE Book ===
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#Arber DA, et al., (2017). Acute myeloid leukaemia with recurrent genetic abnormalities, in World Health Organization Classification of Tumours of Haematopoietic and Lymphoid Tissues, Revised 4th edition. Swerdlow SH, Campo E, Harris NL, Jaffe ES, Pileri SA, Stein H, Thiele J, Arber DA, Hasserjian RP, Le Beau MM, Orazi A, and Siebert R, Editors. IARC Press: Lyon, France, p129-171.
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#Arber DA, et al., (2008). Acute myeloid leukaemia with recurrent genetic abnormalities, in World Health Organization Classification of Tumours of Haematopoietic and Lymphoid Tissues, 4thedition.Swerdlow SH, Campo E, Harris NL, Jaffe ES, Pileri SA, Stein H, Thiele J, Vardiman JW, Editors. IARC Press: Lyon, France, p117-118.
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=== EXAMPLE Journal Article ===
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#Li Y, et al., (2001). Fusion of two novel genes, RBM15 and MKL1, in the t(1;22)(p13;q13) of acute megakaryoblastic leukemia. Nat Genet 28:220-221, PMID 11431691.
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== Notes ==
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==Notes==
 
<nowiki>*</nowiki>Primary authors will typically be those that initially create and complete the content of a page.  If a subsequent user modifies the content and feels the effort put forth is of high enough significance to warrant listing in the authorship section, please contact the CCGA coordinators (contact information provided on the homepage).  Additional global feedback or concerns are also welcome.
 
<nowiki>*</nowiki>Primary authors will typically be those that initially create and complete the content of a page.  If a subsequent user modifies the content and feels the effort put forth is of high enough significance to warrant listing in the authorship section, please contact the CCGA coordinators (contact information provided on the homepage).  Additional global feedback or concerns are also welcome.
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