Compendium of Cancer Genome Aberrations

Changes

CNS5:Diffuse hemispheric glioma, H3 G34-mutant (view source)

Revision as of 10:08, 20 February 2022

2,470 bytes added ,  10:08, 20 February 2022
no edit summary
Line 1: Line 1: −
{{Under Construction}}
   
==Primary Author(s)*==
 
==Primary Author(s)*==
   −
Put your text here (Example: Jane Smith, PhD, Institute of Genomics)
+
Put your text here
    
__TOC__
 
__TOC__
Line 28: Line 27:  
==Clinical Features==
 
==Clinical Features==
   −
Put your text here
+
Put your text here and fill in the table
 +
{| class="wikitable"
 +
|'''Signs and Symptoms'''
 +
|EXAMPLE Asymptomatic (incidental finding on complete blood counts)
 +
 
 +
EXAMPLE B-symptoms (weight loss, fever, night sweats)
 +
 
 +
EXAMPLE Fatigue
 +
 
 +
EXAMPLE Lymphadenopathy (uncommon)
 +
|-
 +
|'''Laboratory Findings'''
 +
|EXAMPLE Cytopenias
 +
 
 +
EXAMPLE Lymphocytosis (low level)
 +
|}
    
==Sites of Involvement==
 
==Sites of Involvement==
Line 40: Line 54:  
==Immunophenotype==
 
==Immunophenotype==
   −
Put your text here and/or fill in the table
+
Put your text here and fill in the table
    
{| class="wikitable sortable"
 
{| class="wikitable sortable"
Line 57: Line 71:  
==Chromosomal Rearrangements (Gene Fusions)==
 
==Chromosomal Rearrangements (Gene Fusions)==
   −
Put your text here and/or fill in the table
+
Put your text here and fill in the table
    
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
 
!Chromosomal Rearrangement!!Genes in Fusion (5’ or 3’ Segments)!!Pathogenic Derivative!!Prevalence
 
!Chromosomal Rearrangement!!Genes in Fusion (5’ or 3’ Segments)!!Pathogenic Derivative!!Prevalence
 +
!Diagnostic Significance (Yes, No or Unknown)
 +
!Prognostic Significance (Yes, No or Unknown)
 +
!Therapeutic Significance (Yes, No or Unknown)
 +
!Notes
 
|-
 
|-
−
|EXAMPLE t(9;22)(q34;q11.2)||EXAMPLE 3'ABL1 / 5'BCR||EXAMPLE der(22)||EXAMPLE 5%
+
|EXAMPLE t(9;22)(q34;q11.2)||EXAMPLE 3'ABL1 / 5'BCR||EXAMPLE der(22)||EXAMPLE 20% (COSMIC)
−
|-
+
EXAMPLE 30% (add reference)
−
|EXAMPLE t(8;21)(q22;q22)||EXAMPLE 5'RUNX1 / 3'RUNXT1||EXAMPLE der(8)||EXAMPLE 5%
+
|Yes
 +
|No
 +
|Yes
 +
|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).
 
|}
 
|}
 
 
−
==Characteristic Chromosomal Aberrations / Patterns==
+
==Individual Region Genomic Gain/Loss/LOH==
   −
Put your text here
+
Put your text here and fill in the table
−
 
  −
==Genomic Gain/Loss/LOH==
  −
 
  −
Put your text here and/or fill in the table
      
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
−
!Chromosome Number!!Gain/Loss/Amp/LOH!!Region
+
!Chr #!!Gain / Loss / Amp / LOH!!Minimal Region Genomic Coordinates [Genome Build]!!Minimal Region Cytoband
 +
!Diagnostic Significance (Yes, No or Unknown)
 +
!Prognostic Significance (Yes, No or Unknown)
 +
!Therapeutic Significance (Yes, No or Unknown)
 +
!Notes
 
|-
 
|-
−
|EXAMPLE 8||EXAMPLE Gain||EXAMPLE chr8:0-1000000
+
|EXAMPLE
 +
 
 +
7
 +
|EXAMPLE Loss
 +
|EXAMPLE
 +
 
 +
chr7:1- 159,335,973 [hg38]
 +
|EXAMPLE
 +
 
 +
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 7||EXAMPLE Loss||EXAMPLE chr7:0-1000000
+
|EXAMPLE
−
|}
+
 
−
+
8
−
==Gene Mutations (SNV/INDEL)==
+
|EXAMPLE Gain
 +
|EXAMPLE
 +
 
 +
chr8:1-145,138,636 [hg38]
 +
|EXAMPLE
 +
 
 +
chr8
 +
|No
 +
|No
 +
|No
 +
|EXAMPLE
 +
 
 +
Common recurrent secondary finding for t(8;21) (add reference).
 +
|}
 +
==Characteristic Chromosomal Patterns==
   −
Put your text here and/or fill in the tables
+
Put your text here
    
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
−
!Gene!!Mutation!!Oncogene/Tumor Suppressor/Other!!Presumed Mechanism (LOF/GOF/Other; Driver/Passenger)!!Prevalence (COSMIC/TCGA/Other)
+
!Chromosomal Pattern
 +
!Diagnostic Significance (Yes, No or Unknown)
 +
!Prognostic Significance (Yes, No or Unknown)
 +
!Therapeutic Significance (Yes, No or Unknown)
 +
!Notes
 
|-
 
|-
−
|EXAMPLE TP53||EXAMPLE R273H||EXAMPLE Tumor Suppressor||EXAMPLE LOF||EXAMPLE 20%
+
|EXAMPLE
−
|}
+
 
−
+
Co-deletion of 1p and 18q
−
===Other Mutations===
+
|Yes
 +
|No
 +
|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)==
 +
 
 +
Put your text here and fill in the table
 +
 
 
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
−
!Type!!Gene/Region/Other
+
!Gene; Genetic Alteration!!'''Presumed Mechanism (Tumor Suppressor Gene [TSG] / Oncogene / Other)'''!!'''Prevalence (COSMIC / TCGA / Other)'''!!'''Concomitant Mutations'''!!'''Mutually Exclusive Mutations'''
−
|-
+
!'''Diagnostic Significance (Yes, No or Unknown)'''
−
|Concomitant Mutations||EXAMPLE IDH1 R123H
+
!Prognostic Significance (Yes, No or Unknown)
−
|-
+
!Therapeutic Significance (Yes, No or Unknown)
−
|Secondary Mutations||EXAMPLE Trisomy 7
+
!Notes
 
|-
 
|-
−
|Mutually Exclusive||EXAMPLE EGFR Amplification
+
|EXAMPLE: TP53; Variable LOF mutations
−
|}
     −
==Epigenomics (Methylation)==
+
EXAMPLE:
   −
Put your text here
+
EGFR; Exon 20 mutations
   −
==Genes and Main Pathways Involved==
+
EXAMPLE: BRAF; Activating mutations
 +
|EXAMPLE: TSG
 +
|EXAMPLE: 20% (COSMIC)
   −
Put your text here
+
EXAMPLE: 30% (add Reference)
 +
|EXAMPLE: IDH1 R123H
 +
|EXAMPLE: EGFR amplification
 +
|
 +
|
 +
|
 +
|EXAMPLE:  Excludes hairy cell leukemia (HCL) (add reference).
 +
<br />
 +
|}
 +
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.
   −
==Diagnostic Testing Methods==
+
==Epigenomic Alterations==
    
Put your text here
 
Put your text here
   −
==Clinical Significance (Diagnosis, Prognosis and Therapeutic Implications)==
+
==Genes and Main Pathways Involved==
   −
Diagnosis: Put your text here
+
Put your text here and fill in the table
 +
{| class="wikitable sortable"
 +
|-
 +
!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome
 +
|-
 +
|EXAMPLE: BRAF and MAP2K1; Activating mutations
 +
|EXAMPLE: MAPK signaling
 +
|EXAMPLE: Increased cell growth and proliferation
 +
|-
 +
|EXAMPLE: CDKN2A; Inactivating mutations
 +
|EXAMPLE: Cell cycle regulation
 +
|EXAMPLE: Unregulated cell division
 +
|-
 +
|EXAMPLE:  KMT2C and ARID1A; Inactivating mutations
 +
|EXAMPLE:  Histone modification, chromatin remodeling
 +
|EXAMPLE:  Abnormal gene expression program
 +
|}
 +
==Genetic Diagnostic Testing Methods==
   −
Prognosis: Put your text here
+
Put your text here
−
 
  −
Therapeutic: Put your text here
      
==Familial Forms==
 
==Familial Forms==
Line 132: Line 223:  
Put your text here
 
Put your text here
   −
==Other Information==
+
==Additional Information==
    
Put your text here
 
Put your text here
Line 138: Line 229:  
==Links==
 
==Links==
   −
Put your links here (use "Link" icon at top of page)
+
Put your text placeholder here (use "Link" icon at top of page)
    
==References==
 
==References==
 
(use "Cite" icon at top of page)
 
(use "Cite" icon at top of page)
−
<references />
   
===EXAMPLE Book===
 
===EXAMPLE Book===
  
Retrieved from "https://content.ccga.io/index.php/Special:MobileDiff/11059"