Compendium of Cancer Genome Aberrations

Disease-Specific Template: Difference between revisions

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''(General Instructions – The main focus of these pages is the clinically significant genetic alterations in each disease type. Use [https://www.genenames.org/ HUGO-approved gene names and symbols] (italicized when appropriate), [https://varnomen.hgvs.org/ HGVS-based nomenclature for variants], as well as generic names of drugs and testing platforms or assays if applicable. Please complete tables whenever possible and do not delete them. The use of bullet points alongside short blocks of text rather than only large paragraphs is encouraged. Additional instructions below in italicized blue text should not be included in the final page content. Please also see [[Author Instructions]] and [[Frequently Asked Questions (FAQs)|FAQs]] as well as contact your [[Leadership|Associate Editor]] or [[Mailto:CCGA@cancergenomics.org|Technical Support]].)''
==Primary Author(s)*==
==Primary Author(s)*==


Put your text here (''Name and affiliation; example:'' Jane Smith, PhD, Institute of Genomics)
Put your text here


__TOC__
__TOC__
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==Definition / Description of Disease==
==Definition / Description of Disease==


Put your text here (''Instructions: Brief description of approximately one paragraph - include disease context relative to other WHO classification categories referring to the specific WHO book pages, diagnostic criteria if applicable, and differential diagnosis if applicable'')
Put your text here


==Synonyms / Terminology==
==Synonyms / Terminology==


Put your text here (''Instructions: Include currently used terms and major historical ones, adding “(historical)” after the latter.'')
Put your text here


==Epidemiology / Prevalence==
==Epidemiology / Prevalence==
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==Clinical Features==
==Clinical Features==


Put your text here and fill in the table (''Instruction: Can include references in the table'')
Put your text here and fill in the table
{| class="wikitable"
{| class="wikitable"
|'''Signs and Symptoms'''
|'''Signs and Symptoms'''
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==Sites of Involvement==
==Sites of Involvement==


Put your text here (''Instruction: Indicate physical sites; Example: nodal, extranodal, bone marrow'')
Put your text here


==Morphologic Features==
==Morphologic Features==
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==Immunophenotype==
==Immunophenotype==


Put your text here and fill in the table (''Instruction: Can include references in the table'')
Put your text here and fill in the table


{| class="wikitable sortable"
{| class="wikitable sortable"
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==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)Signs and Symptoms'''
!Diagnostic Significance (Yes, No or Unknown)
|'''Prognostic Significance (Yes, No or Unknown)Signs and Symptoms'''
!Prognostic Significance (Yes, No or Unknown)
|'''Therapeutic Significance (Yes, No or Unknown)Signs and Symptoms'''
!Therapeutic Significance (Yes, No or Unknown)
|'''NotesSigns and Symptoms'''
!Notes
|-
|-
|EXAMPLE t(9;22)(q34;q11.2)||EXAMPLE 3'ABL1 / 5'BCR||EXAMPLE der(22)||EXAMPLE 20% (COSMIC)
|EXAMPLE t(9;22)(q34;q11.2)||EXAMPLE 3'ABL1 / 5'BCR||EXAMPLE der(22)||EXAMPLE 20% (COSMIC)
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|}
|}
==Characteristic Chromosomal Aberrations / Patterns==
==Individual Region Genomic Gain/Loss/LOH==
 
Put your text here
 
==Genomic Gain/Loss/LOH==


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"
|-
|-
!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


Put your text here and/or fill in the tables
Common recurrent secondary finding for t(8;21) (add reference).
|}
==Characteristic Chromosomal Patterns==
 
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)'''
!Prognostic Significance (Yes, No or Unknown)
!Therapeutic Significance (Yes, No or Unknown)
!Notes
|-
|-
|Concomitant Mutations||EXAMPLE IDH1 R123H
|EXAMPLE: TP53; Variable LOF mutations
|-
|Secondary Mutations||EXAMPLE Trisomy 7
|-
|Mutually Exclusive||EXAMPLE EGFR Amplification
|}


==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==
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Put your text here
Put your text here


==Other Information==
==Additional Information==


Put your text here
Put your text here
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==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==
<references />
(use "Cite" icon at top of page)
(use "Cite" icon at top of page)
<references />
 
===EXAMPLE Book===
'''EXAMPLE Book'''


#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.
#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.


==Notes==
==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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