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"
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==Individual Region Genomic Gain/Loss/LOH==
==Individual Region Genomic Gain/Loss/LOH==


Put your text here and fill in the table (''Instructions: Includes aberrations not involving gene fusions. Can include references in the table. Can refer to CGC workgroup tables as linked on the homepage if applicable.'')
Put your text here and fill in the table


{| class="wikitable sortable"
{| class="wikitable sortable"
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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).
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
8
|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==
==Characteristic Chromosomal Patterns==


Put your text here ''(EXAMPLE PATTERNS: hyperdiploid; gain of odd number chromosomes including typically chromosome 1, 3, 5, 7, 11, and 17; co-deletion of 1p and 19q; complex karyotypes without characteristic genetic findings; chromothripsis)''
Put your text here


{| class="wikitable sortable"
{| class="wikitable sortable"
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==Gene Mutations (SNV/INDEL)==
==Gene Mutations (SNV/INDEL)==


Put your text here and fill in the table (''Instructions: This table is not meant to be an exhaustive list; please include only genes/alterations that are recurrent and common as well either disease defining and/or clinically significant. Can include references in the table. For clinical significance, denote associations with FDA-approved therapy (not an extensive list of applicable drugs) and NCCN or other national guidelines if applicable; Can also refer to CGC workgroup tables as linked on the homepage if applicable as well as any high impact papers or reviews of gene mutations in this entity.)''
Put your text here and fill in the table


{| class="wikitable sortable"
{| class="wikitable sortable"
|-
|-
!Gene; Genetic Alteration!!'''Presumed Mechanism (Tumor Suppressor Gene (TSG) / Oncogene / Other)'''!!'''Prevalence (COSMIC/ TCGA/Other)'''!!'''Concomitant Mutations'''!!'''Mutually Exclusive Mutations'''
!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)'''
!'''Diagnostic Significance (Yes, No or Unknown)'''
!Prognostic Significance (Yes, No or Unknown)
!Prognostic Significance (Yes, No or Unknown)
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==Genes and Main Pathways Involved==
==Genes and Main Pathways Involved==


Put your text here and fill in the table ''(Instructions: 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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|-
|-
|EXAMPLE: BRAF and MAP2K1; Activating mutations
|EXAMPLE: BRAF and MAP2K1; Activating mutations
EXAMPLE: CDKN2A; Inactivating mutations
EXAMPLE:  KMT2C and ARID1A; Inactivating mutations
|EXAMPLE: MAPK signaling
|EXAMPLE: MAPK signaling
EXAMPLE: Cell cycle regulation
EXAMPLE:  Histone modification, chromatin remodeling
|EXAMPLE: Increased cell growth and proliferation
|EXAMPLE: Increased cell growth and proliferation
 
|-
EXAMPLE: Unregulated cell division
|EXAMPLE: CDKN2A; Inactivating mutations
 
|EXAMPLE: Cell cycle regulation
EXAMPLE:  Abnormal gene expression program
|EXAMPLE: Unregulated cell division
|-
|EXAMPLE:  KMT2C and ARID1A; Inactivating mutations
|EXAMPLE:  Histone modification, chromatin remodeling
|EXAMPLE:  Abnormal gene expression program
|}
|}
==Genetic Diagnostic Testing Methods==
==Genetic Diagnostic Testing Methods==
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==Familial Forms==
==Familial Forms==


Put your text here (''Instructions: Include associated hereditary conditions/syndromes that cause this entity or are caused by this entity.'')
Put your text here


==Additional Information==
==Additional Information==
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==Links==
==Links==


Put your text placeholder here (use "Link" icon at top of page) (''Instructions: For example, link to related gene pages within the site. Note: links will be converted using the link icon at top of page in the CCGA site.'')
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)


(''Instruction: Add PMIDs into the text above where references are appropriate - PMIDs will be used to insert references on the CCGA site and the reference list automatically generated'')
'''EXAMPLE Book'''
 
(''Instruction: If a PMID is not available, such as for a book, please include the entire reference in this section'')<references />
===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.
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