Difference between revisions of "GTS5:Familial adenomatous polyposis (APC)"

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<span style="color:#0070C0">(''General Instructions – The main focus of these pages is the clinically significant genetic alterations in each disease type. Use [https://www.genenames.org/ <u>HUGO-approved gene names and symbols</u>] (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 (add N/A if not applicable in the table and delete the examples); to add (or move) a row or column to a table, click nearby within the table and select the > symbol that appears to be given options. Please do not delete or alter the section headings. 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'' </span><u>''[[Author_Instructions]]''</u><span style="color:#0070C0"> ''and [[Frequently Asked Questions (FAQs)|<u>FAQs</u>]] as well as contact your [[Leadership|<u>Associate Editor</u>]] or [mailto:CCGA@cancergenomics.org <u>Technical Support</u>])''</span>
+
{{Under Construction}}
 +
__TOC__
 +
 
 +
<span style="color:#0070C0">(''General Instructions – The focus of these pages is the clinically significant genetic alterations in each disease type, which is based on current knowledge within the WHO classification books and using resources such as PubMed for the latest information. If the same disease is described in multiple WHO classification books, the genetics-related information for that disease will be consolidated into a single main page that has this template (other pages would only contain a link to this main page). Use [https://www.genenames.org/ <u>HUGO-approved gene names and symbols</u>] (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 (add N/A if not applicable in the table and delete the examples); to add (or move) a row or column in a table, click nearby within the table and select the > symbol that appears. Please do not delete or alter the section headings. 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'' </span><u>''[[Author_Instructions]]''</u><span style="color:#0070C0"> ''and [[Frequently Asked Questions (FAQs)|<u>FAQs</u>]] as well as contact your [[Leadership|<u>Associate Editor</u>]] or [mailto:CCGA@cancergenomics.org <u>Technical Support</u>])''</span>
 
==Primary Author(s)*==
 
==Primary Author(s)*==
 
Put your text here<span style="color:#0070C0"> (''<span class="blue-text">EXAMPLE:</span>'' Jane Smith, PhD) </span>
 
Put your text here<span style="color:#0070C0"> (''<span class="blue-text">EXAMPLE:</span>'' Jane Smith, PhD) </span>
 
==WHO Classification of Disease==
 
==WHO Classification of Disease==
<span style="color:#0070C0">(Will be autogenerated; Book will include name of specific book and have a link to the online WHO site)</span>
+
<span style="color:#0070C0">(''Instructions: This table’s content will be autogenerated.'')</span>
 
{| class="wikitable"
 
{| class="wikitable"
 
!Structure
 
!Structure
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|}
 
|}
 
==Definition / Description of Disease==
 
==Definition / Description of Disease==
Put your text here <span style="color:#0070C0">(''Instructions: Brief description of approximately one paragraph - include disease context relative to other WHO classification categories, diagnostic criteria if applicable, and differential diagnosis if applicable. Other classifications can be referenced for comparison.'') </span>
+
Put your text here <span style="color:#0070C0">(''Instructions: Include a brief general clinical description, diagnostic criteria, and differential diagnosis if applicable. Include disease context relative to other WHO classification categories, i.e. describe any organ-specific information pertinent to the genetic aspects of the disease across all applicable WHO classification books.'') </span>
 
==Synonyms / Terminology==
 
==Synonyms / Terminology==
 
Put your text here <span style="color:#0070C0">(''Instructions: Include currently used terms and major historical ones, adding “(historical)” after the latter.'') </span>
 
Put your text here <span style="color:#0070C0">(''Instructions: Include currently used terms and major historical ones, adding “(historical)” after the latter.'') </span>
 
==Epidemiology / Prevalence==
 
==Epidemiology / Prevalence==
 
Put your text here
 
Put your text here
==Clinical Features==
+
==Genetic Abnormalities: Germline==
Put your text here and fill in the table <span style="color:#0070C0">(''Instruction: Can include references in the table. Do not delete table.'') </span>
+
Put your text here and fill in the table <span style="color:#0070C0">(''Instruction: Can include references in the table. Do not delete table. If multiple causes of the syndrome, include relative prevalence of genetic contributions to that syndrome. In the notes, include additional details about most common mutations including founder mutations, mechanisms of molecular pathogenesis, alteration-specific prognosis and any other important genetic-related information with key references.'')</span>
{| class="wikitable"
 
|'''Signs and Symptoms'''
 
|<span class="blue-text">EXAMPLE:</span> Asymptomatic (incidental finding on complete blood counts)
 
<span class="blue-text">EXAMPLE:</span> B-symptoms (weight loss, fever, night sweats)
 
 
 
<span class="blue-text">EXAMPLE:</span> Lymphadenopathy (uncommon)
 
|-
 
|'''Laboratory Findings'''
 
|<span class="blue-text">EXAMPLE:</span> Cytopenias
 
<span class="blue-text">EXAMPLE:</span> Lymphocytosis (low level)
 
|}
 
==Sites of Involvement==
 
Put your text here <span style="color:#0070C0">(''Instruction: Indicate physical sites; <span class="blue-text">EXAMPLE:</span> nodal, extranodal, bone marrow'') </span>
 
==Morphologic Features==
 
Put your text here <span style="color:#0070C0">(''Instructions: Brief description of typically approximately one paragraph'') </span>
 
==Immunophenotype==
 
Put your text here and fill in the table <span style="color:#0070C0">(''Instruction: Can include references in the table. Do not delete table.'') </span>
 
 
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
!Finding!!Marker
+
|'''Gene'''
 +
|'''Genetic Variant or Variant Type'''
 +
|'''Molecular Pathogenesis'''
 +
|'''Inheritance, Penetrance, Expressivity'''
 +
|'''Notes'''
 
|-
 
|-
|Positive (universal)||<span class="blue-text">EXAMPLE:</span> CD1
+
|<span class="blue-text">EXAMPLE:</span> BRCA1||<span class="blue-text">EXAMPLE:</span> Many||<span class="blue-text">EXAMPLE:</span> Multiple variant types leading to loss of function||
 +
|
 
|-
 
|-
|Positive (subset)||
+
|<span class="blue-text">EXAMPLE:</span> Gene X
|-
+
|<span class="blue-text">EXAMPLE:</span> List the specific mutation
|Negative (universal)||
+
|
|-
+
|
|Negative (subset)||
+
|
 
|}
 
|}
==Chromosomal Rearrangements (Gene Fusions)==
+
==Genetic Abnormalities: Somatic==
Put your text here and fill in the table <span style="color:#0070C0">(''Instruction: Can include references in the table. Do not delete table.'')</span>
+
Put your text here and fill in the table <span style="color:#0070C0">(''Instruction: Describe significant second hit mutations, or somatic variants that present as a germline syndrome. Can include references in the table. Do not delete table. In the notes, include details about most common mutations, mechanisms of molecular pathogenesis, alteration-specific prognosis and any other important genetic-related information with key references.'') </span>
 
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
!Chromosomal Rearrangement!!Genes in Fusion (5’ or 3’ Segments)!!Pathogenic Derivative!!Prevalence
+
|'''Gene'''
!Diagnostic Significance (Yes, No or Unknown)
+
|'''Genetic Variant or Variant Type'''
!Prognostic Significance (Yes, No or Unknown)
+
|'''Molecular Pathogenesis'''
!Therapeutic Significance (Yes, No or Unknown)
+
|'''Inheritance, Penetrance, Expressivity'''
!Notes
+
|'''Notes'''
 
|-
 
|-
|<span class="blue-text">EXAMPLE:</span> t(9;22)(q34;q11.2)||<span class="blue-text">EXAMPLE:</span> 3'ABL1 / 5'BCR||<span class="blue-text">EXAMPLE:</span> der(22)||<span class="blue-text">EXAMPLE:</span> 20% (COSMIC)
+
|<span class="blue-text">EXAMPLE:</span> BRCA
<span class="blue-text">EXAMPLE:</span> 30% (add reference)
+
|<span class="blue-text">EXAMPLE:</span> Biallelic inactivation variants
|<span class="blue-text">EXAMPLE:</span> Yes
+
|<span class="blue-text">EXAMPLE:</span> Second hit mutation can occur as copy neutral LOH, inactivating mutation, deletion, promoter hypermethylation, or a structural abnormality disrupting the gene.
|<span class="blue-text">EXAMPLE:</span> No
+
|
|<span class="blue-text">EXAMPLE:</span> Yes
+
|
|<span class="blue-text">EXAMPLE:</span>
 
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).
 
|}
 
==Individual Region Genomic Gain / Loss / LOH==
 
Put your text here and fill in the table <span style="color:#0070C0">(''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. Do not delete table.'') </span>
 
{| class="wikitable sortable"
 
|-
 
!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
 
|-
 
|<span class="blue-text">EXAMPLE:</span>
 
7
 
|<span class="blue-text">EXAMPLE:</span> Loss
 
|<span class="blue-text">EXAMPLE:</span>
 
chr7:1-159,335,973 [hg38]
 
|<span class="blue-text">EXAMPLE:</span>
 
chr7
 
|<span class="blue-text">EXAMPLE:</span> Yes
 
|<span class="blue-text">EXAMPLE:</span> Yes
 
|<span class="blue-text">EXAMPLE:</span> No
 
|<span class="blue-text">EXAMPLE:</span>
 
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).
 
 
|-
 
|-
|<span class="blue-text">EXAMPLE:</span>
+
|<span class="blue-text">EXAMPLE:</span> BRCA
8
 
 
|<span class="blue-text">EXAMPLE:</span> Gain
 
|<span class="blue-text">EXAMPLE:</span> Gain
|<span class="blue-text">EXAMPLE:</span>
+
|<span class="blue-text">EXAMPLE:</span>After exposure to certain therapies (e.g. PARP inhibitors), a second mutation may restore gene function as a resistance mechanism.
chr8:1-145,138,636 [hg38]
+
|
|<span class="blue-text">EXAMPLE:</span>
+
|
chr8
 
|<span class="blue-text">EXAMPLE:</span> No
 
|<span class="blue-text">EXAMPLE:</span> No
 
|<span class="blue-text">EXAMPLE:</span> No
 
|<span class="blue-text">EXAMPLE:</span>
 
Common recurrent secondary finding for t(8;21) (add reference).
 
|}
 
==Characteristic Chromosomal Patterns==
 
Put your text here <span style="color:#0070C0">(''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. Do not delete table.'')</span>
 
{| class="wikitable sortable"
 
|-
 
!Chromosomal Pattern
 
!Diagnostic Significance (Yes, No or Unknown)
 
!Prognostic Significance (Yes, No or Unknown)
 
!Therapeutic Significance (Yes, No or Unknown)
 
!Notes
 
|-
 
|<span class="blue-text">EXAMPLE:</span>
 
Co-deletion of 1p and 18q
 
|<span class="blue-text">EXAMPLE:</span> Yes
 
|<span class="blue-text">EXAMPLE:</span> No
 
|<span class="blue-text">EXAMPLE:</span> No
 
|<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).
 
 
|}
 
|}
==Gene Mutations (SNV / INDEL)==
 
Put your text here and fill in the table <span style="color:#0070C0">(''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. Do not delete table.'') </span>
 
{| class="wikitable sortable"
 
|-
 
!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
 
|-
 
|<span class="blue-text">EXAMPLE:</span> ''TP53''; Variable LOF mutations
 
<span class="blue-text">EXAMPLE:</span>
 
 
''EGFR''; Exon 20 mutations
 
 
<span class="blue-text">EXAMPLE:</span> ''BRAF''; Activating mutations
 
|<span class="blue-text">EXAMPLE:</span> TSG
 
|<span class="blue-text">EXAMPLE:</span> 20% (COSMIC)
 
<span class="blue-text">EXAMPLE:</span> 30% (add Reference)
 
|<span class="blue-text">EXAMPLE:</span> ''IDH1'' R123H
 
|<span class="blue-text">EXAMPLE:</span> ''EGFR'' amplification
 
|<span class="blue-text">EXAMPLE:</span> Yes
 
|<span class="blue-text">EXAMPLE:</span> No
 
|<span class="blue-text">EXAMPLE:</span> No
 
|<span class="blue-text">EXAMPLE:</span> Excludes hairy cell leukemia (HCL) (add reference).
 
|}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.
 
==Epigenomic Alterations==
 
Put your text here
 
 
==Genes and Main Pathways Involved==
 
==Genes and Main Pathways Involved==
 
Put your text here and fill in the table <span style="color:#0070C0">(''Instructions: Can include references in the table. Do not delete table.'')</span>
 
Put your text here and fill in the table <span style="color:#0070C0">(''Instructions: Can include references in the table. Do not delete table.'')</span>
Line 180: Line 93:
 
==Genetic Diagnostic Testing Methods==
 
==Genetic Diagnostic Testing Methods==
 
Put your text here
 
Put your text here
==Familial Forms==
 
Put your text here <span style="color:#0070C0">(''Instructions: Include associated hereditary conditions/syndromes that cause this entity or are caused by this entity.'') </span>
 
 
==Additional Information==
 
==Additional Information==
 
Put your text here
 
Put your text here
 
==Links==
 
==Links==
(use the "Link" icon that looks like two overlapping circles at the top of the page) <span style="color:#0070C0">(''Instructions: Highlight text to which you want to add a link in this section or elsewhere, select the "Link" icon at the top of the page, and search the name of the internal page to which you want to link this text, or enter an external internet address by including the "<nowiki>http://www</nowiki>." portion.'')</span>
+
Put a link here or anywhere appropriate in this page <span style="color:#0070C0">(''Instructions: Highlight the text to which you want to add a link in this section or elsewhere, select the "Link" icon at the top of the page, and search the name of the internal page to which you want to link this text, or enter an external internet address by including the "<nowiki>http://www</nowiki>." portion.'')</span>
 
==References==
 
==References==
(use the "Cite" icon at the top of the page) <span style="color:#0070C0">(''Instructions: Add each reference into the text above by clicking on where you want to insert the reference, selecting the “Cite” icon at the top of the page, and using the “Automatic” tab option to search such as by PMID to select the reference to insert. The reference list in this section will be automatically generated and sorted.''</span> <span style="color:#0070C0">''If a PMID is not available, such as for a book, please use the “Cite” icon, select “Manual” and then “Basic Form”, and include the entire reference''</span><span style="color:#0070C0">''.''</span><span style="color:#0070C0">) </span>
+
<references />(use the "Cite" icon at the top of the page) <span style="color:#0070C0">(''Instructions: Add each reference into the text above by clicking where you want to insert the reference, selecting the “Cite” icon at the top of the page, and using the “Automatic” tab option to search by PMID to select the reference to insert. If a PMID is not available, such as for a book, please use the “Cite” icon, select “Manual” and then “Basic Form”, and include the entire reference. To insert the same reference again later in the page, select the “Cite” icon and “Re-use” to find the reference; DO NOT insert the same reference twice using the “Automatic” tab as it will be treated as two separate references. The reference list in this section will be automatically generated and sorted''</span><span style="color:#0070C0">''.''</span><span style="color:#0070C0">) </span>
 
==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 [[Leadership|''Associate Editor'']] or other CCGA representative.  When pages have a major update by a new author, the new author will be acknowledged at the beginning of the page, and those who contributed previously will be acknowledged below as a prior author.  Additional global feedback or concerns are also welcome.
 +
 
 +
Prior Author(s):

Latest revision as of 17:50, 4 September 2024

(General Instructions – The focus of these pages is the clinically significant genetic alterations in each disease type, which is based on current knowledge within the WHO classification books and using resources such as PubMed for the latest information. If the same disease is described in multiple WHO classification books, the genetics-related information for that disease will be consolidated into a single main page that has this template (other pages would only contain a link to this main page). Use HUGO-approved gene names and symbols (italicized when appropriate), 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 (add N/A if not applicable in the table and delete the examples); to add (or move) a row or column in a table, click nearby within the table and select the > symbol that appears. Please do not delete or alter the section headings. 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 FAQs as well as contact your Associate Editor or Technical Support)

Primary Author(s)*

Put your text here (EXAMPLE: Jane Smith, PhD)

WHO Classification of Disease

(Instructions: This table’s content will be autogenerated.)

Structure Disease
Book
Category
Family
Type
Subtype(s)

Definition / Description of Disease

Put your text here (Instructions: Include a brief general clinical description, diagnostic criteria, and differential diagnosis if applicable. Include disease context relative to other WHO classification categories, i.e. describe any organ-specific information pertinent to the genetic aspects of the disease across all applicable WHO classification books.)

Synonyms / Terminology

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

Epidemiology / Prevalence

Put your text here

Genetic Abnormalities: Germline

Put your text here and fill in the table (Instruction: Can include references in the table. Do not delete table. If multiple causes of the syndrome, include relative prevalence of genetic contributions to that syndrome. In the notes, include additional details about most common mutations including founder mutations, mechanisms of molecular pathogenesis, alteration-specific prognosis and any other important genetic-related information with key references.)

Gene Genetic Variant or Variant Type Molecular Pathogenesis Inheritance, Penetrance, Expressivity Notes
EXAMPLE: BRCA1 EXAMPLE: Many EXAMPLE: Multiple variant types leading to loss of function
EXAMPLE: Gene X EXAMPLE: List the specific mutation

Genetic Abnormalities: Somatic

Put your text here and fill in the table (Instruction: Describe significant second hit mutations, or somatic variants that present as a germline syndrome. Can include references in the table. Do not delete table. In the notes, include details about most common mutations, mechanisms of molecular pathogenesis, alteration-specific prognosis and any other important genetic-related information with key references.)

Gene Genetic Variant or Variant Type Molecular Pathogenesis Inheritance, Penetrance, Expressivity Notes
EXAMPLE: BRCA EXAMPLE: Biallelic inactivation variants EXAMPLE: Second hit mutation can occur as copy neutral LOH, inactivating mutation, deletion, promoter hypermethylation, or a structural abnormality disrupting the gene.
EXAMPLE: BRCA EXAMPLE: Gain EXAMPLE:After exposure to certain therapies (e.g. PARP inhibitors), a second mutation may restore gene function as a resistance mechanism.

Genes and Main Pathways Involved

Put your text here and fill in the table (Instructions: Can include references in the table. Do not delete table.)

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

Put your text here

Additional Information

Put your text here

Links

Put a link here or anywhere appropriate in this page (Instructions: Highlight the text to which you want to add a link in this section or elsewhere, select the "Link" icon at the top of the page, and search the name of the internal page to which you want to link this text, or enter an external internet address by including the "http://www." portion.)

References

(use the "Cite" icon at the top of the page) (Instructions: Add each reference into the text above by clicking where you want to insert the reference, selecting the “Cite” icon at the top of the page, and using the “Automatic” tab option to search by PMID to select the reference to insert. If a PMID is not available, such as for a book, please use the “Cite” icon, select “Manual” and then “Basic Form”, and include the entire reference. To insert the same reference again later in the page, select the “Cite” icon and “Re-use” to find the reference; DO NOT insert the same reference twice using the “Automatic” tab as it will be treated as two separate references. The reference list in this section will be automatically generated and sorted.)

Notes

*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 Associate Editor or other CCGA representative.  When pages have a major update by a new author, the new author will be acknowledged at the beginning of the page, and those who contributed previously will be acknowledged below as a prior author.  Additional global feedback or concerns are also welcome.

Prior Author(s):