Disease-Specific Template with Instructions: Difference between revisions
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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). 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 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 within the table and select the > symbol for 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> | ||
==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> | ||
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|<span class="blue-text">EXAMPLE:</span> Loss | |<span class="blue-text">EXAMPLE:</span> Loss | ||
|<span class="blue-text">EXAMPLE:</span> | |<span class="blue-text">EXAMPLE:</span> | ||
chr7:1- 159,335,973 [hg38] | chr7:1-159,335,973 [hg38] | ||
|<span class="blue-text">EXAMPLE:</span> | |<span class="blue-text">EXAMPLE:</span> | ||
chr7 | chr7 | ||
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|} | |} | ||
==Gene Mutations (SNV / INDEL)== | ==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 | 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 as 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" | {| class="wikitable sortable" | ||
|- | |- | ||
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!Notes | !Notes | ||
|- | |- | ||
|<span class="blue-text">EXAMPLE:</span> TP53; Variable LOF mutations | |<span class="blue-text">EXAMPLE:</span> ''TP53''; Variable LOF mutations | ||
<span class="blue-text">EXAMPLE:</span> | <span class="blue-text">EXAMPLE:</span> | ||
EGFR; Exon 20 mutations | ''EGFR''; Exon 20 mutations | ||
<span class="blue-text">EXAMPLE:</span> BRAF; Activating mutations | <span class="blue-text">EXAMPLE:</span> ''BRAF''; Activating mutations | ||
|<span class="blue-text">EXAMPLE:</span> TSG | |<span class="blue-text">EXAMPLE:</span> TSG | ||
|<span class="blue-text">EXAMPLE:</span> 20% (COSMIC) | |<span class="blue-text">EXAMPLE:</span> 20% (COSMIC) | ||
<span class="blue-text">EXAMPLE:</span> 30% (add Reference) | <span class="blue-text">EXAMPLE:</span> 30% (add Reference) | ||
|<span class="blue-text">EXAMPLE:</span> IDH1 R123H | |<span class="blue-text">EXAMPLE:</span> ''IDH1'' R123H | ||
|<span class="blue-text">EXAMPLE:</span> EGFR amplification | |<span class="blue-text">EXAMPLE:</span> ''EGFR'' amplification | ||
|<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> No | ||
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!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome | !Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome | ||
|- | |- | ||
|<span class="blue-text">EXAMPLE:</span> BRAF and MAP2K1; Activating mutations | |<span class="blue-text">EXAMPLE:</span> ''BRAF'' and ''MAP2K1''; Activating mutations | ||
|<span class="blue-text">EXAMPLE:</span> MAPK signaling | |<span class="blue-text">EXAMPLE:</span> MAPK signaling | ||
|<span class="blue-text">EXAMPLE:</span> Increased cell growth and proliferation | |<span class="blue-text">EXAMPLE:</span> Increased cell growth and proliferation | ||
|- | |- | ||
|<span class="blue-text">EXAMPLE:</span> CDKN2A; Inactivating mutations | |<span class="blue-text">EXAMPLE:</span> ''CDKN2A''; Inactivating mutations | ||
|<span class="blue-text">EXAMPLE:</span> Cell cycle regulation | |<span class="blue-text">EXAMPLE:</span> Cell cycle regulation | ||
|<span class="blue-text">EXAMPLE:</span> Unregulated cell division | |<span class="blue-text">EXAMPLE:</span> Unregulated cell division | ||
|- | |- | ||
|<span class="blue-text">EXAMPLE:</span> KMT2C and ARID1A; Inactivating mutations | |<span class="blue-text">EXAMPLE:</span> ''KMT2C'' and ''ARID1A''; Inactivating mutations | ||
|<span class="blue-text">EXAMPLE:</span> Histone modification, chromatin remodeling | |<span class="blue-text">EXAMPLE:</span> Histone modification, chromatin remodeling | ||
|<span class="blue-text">EXAMPLE:</span> Abnormal gene expression program | |<span class="blue-text">EXAMPLE:</span> Abnormal gene expression program | ||
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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> | |||
==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> | (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> | ||
==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. | ||