Gene-Specific Template (Updated 9-28-21)
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(General Instructions –The main focus of these pages is providing a quick reference for cancer associations and linking to internal and external resources providing genetics-related information for the gene of interest. 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. The use of bullet points rather than 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 , How to Curate a Gene Page, and FAQs as well as contact your Associate Editor or Technical Support.)
Primary Author(s)*
Put your text here (Name and affiliation; EXAMPLE: Jane Smith, PhD, Institute of Genomics)
Gene Characteristics
| Synonyms | EXAMPLE: Tumor protein p53, 'LFS1, p53, BCC7, TRP53 |
| Cytoband | EXAMPLE: 17p13.1 |
| Genomic Coordinates | EXAMPLE: chr17:7,668,402-7,687,538 [GRCh38/hg38]
EXAMPLE: chr17:7,571,720-7,590,868 [GRCh37/hg19] |
| Gene/Protein Native Function | EXAMPLES: Growth factor, DNA repair, Apoptosis |
Gene in Cancer Overview
- Put your text here
- Put your text here
- Put your text here
(Instruction: Use a list of three bullets, targeting one to three sentences each for gene function, germline associations, and somatic associations. Include gene/protein function in cancer such as tumor suppressor, oncogene or other. The information provided can include high level clinically significant details such as if mutations in this gene confirm or exclude certain diseases. Of note, this gene page is not meant to recapitulate the very detailed content on related linked disease entity pages.)
EXAMPLE:
- TP53 is a well-described tumor suppressor gene that functions in apoptosis, genomic stability and inhibition of angiogenesis (RefSeq, Dec 2016).
- Germline loss-of-function alterations, including deletions, are associated with Li-Fraumeni cancer predisposition syndrome (LFS). Individuals with LFS are at an increased risk of developing cancer, particularly sarcomas (PMID: 20586629, 27621308, 25896519).
- Somatic TP53 alterations are reported at a high frequency across a wide range of tumors, arising in ~30% of all cancer patients (PMID: 25400752, 27239089, cbioportal.org accessed 6/2/21).
Clinical Cancer Associations (Somatic)
(Instruction: include references and links to related internal CCGA pages)
| Tumor Type | Alteration Type(s) | Diagnostic Significance (Yes, No or Unknown) | Prognostic Significance (Yes, No or Unknown) | Therapeutic Significance (Yes, No or Unknown) |
| EXAMPLE: Chronic Myeloid Leukemia (CML), BCR-ABL1 Positive (link this name to internal page using link icon above) | EXAMPLES: Copy Number Loss, Copy Number Gain, LOH, Loss-of-Function Mutation, Gain-of-Function Mutation, Translocation/Fusion, Expression Changes (Biomarker), Somatic Hypermutation | |||
Clinical Cancer Associations (Germline)
(Instruction: include references and links to related internal CCGA pages)
| Tumor Type | Alteration Type(s) | Diagnostic Significance (Yes, No or Unknown) | Prognostic Significance (Yes, No or Unknown) | Therapeutic Significance (Yes, No or Unknown) |
| EXAMPLE: Myeloid Neoplasms with Germline ANKRD26 Mutation (link this name to internal page using link icon above) | EXAMPLES: Copy Number Loss, Copy Number Gain, LOH, Loss-of-Function Mutation, Gain-of-Function Mutation, Translocation/Fusion, | |||
Association with Other Diseases
Put your text here
External Links
Put your text here (Instruction: Include as applicable links to: 1) Atlas of Genetics and Cytogenetics in Oncology and Haematology, 2) COSMIC, 3) CIViC, 4) St. Jude ProteinPaint, 5) Precision Medicine Knowledgebase (Weill Cornell), 6) Cancer Index, 7) OncoKB, 8) NCBI Gene 9) My Cancer Genome, 10) UniProt, 11) Pfam, 12) GeneCards, 13) OMIM 14) LOVD(3) - Leiden Open Variation Database 15) TICdb - database of Translocation breakpoints In Cancer 16) GeneReviews, 17) ClinGen, and 18) Any gene-specific databases.)
EXAMPLES (these may be filled in already and if not, click on the link and select edit to change)
TP53 by Atlas of Genetics and Cytogenetics in Oncology and Haematology - detailed gene information
TP53 by COSMIC - sequence information, expression, catalogue of mutations
TP53 by CIViC - general knowledge and evidence-based variant specific information
TP53 by IARC - TP53 database with reference sequences and mutational landscape
TP53 by St. Jude ProteinPaint mutational landscape and matched expression data.
TP53 by Precision Medicine Knowledgebase (Weill Cornell) - manually vetted interpretations of variants and CNVs
TP53 by Cancer Index - gene, pathway, publication information matched to cancer type
TP53 by OncoKB - mutational landscape, mutation effect, variant classification
MECOM by NCBI Gene - brief gene overview
TP53 by My Cancer Genome - brief gene overview
TP53 by UniProt - protein and molecular structure and function
TP53 by Pfam - gene and protein structure and function information
TP53 by GeneCards - general gene information and summaries
MECOM by OMIM - compendium of human genes and genetic phenotypes
MECOM by LOVD(3) - Leiden Open Variation Database
MECOM by TICdb - database of Translocation breakpoints In Cancer
[1] - germline gene significance with expert curation
GeneReviews - information on Li Fraumeni Syndrome
Additional Information
Put your text here
References
(Instruction: Use "Cite" icon at top of page for automatic insertion using PMID; If a PMID is not available, manually add the reference information such as for the example book or internet resource below)
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, p130-149.
EXAMPLE Internet Resource
Author name(s). Date (if possible). page title, website title, web address, and date accessed.
- Cingam, S. R. and Koshy, N.V. (2017). Cancer, Leukemia, Promyelocytic, Acute (APL, APML). https://www.ncbi.nlm.nih.gov/books/NBK459352/ Accessed August 3, 2018.
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 CCGA coordinators (contact information provided on the homepage). Additional global feedback or concerns are also welcome.