Atlas of Genetics and Cytogenetics in Oncology and Haematology

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  • Modification of the gene fusion nomenclature :
    Fusion genes are now written as Symb1::Symb2 instead of Symb1/Symb2
    Leukemia¬. 2021 Oct 6. doi: 10.1038/s41375-021-01436-6. Online ahead of print. HUGO Gene Nomenclature Committee (HGNC) recommendations for the designation of gene fusions Elspeth A Bruford 1 2 , Cristina R Antonescu 3 , Andrew J Carroll 4 , Arul Chinnaiyan 5 6 , Ian A Cree 7 , Nicholas C P Cross 8 9 , Raymond Dalgleish 10 , Robert Peter Gale 11 , Christine J Harrison 12 , Rosalind J Hastings 13 , Jean-Loup Huret 14 , Bertil Johansson 15 , Michelle Le Beau 16 , Cristina Mecucci 17 , Fredrik Mertens 15 , Roel Verhaak 18 19 , Felix Mitelman 15 Affiliations PMID: 34615987 DOI: 10.1038/s41375-021-01436-6 Abstract Gene fusions have been discussed in the scientific literature since they were first detected in cancer cells in the early 1980s. There is currently no standardized way to denote the genes involved in fusions, but in the majority of publications the gene symbols in question are listed either separated by a hyphen (-) or by a forward slash (/). Both types of designation suffer from important shortcomings. HGNC has worked with the scientific community to determine a new, instantly recognizable and unique separator-a double colon (::)-to be used in the description of fusion genes, and advocates its usage in all databases and articles describing gene fusions.


  • Update of pages for chromosomal bands
    For each (on 440 bands) you will find 2 parts : example : 2p16
    Update with COSMIC (release 92 August 27, 2020) and Mitelman database (July 15, 2020)
  • Regular update of External Links for Genes (with Entrez, Ensembl, UCSC, Uniprot ... data).


  • Update of pages for chromosomal bands
    For each (on 440 bands) you will find 2 parts : example : 2p16
    1. Translocations and other gene rearrangements
      abnormalilties without a precise knowledge of the genome breakpoint coordinates. These abnormalities are essentially (for gene fusions) from cytogenetic observations (and published in literature).
    2. Genes by bands
      Location of genes and gene fusions .
      All these informations are from several sources (with different informations either for location or for topographical or morphological descriptions. which have not normalized).
      That is why there are often several item for a same fusion.
      This section describe also genes (by their location), some genetic markers (fishClone file), or gene fusions which are present in normal tissues (and can be considered as false positive).
    3. Two other sections describe
      External links and Global files (in tabulated txt format)
    In all the pages (and files) original symbol of genes are replaced by the official symbol.


  • Update of presentation of Solid Tumors with a new section : Pediatric Tumors.

  • Access on line


  • Nomination of several Section Editors (see Editorial Board).
  • Update of presentation of Leukemia (with Lymphoma and Myeloid malignancies sections).
  • Update of presentation of Solid Tumors (with several sections).
  • Data for human genome is now referenced to GCRCh38 build) for chromosomal coordonates, chromosomal and cytogenetic band pages.


  • A new table for ICD Classification.
    This table gives access to International Classification of Diseases [ ICD-O-3 ] and the neoplasm part of ICD10.
    The first part gives access at the topographical classification with links to Atlas tumors and secondly to the morphological codes.
  • The searchbox on the Home page has been updated with a full indexation of fields NAME, ALIAS, GENE SYMBOL .. with a simple or an advanced form.
    For a complementary search in full text, the Google indexation of Atlas can also be queried.


  • A new table for a new integrated portal at NCI : Genomic Data Commons DataPortal.
    The GDC Portal offers simple access to data from TCGA and TARGET programs.
    A great part of data have been reanalysed with new pipeline and annotations. see the Release Note.


  • How to link the data in the Atlas :
  • New table for the different projects on the IntoGen Portal (Barcelona)
    IntOGen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes (list of 459 mutational cancer driver genes. )
  • New table for the different projects on the OASIS Portal (developped by Pfizer).
    OASIS portal presents a set of cancer data (TCGA nd some other) with somatic mutations, copy number ....). with the possibility of retrieving the data.


  • On Atlas : Update of the Entities by Chromosomal bands (Chromosomal abnormalities, Gene locations and Gene fusions)
  • Update of the list of TCGA programs with new links to the Broad Firehose portal and list of ICGC programs.


  • Update of interfaces for chromosome abnormalities with structural variations of COSMIC.
  • Update of Atlas Status with list of Atlas' authors


  • New interfaces for chromosome abnormalities and genes (and gene fusions) classified by chromosomal bands ex : 1p36.
    This development is an attempt to integrate major informations about chromosome abnormalities and fusion genes from different sources. The result is probably not exhaustive and may have some errors. Please send your remarks.
    These 440 pages (one for each band) are split in 2 parts : Abnormalities and Genes
    All these informations are from the following sources :


  • Nosology, Thesaurus and Census of Solid Tumors Several new Tables for Solid Tumors describe a Classification of Tumors in Atlas in relation with the International Classification of Disease s (ICD-O3) with references to nosology and phylums/phyla and sub tables for 11 sub classifications (access from the page Solid Tumors


    Atlas Status These pages describe the status of objects/items (Genes, Leukemia, Tumors and Cancer-prones) with their status (date of creation and /or update of expertise), some information as chromosomal locations, ICD classification ..) These tables (updated regularly at each indexation) may decide an author to submit a new paper. See : How to contribute


  • Tumor Cell lines This page was updated with reference to the paper in Nature on a comprehensive transcriptional portrait of human cancer cell line, by GenenTech. Klijn C et al. A comprehensive transcriptional portrait of human cancer cell lines.Nat Biotechnol. 2015 Mar;33(3): 306-12. PMID: [PubMed]


  • The list of genes maintained in the Atlas is now extended to all genes (symbol) present in Entrez Gene which have a location on the human genome (build hg19) on the UCSC database. The list consist on an expertised list (> 1,400) and a raw list (> 26,000) which contains either a part which is implicated in cancer and an other part with no know implication in cancer (In Atlas the difference is based on the presence of a list of "cancer" terms present in different files (description, geneRIF ..).

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