Added value of the Atlas


Encyclopedia containing original monographs written by different authors, the Atlas combines different types of knowledge. No other web site presents so many monographs on genes, very rich iconography. It is a tool for researchers in genomics, for clinicians as a help in diagnosis and therapeutic decision, for a personalized cancer medicine. The Atlas is not only a web site and an encyclopedia, but also a scientific journal.

In conclusion, it is an original/unique database without equivalent.


Positive aspects of the Atlas


Encyclopedia composed of documents that are original monographs written by invited authors, based on their expertise in a given field (ex: Carlo M Croce on "Common fragile sites and genomic instability", Rolf Marschalek on the KMT2A (MLL) gene, George C Prendergast on the IDO1 and 2 genes, Cécile Badoual on "Head and Neck paragangliomas", Maurizio Genuardi on "MUTYH-associated polyposis", Felix Mitelman on "Cancer Cytogenetics"). Other databases present texts on genes (for example Aceview) but these are non-expertized texts, resulting from data mining. GeneCards is a database with links to other databases, with few data copied from these databases.


Starting first from cytogenetics, the Atlas combines different types of knowledge in a single web site: genes and their function, cell biology (ex: Apoptosis:, pathological data, diseases and their clinical implications, cytogenetics, but also medical genetics, with hereditary disorders associated with an increased risk of cancer. This gives a wider and more global view of cancer genetics, while these data are usually dispersed[1]. The Atlas is the only genetic site where the prognosis is included; it has always surprised us that data so important such as prognosis could be absent in other sites… even more now in the context of personalized cancer medicine.


No other site, journal or book has so many monographs on genes (more than 1,400 genes; ex:, together with 28,000 non-annotated cards based on the GeneCard type (ex:, see paragraph on "Other genes").


Very rich iconography on chromosomal aberrations (700 images, ex:, on genes (3,000 images ex:, on clinics and pathology (400 images, ex:


Research axis: the Atlas is a tool for researchers in genomics (see Science, 2011). Documents on genes having more and more importance in the analysis of an abnormality, mutations and fusions in relation with NGS: the Atlas is a tool allowing an expert selection of genes involved in cancer. It has been referenced several times as a pertinent source in relation with an abnormality, more particularly as identification of genes associated with the abnormality.


Help in diagnosis and therapeutic decision: the Atlas guides the cytogeneticist by its iconography on chromosomal abnormalities, informs the clinician on rare pathologies, allowing him to adjust his treatment. The Atlas is particularly indispensable in rare diseases (because rare diseases are numerous, these are frequent). All the cytogeneticists from all around the world regularly use the Atlas, as it appeared with recent financial issues[2].


Towards a personalized cancer medicine: 322 genes involved in colon cancer, 457 in breast cancer and 589 in prostate cancer can be extracted from the "gene" section (see paragraph "Other genes implicated" With the development of new techniques, it is now evident than solid tumors, as leukemia, have numerous sub-types (how many hundreds of breast cancer with different genetic profiles?). This, added to the development in cell biology, shows that the encyclopedic contents of the Atlas is potentially a basis for the development of personalized cancer medicine.


The Atlas is not only a web site and an encyclopedia, but also a scientific journal. The pdf format of the Atlas ( constitutes the archives of a journal published 4 times a year since 1997, then 6 times in 2008, and 12 times in 2009. It includes 2,500 articles in more than 100 volumes, and 9,000 pages to allow us to be referenced by PubMed in the future.


Ergonomy: Access by pages (ex: chromosomes , by table of anomalies, genes and fusion genes by chromosomal band (ex:, with the more recent data on chromosomal abnormalities and fusion genes compiled (TCGA, Cosmic, TicDB, etc.). Synthetic tables (ex: nosology, patterns, categories, etc.).


The initial structure (independent documents) was improved to allow numerous internal hypertext links: i) direct links and ii) call for links from a given document to a wide range of other documents (ex: tumors associated with a given gene). The Atlas contains more than 17,000 internal links. It is bound to get enriched from its own contents by meta-analysis scripts.

Gestion of external links towards the majority of interesting public databases is automatic.

The Atlas is referenced by other web sites (NextProt, GeneCards, Mitelman database, COSMIC, etc.).

The Atlas benefits from the material support of INIST (CNRS-INSERM), allowing an excellent internet access (more than 1.5 million visits in a year).


In conclusion: original database with no equivalent or concurrence, therefore necessary, besides several other databases, for an in-depth analysis (ex: Atlas + Mitelman + Gene at NCBI + Cosmic).


… However …


Lack of exhaustivity and lack of update of the existing documents (due to lack of staff and the amount of work to be done - the Atlas has already more than 50,000 pages).

Need for the database restructuration, with an editorial system and a more performing ergonomics of consultation.

A need, very soon, for new developments concerning new techniques in genetics.


Note: Some addresses

- New developments:

- Atlas Journal Pdf/Scientific side of the Atlas:


- Cell Biology: e.g.

- Cell lines:

- Nosology:

- Physical maps of genes, markers, and diseases at the level of the chromosome band: e.g.



[1]Given the magnitude of the task, it could be very tempting to limit the Atlas to only a part of it, let's say the leukemias part.

However, it would ruin a specificity/originality of the Atlas: bringing together the diverse and complementary knowledge, to offer a broader view concerning cancer genetics processes. All the more so as a gene can be translocated in a leukemia and overexpressed in a carcinoma, or the opposite, and as the t(16;21)(p11;q22) FUS/ERG may be found in the Ewing?PNET spectrum and in acute myeloid leukemia!.