Atlas of Genetics and Cytogenetics in Oncology and Haematology

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Atlas of Genetics and Cytogenetics in Oncology and Haematology
Content
DescriptionThe Atlas is a peer reviewed on-line journal / encyclopedia / database in open access dealing with chromosomes, genes and cancers and the biology of normal and cancerous cells.
Data types
captured		Annotation on chromosomes, genes and cancers
Organisms Human
Miscellaneous
Versioning Yes
Data release
frequency		every week
Curation policyYes – manual (over 10,000 pages) and automatic (30,000 pages). Full review articles vs automatic annotation.

The Atlas of Genetics and Cytogenetics in Oncology and Haematology, created in 1997 by Jean-Loup Huret (with bioinformatics by Philippe Dessen) is a collection of resources on genes, chromosomes anomalies, leukemias, solid tumours, and cancer-prone diseases. The project is accessible through Internet and is made of encyclopedic-style files, as well as traditional overviews, links towards websites and databases devoted to cancer and/or genetics, case reports in haematology. It also encompasses teaching items in various languages. [1]

Contents

Starting first from cytogenetics in the nineteens, the Atlas now combines different types of knowledge in a single web site: genes and their function, cell biology (ex: Apoptosis), [2] 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. [3] It includes a large iconography of about 35,000 images. Dan van Dyke said "This is one stop shopping that unifies cancer genetics information", and Lidia Larizza said that the Atlas was an "interdisciplinary resource". Felix Mitelman said "This systematic collection of cytogenetic and genetic aberrations (…) the molecular outcome (…) and the clinical consequences (….) has grown into a truly monumental encyclopedic work of great importance"; Janet Rowley said: "In the future I will undoubtedly rely on your Website rather than trying to keep up with the literature myself" [4]

The Atlas is part of the genome project and participates in research on cancer epidemiology. The Atlas is accessed by: 1- researchers in cytogenetics, molecular biology, cell biology; 2- clinicians, haematologists, cytogeneticists, pathologists, from the university hospitals, indeed, but also from general hospitals where the Atlas is one of the rare free resources. Junior doctors in haematology or oncology, are also most receptive to the Atlas that they see as a training and educational tool; 3-Students in medicine and life sciences. [5]

In 2017, it contains review articles on 1,500 genes, 700 papers on leukemias, 220 on solid tumors, and 110 on hereditary disease with a cancer-prone condition and 110 "Deep Insights" on related subjects, 40,000 internal links and 730,000 external links. This represents 45,000 "web pages" (i.e. about 200,000 printed pages). More than 3,300 authors have/are contributing (1 130 North-American, 400 French, 300 Italian, 200 Japanese, 180 Spanish, 170 German, 160 English, 140 Chinese, etc...) . [6] It includes an iconography of about 35,000 images.

In 2018, Jesús María Hernández Rivas (Salamanca, Spain) and Paola Dal Cin (Boston, Massachusetts) joined Jean-Loup Huret as Co-Editors in Chief, and in April 2021 Alessandro Beghini (Milano, Italy) and João Agostinho Machado-Neto (São Paulo, Brazil) replace Jean-Loup Huret. "After 25 years building the Atlas day after day, Jean-Loup Huret and Philippe Dessen will take a little rest", as is said on the web site. [7]

The Atlas is also published as a scientific journal by CNRS, [8] and is referenced by Scopus et Embase. The Atlas is financially supported by scientific societies, charities and individual donations. More data is available from the site of the association in charge of the Atlas. [9]

See also

Related Research Articles

<span class="mw-page-title-main">Autosome</span> Any chromosome other than a sex chromosome

An autosome is any chromosome that is not a sex chromosome. The members of an autosome pair in a diploid cell have the same morphology, unlike those in allosomal pairs, which may have different structures. The DNA in autosomes is collectively known as atDNA or auDNA.

<span class="mw-page-title-main">Chromosome</span> DNA molecule containing genetic material of a cell

A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are the histones. These proteins, aided by chaperone proteins, bind to and condense the DNA molecule to maintain its integrity. These chromosomes display a complex three-dimensional structure, which plays a significant role in transcriptional regulation.

<span class="mw-page-title-main">Molecular genetics</span> Scientific study of genes at the molecular level

Molecular genetics is a sub-field of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the structure and/or function of genes in an organism's genome using genetic screens. The field of study is based on the merging of several sub-fields in biology: classical Mendelian inheritance, cellular biology, molecular biology, biochemistry, and biotechnology. Researchers search for mutations in a gene or induce mutations in a gene to link a gene sequence to a specific phenotype. Molecular genetics is a powerful methodology for linking mutations to genetic conditions that may aid the search for treatments/cures for various genetics diseases.

<span class="mw-page-title-main">Cytogenetics</span> Branch of genetics

Cytogenetics is essentially a branch of genetics, but is also a part of cell biology/cytology, that is concerned with how the chromosomes relate to cell behaviour, particularly to their behaviour during mitosis and meiosis. Techniques used include karyotyping, analysis of G-banded chromosomes, other cytogenetic banding techniques, as well as molecular cytogenetics such as fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH).

<span class="mw-page-title-main">Fusion gene</span>

A fusion gene is a hybrid gene formed from two previously independent genes. It can occur as a result of translocation, interstitial deletion, or chromosomal inversion. Fusion genes have been found to be prevalent in all main types of human neoplasia. The identification of these fusion genes play a prominent role in being a diagnostic and prognostic marker.

<span class="mw-page-title-main">Locus (genetics)</span> Location of a gene or region on a chromosome

In genetics, a locus is a specific, fixed position on a chromosome where a particular gene or genetic marker is located. Each chromosome carries many genes, with each gene occupying a different position or locus; in humans, the total number of protein-coding genes in a complete haploid set of 23 chromosomes is estimated at 19,000–20,000.

<span class="mw-page-title-main">Genetic analysis</span>

Genetic analysis is the overall process of studying and researching in fields of science that involve genetics and molecular biology. There are a number of applications that are developed from this research, and these are also considered parts of the process. The base system of analysis revolves around general genetics. Basic studies include identification of genes and inherited disorders. This research has been conducted for centuries on both a large-scale physical observation basis and on a more microscopic scale. Genetic analysis can be used generally to describe methods both used in and resulting from the sciences of genetics and molecular biology, or to applications resulting from this research.

A chromosomal abnormality, chromosomal anomaly, chromosomal aberration, chromosomal mutation, or chromosomal disorder, is a missing, extra, or irregular portion of chromosomal DNA. These can occur in the form of numerical abnormalities, where there is an atypical number of chromosomes, or as structural abnormalities, where one or more individual chromosomes are altered. Chromosome mutation was formerly used in a strict sense to mean a change in a chromosomal segment, involving more than one gene. Chromosome anomalies usually occur when there is an error in cell division following meiosis or mitosis. Chromosome abnormalities may be detected or confirmed by comparing an individual's karyotype, or full set of chromosomes, to a typical karyotype for the species via genetic testing.

<span class="mw-page-title-main">B-cell maturation antigen</span> Protein-coding gene in the species Homo sapiens

B-cell maturation antigen, also known as tumor necrosis factor receptor superfamily member 17 (TNFRSF17), is a protein that in humans is encoded by the TNFRSF17 gene.

<span class="mw-page-title-main">Extracellular matrix protein 1</span> Protein-coding gene in the species Homo sapiens

Extracellular matrix protein 1 is a protein that in humans is encoded by the ECM1 gene.

<span class="mw-page-title-main">BIRC6</span> Protein-coding gene in the species Homo sapiens

Baculoviral IAP repeat-containing protein 6 is a protein that in humans is encoded by the BIRC6 gene.

<span class="mw-page-title-main">Felix Mitelman</span> Swedish geneticist and professor

Felix Mitelman is a Swedish geneticist and is professor of clinical genetics in Lund, Sweden. He is best known for his pioneering work on chromosome changes in cancer.

TOX high mobility group box family member 3, also known as TOX3, is a human gene.

Virtual karyotype is the digital information reflecting a karyotype, resulting from the analysis of short sequences of DNA from specific loci all over the genome, which are isolated and enumerated. It detects genomic copy number variations at a higher resolution for level than conventional karyotyping or chromosome-based comparative genomic hybridization (CGH). The main methods used for creating virtual karyotypes are array-comparative genomic hybridization and SNP arrays.

COSMIC is an online database of somatically acquired mutations found in human cancer. Somatic mutations are those that occur in non-germline cells that are not inherited by children. COSMIC, an acronym of Catalogue Of Somatic Mutations In Cancer, curates data from papers in the scientific literature and large scale experimental screens from the Cancer Genome Project at the Sanger Institute. The database is freely available to academic researchers and commercially licensed to others.

<span class="mw-page-title-main">Breakage-fusion-bridge cycle</span>

Breakage-fusion-bridge (BFB) cycle is a mechanism of chromosomal instability, discovered by Barbara McClintock in the late 1930s.

The Cancer Genome Anatomy Project (CGAP), created by the National Cancer Institute (NCI) in 1997 and introduced by Al Gore, is an online database on normal, pre-cancerous and cancerous genomes. It also provides tools for viewing and analysis of the data, allowing for identification of genes involved in various aspects of tumor progression. The goal of CGAP is to characterize cancer at a molecular level by providing a platform with readily accessible updated data and a set of tools such that researchers can easily relate their findings to existing knowledge. There is also a focus on development of software tools that improve the usage of large and complex datasets. The project is directed by Daniela S. Gerhard, and includes sub-projects or initiatives, with notable ones including the Cancer Chromosome Aberration Project (CCAP) and the Genetic Annotation Initiative (GAI). CGAP contributes to many databases and organisations such as the NCBI contribute to CGAP's databases.

<span class="mw-page-title-main">Jean-Loup Huret</span>

Jean Loup Huret is a French scientist and medical practitioner specialist in genetics, honorary associate professor of medical genetics of the French Universities, working on chromosome abnormalities.

The Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer is a free access database devoted to chromosomes, genes, and cancer. It was first published in 1983 as a book named "Catalog of Chromosome aberrations in Cancer" in the Journal of Cytogenetics and Cell Genetics, containing 3,844 cases. Subsequent editions of the Catalog were published 1985, 1988, 1991, 1994 (22,076 cases), and 1998. In 2000, it became an online database on open access hosted by the NCI.

Henry HQ Heng is a professor of molecular medicine and genetics and of pathology at the Wayne State University School of Medicine. Heng first received his PhD from the University of Toronto Hospital for Sick Children in 1994, mentored by Lap-Chee Tsui. He then completed his post-doc under Peter Moens at York University, before joining the Wayne State University School of Medicine faculty.

References

  1. ↑ Huret, Jean-Loup; Ahmad, Mohammad; Arsaban, Mélanie; Bernheim, Alain; Cigna, Jérémy; Desangles, François; Guignard, Jean-Christophe; Jacquemot-Perbal, Marie-Christine; Labarussias, Maureen; Leberre, Vanessa; Malo, Anne; Morel-Pair, Catherine; Mossafa, Hossein; Potier, Jean-Claude; Texier, Guillaume; Viguié, Franck; Yau Chun Wan-Senon, Sylvie; Zasadzinski, Alain; Dessen, Philippe (17 November 2012). "Atlas of Genetics and Cytogenetics in Oncology and Haematology in 2013". Nucleic Acids Research. 41 (D1): D920–D924. doi:10.1093/nar/gks1082. PMC   3531131 . PMID   23161685.
  2. ↑ "Apoptosis". Atlas of Genetics and Cytogenetics in Oncology and Haematology. Archived from the original on 2010-06-05.
  3. ↑ "Chromosomes in Cancer - Argument". chromosomesincancer.org/en.
  4. ↑ "Atlas backpage". atlasgeneticsoncology.org.
  5. ↑ "General Pediatric Brain Tumor". Pediatric Oncology Education Materials.
  6. ↑ "Atlas_status". atlasgeneticsoncology.org.
  7. ↑ "Atlas backpage". atlasgeneticsoncology.org.
  8. ↑ "Atlas of Genetics and Cytogenetics in Oncology and Haematology". I-Revues. hdl:2042/15655. Archived from the original on 2018-06-02.
  9. ↑ "Chromosomes in Cancer - Homepage". chromosomesincancer.org/en.

Sources

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