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MSY Breakpoint Mapper

http://breakpointmapper.wi.mit.edu/

Description :
Sequence-tagged sites in the human Y chromosome

Atlas of Genetics and Cytogenetics in Oncology and Haematology

http://atlasgeneticsoncology.org/

Description :
The Atlas of Genetics and Cytogenetics in Oncology and Haematology http://atlasgeneticsoncology.org/ contains concise and updated cards on cancer related genes, chromosomal abnormalities, cancers, and cancer-prone diseases, a portal towards genetics/cancer, and teaching materials in genetics (1-3). This database is made for and by researchers and clinicians, who are encouraged to contribute. Contributions are reviewed before acceptance.

Database Structure
Cards: well structured papers which represent the body of the Atlas. Cards on genes include data on: DNA/RNA, protein, mutations, and diseases. Cards on leukemias and solid tumours include data on: clinics, cytogenetics, genes, hybrid gene and fusion protein. Cards on cancer-prone diseases include data on: inheritance mode, clinics, neoplastic risk, cytogenetics, genes and proteins, mutations. Cards also include hyperlinks towards Medline, and towards the main complementary databases (nomenclature, cartography, gene structure, transcripts, proteins, domain families, diseases, mutations, probes). Pages classified by chromosome present genes and diseases and also point towards external resources.
Deep Insights/Case Reports: Deep insights are review articles. The Case Reports Section is dedicated to rare cytogenetic entities of leukemia to document these poorly known entities, to further delineate their epidemiology, including the associated prognosis: the Atlas intend to provide new information in cancer epidemiology.
Portal: towards Internet databases devoted to genetics and/or cancer, and towards 100 journals, with specific pages on both the lattest issue and the archives, with indications on free access when available. Teaching materials in Genetics are being developed in English, French, German, Portuguese, and Spanish, and we are (still) looking for an Italian translation. We are happy that some Universities already use the Atlas for teaching; they can also provide us with more authors.

Comments
The Atlas is a peer reviewed on-line journal and database indexed by the Current Contents. More than a 260 collaborators are contributing and more than 600 papers are available. More than 28 000 individual machines connect each month. The Atlas is part of the genome project and participates in the research in cancer epidemiology. The Atlas is at the crossroads of research, university and post-university teaching (virtual medical university), and telemedicine. It contributes to meta-medicine, this mediation, using new information technology, between the overflowing information provided by the scientific community and the individual practitioner. Contributions and collaborations are MOST welcome. It will serve the entire community of clinicians, researchers, and students

Aknowledgement :
The Atlas is funded by: Ministère de la Recherche, Ministère de lí Education Nationale, Département de la Vienne, Communauté dí Agglomération de Poitiers, Ligue Nationale contre le Cancer (Charente, Cher, Corrèze, Indre, et Poitou-Charentes), and benefits from INFOBIOGEN resources.

References :

  1. Huret,J.L., Dessen,P. and Bernheim,A. (2001) Atlas of Genetics and Cytogenetics in Oncology and Haematology, Updated. Nucleic Acids Res., 29, 303-304.
  2. Kaiser,J. (2001) Fingerprinting a killer. Science 292, 1803. http://www.sciencemag.org/cgi/content/summary/292/5523/1803b
  3. Pearson,H. (2001) Lifelines: browsing the cancer catalogue. Nature Science Update 30 May 2001. http://www.nature.com/nsu/010531/010531-8.html#

Cancer Chromosomes

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cancerchromosomes

Description :
Cancer Chromosomes is an Entrez database that integrates data from three sources: the NCI/NCBI SKY/M-FISH & CGH Database, the NCI Mitelman Database of Chromosome Aberrations in Cancer, and the NCI Recurrent Aberrations in Cancer. Provides the ability to search for cytogenetic, clinical, and/or reference information. Similarity Reports demonstrate cytogenetic and clinical relatedness at varying levels of specificity. Linking between entries based on similarity of genetic features is supported.

SKY/M-FISH and CGH

http://www.ncbi.nlm.nih.gov/sky/

Description :
The NCI and NCBI SKY/M-FISH and CGH Database is a repository of publicly submitted data from Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH), and Comparative Genomic Hybridization (CGH), which are complementary fluorescent molecular cytogenetic techniques. SKY/M-FISH permits the simultaneous visualization of each human or mouse chromosome in a different color, facilitating the identification of chromosomal aberrations; CGH can be used to generate a map of DNA copy number changes in tumor genomes. Collaborative project with the National Cancer Institute.

HCAD - Human Chromosome Aberration Database

http://www.pdg.cnb.uam.es/UniPub/HCAD/

Description :
Chromosomal breakpoints and affected genes

The Autism Chromosome Rearrangement Database

http://projects.tcag.ca/autism

Description :
A curated database of chromosomal breakpoints and other genomic features related to autism.

The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature, databases and unpublished data. The database is continuously updated with information from in-house experimental data as well as data from published research studies. We welcome submission of data and comments regarding the database from the research community.

Recent develoments :
Keyword searches of the database have been implemented and links to NCBI and UCSC are available for relevant publications and sequence links.

Aknowledgement :
We thank The Centre for Applied Genomics at the Hospital for Sick Children (HSC) as well as collaborators worldwide. Supported by Genome Canada, the McLaughlin Centre for Molecular Medicine, the Howard Hughes Medical Institute International Scholar Program (to S.W.S.). and the HSC Foundation.

References :
1. Xu, J., Zwaigenbaum, L., Szatmari, P. and Scherer, S.W. 2004. Molecular Cytogenetics of Autism. Current Genomics 5(4), 347-364.

KaryotypeDB

http://www.nenno.it/karyotypedb/

Description :
The Karyotype database (KaryotypeDB) contains karyotype and chromosome information like chromosome number, length, karyotype features, idiograms, physical localizations of DNA sequences by fluorescence in situ hybridizion (FISH), and cell material for metaphase chromosomes and polytene chromosomes from different animal and plant species together with literature references and links.

Cancer Genome Anatomy Project

http://cgap.nci.nih.gov/

Description :
Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data.

CAPweb

http://bioinfo.curie.fr/CAPweb/

Description :
CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.

ISACGH

http://isacgh.bioinfo.cipf.es/

Description :
ISACGH (In Silico Array CGH) is a tool for visualizing array CGH data and/or expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. ISACGH is included in the GEPAS package.

PROGENETIX CGH database: Cytogenetics in Leukemia and Cancer

http://www.progenetix.de/~pgscripts/progenetix/Aboutprogenetix.html This database is a collection of published cytogenetic abnormalities in human malignancies, mostly from CGH experiments. For all cases registered in Pprogenetix, band specific chromosomal aberration data is available to be included in data mining projects. The complete dataset can be accessed for download (You have to check on the website for the License terms).

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