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  Blood Group Antigen Gene Mutation Database
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BGMUT Resources
 Last Updated, July 2010

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Publications

Peer-reviewed publications about the database
Blumenfeld OO.  Mutation databases and other online sites as a resource for transfusion medicine: history and attributes.  Transfus Med Rev. 2002 Apr;16(2):103-14.  PubMed 11941573

Claustres M, Horaitis O, Vanevski M, Cotton RG.  Time for a unified system of mutation description and reporting: a review of locus-specific mutation databases.  Genome Res. 2002 May;12(5):680-8.  PubMed 11997335
Annotation: This publication reviewed more than 200 locus specific databases for 10 characteristics concerning ease of use and quality and quantity of information.  Only 3 databases received the highest score (9/10): BGMUT, hemoglobin variants, and phenylalanine hydroxylase.

Blumenfeld OO, Patnaik SK.  Allelic genes of blood group antigens: a source of human mutations and cSNPs documented in the Blood Group Antigen Gene Mutation Database.  Hum. Mutat. 2004 Jan;23(1):8-16.  PubMed 14695527

Patnaik SK, Blumenfeld OO.  Patterns of human genetic variation inferred from comparative analysis of allelic mutations in blood group antigen genes.  Hum. Mutat. 2011 Mar;32(3):263-71.  PubMed 21312314

Patnaik SK, Helmberg W, Blumenfeld OO.  BGMUT: NCBI dbRBC database of allelic variations of genes encoding antigens of blood group systems.  Nucleic Acids Res. 2012 Jan;40(1):D1023-9.  PubMed 22084196

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Acknowledgement

Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, New York for supporting our efforts towards the development and growth of the database from 1999 to 2011.

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Tutorials

External Links

Websites about blood group antigens

SCARF (Serum, Cells, and Rare Fluid) Exchange is a scientific consortium sharing samples with unique blood group phenotypes, rare antibodies, and genomic DNA samples.  This site provides brief descriptions of 26 blood group systems.

The Rhesus site provides a thorough and comprehensive description of the RH gene locus including a database of RHD alleles.

The International Society for Blood Transfusion (ISBT) has specific blood group terminology and classification nomenclature for Red Cell Surface Antigens, including information on blood group genotyping workshops.

The Bristol Institute for Transfusion Sciences and The International Blood Group Reference Laboratory provide the most complete list of links to a large number of sites useful to the transfusion medicine community.

dbLRC is a database of DNA sequences and typing reagents related to the human Leukocyte Receptor Complex.  dbMHC is a database of DNA and clinical data related to the human Major Histocompatibility Complex.

Websites on human gene mutations and polymorphisms

Human Gene Mutation Database (HGMD): At the University of Wales, College of Medicine, Cardiff and now associated with BIOBASE Biological Databases.  This database contains a collection of data on germ-line mutations in nuclear genes responsible for human inherited disease.  Access is limited to registered users from academic and non-profit institutions.  Access to commercial users requires a license purchased from BIOBASE.  Such a license is also required for all users for access to the most up-to-date version of the database.

Human Genome Variation Society (HGVS), previously known as HUGO Mutation Database Initiative (HMDI), is the key organization concerned with the planning and coordination of the catalog of human genetic variation (see R.G.H. Cotton, Human Mutation. 15:4, 2000).  Its aim is to "foster the discovery and characterization of genomic variation."  The home page at the University of Melbourne provides access to a list of a large number of mutation databases and related sites including databases dealing with mutations in an ever-growing number of individual genes, Locus Specific Mutation databases, two kinds of central mutation databases and other large databases that include National and Ethnic, Mitochondrial, Chromosomal, Non-human and others.  This important resource is the most complete list of databases dealing with DNA changes.

Human Genome Variation Database of Genotype-to-Phenotype information (HGVbaseG2P) focuses on genetic association studies.  It can be queried for the actual studies, phenotypes or markers.  In the first two cases a brief summary of results, a list of contributors and citations is provided.  Markers can be searched by SNP identifiers.

dbSNP.  A Database of Single Nucleotide Polymorphisms (SNPs) and other non-polymorphic variants serves as a central repository for single base nucleotide substitutions and short deletions and insertions.  These are the most common variations that occur in the human genome found approximately once every 100 to 300 bases.  The SNPs can be viewed on the gene map or, in more detail, on the gene of interest.  Clinical association, frequency, and validation data are available.  The database can be searched and information can be submitted.  SNPs for non-human species (including horse, cow, rat, platypus, and zebrafish) are also provided.  The data in dbSNP is integrated with other NCBI genomic data and is publicly and freely available.

The Human Genome Project is sponsored by the US Department of Energy and the NIH.  Its goal is the "understanding of genetic material on a large scale" and the application of studies of genomics to human health.  It is the most comprehensive site about the human genome, genomes of some other species, the related technologies, and the ethical, social and legal issues resulting from the projects available.  It provides a valuable list of links to most aspects of research related to human and other genomes.  The site is an invaluable resource.

OMIM.  Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.  OMIM focuses on the "relationship of phenotype and genotype" presenting information on best known Mendelian disorders.  Molecular information includes a historical narrative with links to key publications.  The functional role of the gene also is summarized in text form with a timeline perspective.  Selected examples of allelic variants are listed and briefly summarized.  This is an authoritative resource for association of genes with human disease.

The UCSC (University of California at Santa Cruz) Genome Browser provides a display of requested portions of genomes together with aligned annotation tracks of features of interest within the requested region.  A large number of features are available.  They include location of neighboring genes, ESTs, mRNAs, SNPs, patterns of orthologues, and levels of conservation or expression.  Information from the ENCODE project at NHGRI is also included.  The goal is to show interrelated information contained within the sequence of the human genome with locations of functional regulatory elements such as transcriptional regulatory sequences or determinants of chromosomal structure and function.  An important feature of the Genome Browser is its connection to the PhenCode site (see below) which displays DNA changes documented in selected Locus Specific Databases, (including BGMUT).  Annotations are assembled by the UCSC Bioinformatics Group and are based on publicly available data contributed by many labs and research groups throughout the world.

PhenCode.  This site connects DNA changes compiled in locus specific databases (LSDB) with genotypic and functional data available.  DNA changes in about 30 LSDBs can be viewed as tracts on the UCSC Genome Browser.  In addition, users may be "able to query on phenotype across loci (e.g. all mutations that cause anemia, regardless of gene)."

The GeneCards Database originates from the Crown Human Genome Center at the Weizmann Institute of Sciences in Israel.  Its unique feature is that it extracts relevant information from a number of specialized databases and assembles and integrates it to relate it to a particular gene.  Total molecular information is provided, including genomic location, DNA and protein sequences, 3D structure, post-transitional modifications, subcellular localization, availability of antibodies, RNAi, clones, primers etc.  Functional features and protein features, such as domains are summarized.  The database is a comprehensive and valuable resource.

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