- Email: [email protected]
Genetics of disease
261
Genetics of disease Web alert Izabela Makalowska*, Tyra G Wolfsberg† and Anna Lorenc‡ A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Genetics & Development. Addresses *Life Sciences Consortium, The Pennsylvania State University, 506 Wartik Lab, University Park, Pennsylvania 16802, USA †National Human Genome Research Institute, National Institutes of Health, Building 50, Room 5228B, 50 South Drive, Bethesda, Maryland 20892-8004, USA ‡Department of Biology, The Pennsylvania State University, 514 Mueller Lab, University Park, Pennsylvania 16802, USA Current Opinion in Genetics & Development 2002, 12:261–262
Human Gene Mutation Database http://www.hgmd.org Hosted by University of Wales College of Medicine. Contains lists of all known to date human disease-associated mutations (i.e. 25,256 mutations in 1132 nuclear genes for 14th February, 2002). Provides also reference cDNA sequences for presented genes, literature references and links to many external resources. Online Mendelian Inheritance in Man (OMIM) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM OMIM is a catalog of human genes and genetic disorders authored and edited by Victor McKusick and his colleagues. Queries to OMIM are now even more powerful, as it has recently been integrated into the NCBI’s Entrez system. OMIM contains textual information, pictures, and reference information, as well as links to MEDLINE articles and sequence information already in Entrez. Genes and Disease http://www.ncbi.nlm.nih.gov/disease/ This site, sponsored by the NCBI, provides information about many mapped human disease genes. It includes information about the disease, sequence, genetic, and literature databases, as well as patient information sites. Rare Genetic Diseases In Children: The Rare Disease Catalogue http://mcrcr2.med.nyu.edu/murphp01/disease.htm This ‘Disease Catalog’ provides a comprehensive list of web sites dedicated to specific genetic diseases. Diseases are listed alphabetically, and each entry is linked to the appropriate OMIM citation, as well as to organizations that can provide additional information. Gene Cards Project http://bioinformatics.weizmann.ac.il/cards/ ‘GeneCards’ is a dictionary-like database that integrates biomedical knowledge from several sources and presents it as an overview. An individual GeneCard gives the information about important features of a gene, e.g. the official name, a list of synonyms, homologous genes in the mouse, the locus of the
gene and of its homologs, the name of its product(s), the main features of this/these product(s), a list of disorders in which the gene is involved, and medical applications, like new therapies and diagnoses. Mouse Knockout and Mutation Database http://research.bmn.com/mkmd/ Mouse Models of Human Disease http://research.bmn.com/mkmd/reviews BioMedNet’s ‘Mouse Knockout and Mutation Database (MKMD)’ is a fully searchable database of phenotypic information related to knockout and classical mutations in mice. It provides comprehensive coverage of neurological, immunological and physiological knockouts and contains >7000 entries and >2000 unique genes. There is also a section dedicated to human disease, including reviews. Updated weekly and with all entries filtered through an international editorial board, MKMD provides information of a high-quality and accuracy. GeneDis http://life2.tau.ac.il/GeneDis/ ‘GeneDis’ is a human genetic disease database with a user graphical interface to a sequence search engine. GeneDis currently includes 12 human genetic diseases. An individual page for each disease presents primary sequences of genes and proteins involved in these human genetic diseases, mutation tables, experimentally determined or modeled 3D structures, sequence alignments and links to other databases. HuGENet http://www.cdc.gov/genomics/hugenet/ The ‘Human Genome Epidemiology Network (HuGENet)’ is a worldwide collaborative project to develop and communicate human genome-related epidemiological information. HuGENet reviews are written by experts in the field and summarize data about a gene’s allelic variants. HuGENet fact-sheets summarize clinical information about genes. The ‘Weekly Update’ provides a summary of ‘Genetics in the News’, as well as ‘Genetics in the Scientific Literature’. A Human Mitochondrial Genome Database MITOMAP http://gen.emory.edu/mitomap.html Maintained by the Center for Molecular Medicine at Emory University, ‘MITOMAP’ brings together information on human mitochondrial genome structure and function, pathogenic mutations and population-associated variation. Provides an exhaustive list of mitochondrial references, as well as links to other mitochondria-oriented sites. Contains database of all known mtDNA mutations and polymorphisms and a collection of unpublished polymorphisms. Contains also The Report of the Committee on the Human Mitochondrial Genome (1995), which is still a comprehensive source of information on mitochondrial DNA mutations and disorders in which the mitochondrial DNA deficiencies have been observed.
262
Web alert
MITOP — Database for Mitochondria-related Genes, Proteins and Diseases http://www.mips.biochem.mpg.de/proj/medgen/mitop/ ‘MITOP’ is a comprehensive database for genetic and functional information on nuclear- and mitochondrial-encoded mitochondrial proteins and their genes. Proteins from five species: Saccharomyces cerevisiae, Mus musculus, Caenorhabditis elegans, Neurospora crassa and Homo sapiens are classified in various ways (e.g. by molecular characteristics, functional categories, metabolic pathways, protein complexes, genomic location) allowing extensive searching. For each of the species, MITOP provides information on mitochondrial genes’ orthologs, including some prokaryotic orthologs. Cancer Genome Anatomy Project (CGAP) http://www.ncbi.nlm.nih.gov/CGAP/ The goal of CGAP, administered by the National Cancer Institute and other institutes at the National Institutes of Health, is to decipher the molecular anatomy of the cancer cell. It includes five initiatives: the ‘Human Tumor Gene Index’ and the ‘Mouse Tumor Gene Index’ identify genes expressed during tumor development; ‘Molecular Profiling’ demonstrates molecular analysis of human tissue specimens; the ‘Cancer Chromosome Aberration Project’ characterizes chromosomal alterations associated with malignant transformation; and the ‘Genetic Annotation Index’ identifies and characterizes cancer polymorphisms. ClinicalTrials.gov http://www.clinicaltrials.gov/ This web resource was developed by National Institutes of Health through its National Library of Medicine. The main goal is to provide patients, family members and members of the public current information about clinical research studies. The site currently contains 5800 clinical studies sponsored by the National Institutes of Health, other Federal agencies, and the pharmaceutical industry in >63,000 locations worldwide. GeneTests GeneClinics http://www.geneclinics.org/ GeneTests GeneClinics provides information about genetic testing, including lists of laboratories and clinics, as well as GeneReviews, with information about the use of genetic testing for patients with inherited diseases. It is intended for genetics professionals, although other healthcare providers and patients may benefit as well. The site is free, but it requires a one-time registration. Hereditary Disease Foundation http://www.hdfoundation.org/ This web site of Hereditary Disease Foundation contains information about research grants, clinical trials, newest discoveries, and testing. It also includes links to the latest publications and hereditary disease related web pages.
WHO Human Genetics Programme http://www.who.int/ncd/hgn/ The Human Genetics Programme is an arm of the World Health Organization (WHO) that develops genetic approaches to prevent and control common hereditary diseases. The Breast Cancer Information Core (BIC) http://www.nhgri.nih.gov/Intramural_research/Lab_transfer/Bic/ The Breast Cancer Information Core (BIC) was established to facilitate the detection and characterization of breast cancer susceptibility genes. It is a repository for all mutations and polymorphisms in these genes, and also provides techniques, primers, and support. Access is open to all who agree to abide by rules governing the use of the pre-publication data found at the site. Neuromuscular Disease Center http://www.neuro.wustl.edu/neuromuscular/index.html A compendium on neuromuscular disease created by Alan Pestronk, a neurologist at Washington University Medical School in St. Louis, gathering information on clinical medicine and molecular biology. An easy-to-follow tabular form provides links to more detailed information. There are pages on neuromuscular evaluation and an impressive collection of pathology specimens as well as ‘Wallet Websites’, summaries of neuromuscular differential diagnoses that can be especially useful for clinicians. The Hereditary Hearing loss Homepage http://www.uia.ac.be/dnalab/hhh/ ‘Hereditary Hearing loss Homepage’ lists all known loci and genes involved in hearing impairment (mostly nonsyndromic). Provides literature references and external links. Leiden Molecular Dystrophy Pages http://www.dmd.nl/index.html ‘Leiden Molecular Dystrophy Pages’ are dedicated to scientists interested in either research or diagnosis in Duchenne and Duchenne-like muscular dystrophies. Apart from mutation databases of various muscular dystrophies, it contains description of genes and proteins involved in dystrophy pathogenesis. Provides laboratory protocols and presents the latest news in the field. The site is maintained by Johan T den Dunnen from the Center for Human and Clinical Genetics at Leiden University Medical Center. Familial Dysautonomia Foundation http://www.familialdysautonomia.org/ The Familial Dysautonomia (FD) Foundation maintains this site, providing broad information related to this disease. It contains information about current research, treatment, genetics, patient care, advocacy as well as services and resources. It also provides links to pages related to FD and other genetic diseases.
Genetics of disease Web alert Izabela Makalowska*, Tyra G Wolfsberg† and Anna Lorenc‡ A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Genetics & Development. Addresses *Life Sciences Consortium, The Pennsylvania State University, 506 Wartik Lab, University Park, Pennsylvania 16802, USA †National Human Genome Research Institute, National Institutes of Health, Building 50, Room 5228B, 50 South Drive, Bethesda, Maryland 20892-8004, USA ‡Department of Biology, The Pennsylvania State University, 514 Mueller Lab, University Park, Pennsylvania 16802, USA Current Opinion in Genetics & Development 2002, 12:261–262
Human Gene Mutation Database http://www.hgmd.org Hosted by University of Wales College of Medicine. Contains lists of all known to date human disease-associated mutations (i.e. 25,256 mutations in 1132 nuclear genes for 14th February, 2002). Provides also reference cDNA sequences for presented genes, literature references and links to many external resources. Online Mendelian Inheritance in Man (OMIM) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM OMIM is a catalog of human genes and genetic disorders authored and edited by Victor McKusick and his colleagues. Queries to OMIM are now even more powerful, as it has recently been integrated into the NCBI’s Entrez system. OMIM contains textual information, pictures, and reference information, as well as links to MEDLINE articles and sequence information already in Entrez. Genes and Disease http://www.ncbi.nlm.nih.gov/disease/ This site, sponsored by the NCBI, provides information about many mapped human disease genes. It includes information about the disease, sequence, genetic, and literature databases, as well as patient information sites. Rare Genetic Diseases In Children: The Rare Disease Catalogue http://mcrcr2.med.nyu.edu/murphp01/disease.htm This ‘Disease Catalog’ provides a comprehensive list of web sites dedicated to specific genetic diseases. Diseases are listed alphabetically, and each entry is linked to the appropriate OMIM citation, as well as to organizations that can provide additional information. Gene Cards Project http://bioinformatics.weizmann.ac.il/cards/ ‘GeneCards’ is a dictionary-like database that integrates biomedical knowledge from several sources and presents it as an overview. An individual GeneCard gives the information about important features of a gene, e.g. the official name, a list of synonyms, homologous genes in the mouse, the locus of the
gene and of its homologs, the name of its product(s), the main features of this/these product(s), a list of disorders in which the gene is involved, and medical applications, like new therapies and diagnoses. Mouse Knockout and Mutation Database http://research.bmn.com/mkmd/ Mouse Models of Human Disease http://research.bmn.com/mkmd/reviews BioMedNet’s ‘Mouse Knockout and Mutation Database (MKMD)’ is a fully searchable database of phenotypic information related to knockout and classical mutations in mice. It provides comprehensive coverage of neurological, immunological and physiological knockouts and contains >7000 entries and >2000 unique genes. There is also a section dedicated to human disease, including reviews. Updated weekly and with all entries filtered through an international editorial board, MKMD provides information of a high-quality and accuracy. GeneDis http://life2.tau.ac.il/GeneDis/ ‘GeneDis’ is a human genetic disease database with a user graphical interface to a sequence search engine. GeneDis currently includes 12 human genetic diseases. An individual page for each disease presents primary sequences of genes and proteins involved in these human genetic diseases, mutation tables, experimentally determined or modeled 3D structures, sequence alignments and links to other databases. HuGENet http://www.cdc.gov/genomics/hugenet/ The ‘Human Genome Epidemiology Network (HuGENet)’ is a worldwide collaborative project to develop and communicate human genome-related epidemiological information. HuGENet reviews are written by experts in the field and summarize data about a gene’s allelic variants. HuGENet fact-sheets summarize clinical information about genes. The ‘Weekly Update’ provides a summary of ‘Genetics in the News’, as well as ‘Genetics in the Scientific Literature’. A Human Mitochondrial Genome Database MITOMAP http://gen.emory.edu/mitomap.html Maintained by the Center for Molecular Medicine at Emory University, ‘MITOMAP’ brings together information on human mitochondrial genome structure and function, pathogenic mutations and population-associated variation. Provides an exhaustive list of mitochondrial references, as well as links to other mitochondria-oriented sites. Contains database of all known mtDNA mutations and polymorphisms and a collection of unpublished polymorphisms. Contains also The Report of the Committee on the Human Mitochondrial Genome (1995), which is still a comprehensive source of information on mitochondrial DNA mutations and disorders in which the mitochondrial DNA deficiencies have been observed.
262
Web alert
MITOP — Database for Mitochondria-related Genes, Proteins and Diseases http://www.mips.biochem.mpg.de/proj/medgen/mitop/ ‘MITOP’ is a comprehensive database for genetic and functional information on nuclear- and mitochondrial-encoded mitochondrial proteins and their genes. Proteins from five species: Saccharomyces cerevisiae, Mus musculus, Caenorhabditis elegans, Neurospora crassa and Homo sapiens are classified in various ways (e.g. by molecular characteristics, functional categories, metabolic pathways, protein complexes, genomic location) allowing extensive searching. For each of the species, MITOP provides information on mitochondrial genes’ orthologs, including some prokaryotic orthologs. Cancer Genome Anatomy Project (CGAP) http://www.ncbi.nlm.nih.gov/CGAP/ The goal of CGAP, administered by the National Cancer Institute and other institutes at the National Institutes of Health, is to decipher the molecular anatomy of the cancer cell. It includes five initiatives: the ‘Human Tumor Gene Index’ and the ‘Mouse Tumor Gene Index’ identify genes expressed during tumor development; ‘Molecular Profiling’ demonstrates molecular analysis of human tissue specimens; the ‘Cancer Chromosome Aberration Project’ characterizes chromosomal alterations associated with malignant transformation; and the ‘Genetic Annotation Index’ identifies and characterizes cancer polymorphisms. ClinicalTrials.gov http://www.clinicaltrials.gov/ This web resource was developed by National Institutes of Health through its National Library of Medicine. The main goal is to provide patients, family members and members of the public current information about clinical research studies. The site currently contains 5800 clinical studies sponsored by the National Institutes of Health, other Federal agencies, and the pharmaceutical industry in >63,000 locations worldwide. GeneTests GeneClinics http://www.geneclinics.org/ GeneTests GeneClinics provides information about genetic testing, including lists of laboratories and clinics, as well as GeneReviews, with information about the use of genetic testing for patients with inherited diseases. It is intended for genetics professionals, although other healthcare providers and patients may benefit as well. The site is free, but it requires a one-time registration. Hereditary Disease Foundation http://www.hdfoundation.org/ This web site of Hereditary Disease Foundation contains information about research grants, clinical trials, newest discoveries, and testing. It also includes links to the latest publications and hereditary disease related web pages.
WHO Human Genetics Programme http://www.who.int/ncd/hgn/ The Human Genetics Programme is an arm of the World Health Organization (WHO) that develops genetic approaches to prevent and control common hereditary diseases. The Breast Cancer Information Core (BIC) http://www.nhgri.nih.gov/Intramural_research/Lab_transfer/Bic/ The Breast Cancer Information Core (BIC) was established to facilitate the detection and characterization of breast cancer susceptibility genes. It is a repository for all mutations and polymorphisms in these genes, and also provides techniques, primers, and support. Access is open to all who agree to abide by rules governing the use of the pre-publication data found at the site. Neuromuscular Disease Center http://www.neuro.wustl.edu/neuromuscular/index.html A compendium on neuromuscular disease created by Alan Pestronk, a neurologist at Washington University Medical School in St. Louis, gathering information on clinical medicine and molecular biology. An easy-to-follow tabular form provides links to more detailed information. There are pages on neuromuscular evaluation and an impressive collection of pathology specimens as well as ‘Wallet Websites’, summaries of neuromuscular differential diagnoses that can be especially useful for clinicians. The Hereditary Hearing loss Homepage http://www.uia.ac.be/dnalab/hhh/ ‘Hereditary Hearing loss Homepage’ lists all known loci and genes involved in hearing impairment (mostly nonsyndromic). Provides literature references and external links. Leiden Molecular Dystrophy Pages http://www.dmd.nl/index.html ‘Leiden Molecular Dystrophy Pages’ are dedicated to scientists interested in either research or diagnosis in Duchenne and Duchenne-like muscular dystrophies. Apart from mutation databases of various muscular dystrophies, it contains description of genes and proteins involved in dystrophy pathogenesis. Provides laboratory protocols and presents the latest news in the field. The site is maintained by Johan T den Dunnen from the Center for Human and Clinical Genetics at Leiden University Medical Center. Familial Dysautonomia Foundation http://www.familialdysautonomia.org/ The Familial Dysautonomia (FD) Foundation maintains this site, providing broad information related to this disease. It contains information about current research, treatment, genetics, patient care, advocacy as well as services and resources. It also provides links to pages related to FD and other genetic diseases.