The Spencer S. Eccles
Health Sciences Library
Health Sciences Library
General Resources:
Spezialised Resources:
Molecular Databases:
References and Further Information
Credits and Disclaimer
Malignant neoplasm ranked second as a cause of death in the United States in 1999 (Minino and Smith, 2001). A correlation between the malfunction of the breast cancer gene, BRCA1, and the occurrence of cancer has been established (Hall et al., 1992). Media and consumer health services quickly spread the word that our health lies in our genes. Diseases of the heart ranked first as a cause of death in the United States in 1999 (Minino and Smith, 2001). Is there a correlation of a gene malfunction and heart disease, too? Which genes are involved in a particular kind of cancer or heart disease? The genetic predisposition to complex diseases such as cancer or heart disease, where environmental factors influence health, becomes a valuable tool for predicting the possibility, not the guarantee of disease.
The progress of the Human Genome Project over the last few years has lead to the development of many resources that compile information and unfold the links between biological data, such as gene mutations and diseases. The resources discussed below represent catalogs of genetic diseases as well as include tools to locate genes and view chromosome maps. With this article we focus on genetic information resources that receive federal funding, but many will provide links to valuable clinical information from resources not highlighted here. The resources are developed to empower the clinical geneticist as well as other professionals in the field of genetics research to make informed choices. An attempt is made to distinguish between general and specialized resources. However, the users should be familiar with Evaluating Internet Resources since publishing on the Web does not require a traditional review process as does publishing in professional journals.
OMIM is a database of human genes and genetic disorders. The first compendium of Mendelian Inheritance in Man was published in 1966, when Dr. Victor A. McKusick and his colleagues at the Johns Hopkins University School of Medicine made the effort to catalog genetic traits. The online version of MIM (OMIM) became available in 1987 from Johns Hopkins and 1995 from the National Center of Biotechnolgy Information (NCBI). OMIM records include phenotypic descriptions and references for genetic disorders as well as molecular information such as allelic variations, mapping information and links to relevant molecular databases and maps. Cited references are linked to PubMed, but an exhaustive review of the literature would require a separate PubMed search. OMIM is still curated at the Johns Hopkins School of Medicine and updated daily. Since OMIM concentrates on inherited disorders, the database contains only little information on chromosomal aberrations.
OMIM is open to the public but targeted to a professional audience as e.g., physicians, genetics researchers and students in science and medicine.
Since OMIM is integrated in NCBI's ENTREZ retrival system, it is subject to
Gene symbols as well as the full name of the gene can be entered. Also available are Entrez features such as
GeneTestsGeneClinics is an initiative of University of Washington Children's Hospital Regional Center in Seattle, Washington, to provide centralized access to information for professionals in the field of clinical genetics. The contribution of information and service-information is voluntary and therefore not comprehensive. GeneTestsGeneClinics is free, but does require a one-time registration, and a User Name and Password to access the information. The information is provided under the following categories:
The sections Gene Reviews, the Laboratory and the Clinics Directory each have their own search interface,
which is available from the homepage by clicking on the section name on the top bar of the page after the
user log-on.
The search options include searching by
GeneCards is an electronic encyclopedia of biological and medical information produced by the Crown Human Genomics Center and the Bioinformatics Unit of the Weizmann Institute of Science in Rehovot, Israel. The aim is to provide a user-friendly and easy-to-navigate access to information for human genes by making use of standardized gene nomenclature. The GeneCards database currently (April 2002) contains 72704 GeneCards (Genes). The data is extracted from many different sources and initiatives and is presented in a table with extensive link-outs for the ease of use. The table rows are organized as follows:
GeneCards can be searched by keyword, gene symbol of alias or by using boolean operators. The exact word match is used when nothing else is specified (case doesn't matter).
In 1996 the National Cancer Institute (NCI) launched the Cancer
Genome Anatomy Project (CGAP) as an interdisciplinary program to study the molecular differences between
a normal cell and a cancer cell. Background information on the project can be viewed by following the
Educational Resources link from
the homepage, whereas the slide tour provides an overview
of the CGAP concept.
In brief, CGAP provides access to
An effort is made to categorize the information into:
However, resources within these categories are overlapping. The Gene Ontology Browser (GO Browser), for example, a tool to classify human and mouse genes by molecular function, biological process, and cellular component, can be found in the Genes as well as in the Tools section.
The Chromosome section provides 4 maps to examine chromosomes:
The database is hosted at the National Library of Medicine and contains over 700 (of approximately 1600 - 2000) descriptions of congenital abnormalities associated with mental retardation including their clinical features. X-linked and chromosomal aberrations that have syndrome characteristics but are not routinely classified as syndromes in the literature can also be found.
Despite looking up the alphabetic table of contents, the database can be searched by
"OrphaNet is a relational database of rare diseases and orphan drugs for the general public. It aims to improve diagnosis, management and treatment of rare diseases. OrphaNet contains an on-line encyclopedia written by European experts and a list of services for patients and professionals. This list includes information about specialized outpatient clinics, diagnostic laboratories, current research projects and support groups."
OphaNet currently contains information on 1,150 rare diseases that can be searched using a variety of search options (e.g. Disease, Signs, Outpatient clinics, Research programs, Clinical trials, Registry, Clinical test, Accreditation, Support group).
The search options are made available under the categories "patients", "professionals", "support groups", "industry" and "public" to meet the users need. Most search options include the ability to type in own search requests or access an alphabetical listing or a thesaurus. OrphaNet is under development and will be available in multiple languages in the future.
The Human Genome Epidemiology Network (HuGENet), hosted on the Center of Disease Control and Prevention (CDC) website, aims to develop a network to exchange information on population-based human genome epidemiology. The database contains peer-reviewed literature on population-specific prevalence data on human gene variants, gene-environment interaction and more.
The atlas is a collaborative project by GFCO, INFOBIOGEN and the University Hospital of Poitiers, France. The resource is a peer reviewed on-line journal and database containing information on genes involved in cancer, cytogenetics and clinical entities in cancer, and cancer-prone diseases. It is made and maintained by professionals in the field of cancer research and genomics and the contributions are reviewed before acceptance.
The contents can be searched by chromosome number or by entering one of the following categories:
"Spectral Karyotyping (SKY) and Comparative Genomic Hybridization (CGH) are complementary fluorescent molecular cytogenetic techniques. SKY permits the simultaneous visualization of all human or mouse chromosomes in a different color, facilitating the identification of chromosomal aberrations. CGH utilizes the hybridization of differentially labeled tumor and reference DNA to generate a map of DNA copy number changes in tumor genomes."
The database can be searched by entering
Searchable Topics are
Special features of the page are:
Single nucleotide polymorphisms (SNPs) are the most common variations within populations. In order to
facilitate genetics studies the National Human Genome Research
Institute (NHGRI) in collaboration with the National
Center for Biotechnology Information (NCBI) launched dbSNP, which currently contains over
4.100.000 submissions of SNPs (April 2002) of both single base nucleotide substitutions and short deletion
and insertion polymorphism.
The database can be searched for genetic variations by using
"dbSTS is an NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites."
Databases:
Gateways and Newsletters:
Information on the Human Genome Project and Educational Pages:
Ethics and Genetics:
References and Readings:
This material was adapted from NCBI's Educational Collaboration with course modules developed by Janet Ohles (Medical Sciences Library, New York Medical College), Kris Alpi (Weill Cornell Medical Library, New York), Michele R. Tennant, Ph.D. (Health Science Center Libraries, University of Florida), Jennifer Lyon (Eskind Biomedical Library, Vanderbilt University Medical Center) and others.
These databases are ment to compile and disseminate information. They are in no way substitute for a visit to the health care provider.
