Genetics & Medicine

Databases

A collection of biomedical books that can be searched directly or from linked data in other NCBI databases. The collection includes biomedical textbooks, other scientific titles, genetic resources such as GeneReviews, and NCBI help manuals.

ClinVar

A resource to provide a public, tracked record of reported relationships between human variation and observed health status with supporting evidence. Related information in the NIH Genetic Testing Registry (GTR)MedGenGeneOMIMPubMed and other sources is accessible through hyperlinks on the records.

An archive and distribution center for the description and results of studies which investigate the interaction of genotype and phenotype. These studies include genome-wide association (GWAS), medical resequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. 

Database of Major Histocompatibility Complex (dbMHC)

An open, publicly accessible platform where the HLA community can submit, edit, view, and exchange data related to the human major histocompatibility complex.  It consists of an interactive Alignment Viewer for HLA and related genes, an MHC microsatellite database, a sequence interpretation site for Sequencing Based Typing (SBT), and a Primer/Probe database.

A searchable database of genes, focusing on genomes that have been completely sequenced and that have an active research community to contribute gene-specific data. Information includes nomenclature, chromosomal localization, gene products and their attributes (e.g., protein interactions), associated markers, phenotypes, interactions, and links to citations, sequences, variation details, maps, expression reports, homologs, protein domain content, and external databases.

GeneReviews

A collection of expert-authored, peer-reviewed disease descriptions on the NCBI Bookshelf that apply genetic testing to the diagnosis, management, and genetic counseling of patients and families with specific inherited conditions.

Genes and Disease

Summaries of information for selected genetic disorders with discussions of the underlying mutation(s) and clinical features, as well as links to related databases and organizations.

Genetic Testing Registry (GTR)

A voluntary registry of genetic tests and laboratories, with detailed information about the tests such as what is measured and analytic and clinical validity.  GTR also is a nexus for information about genetic conditions and provides context-specific links to a variety of resources, including practice guidelines, published literature, and genetic data/information. The initial scope of GTR includes single gene tests for Mendelian disorders, as well as arrays, panels and pharmacogenetic tests.

HIV-1, Human Protein Interaction Database

A database of known interactions of HIV-1 proteins with proteins from human hosts. It provides annotated bibliographies of published reports of protein interactions, with links to the corresponding PubMed records and sequence data.

Influenza Virus

A compilation of data from the NIAID Influenza Genome Sequencing Project and GenBank.  It provides tools for flu sequence analysis, annotation and submission to GenBank. This resource also has links to other flu sequence resources, and publications and general information about flu viruses.

MedGen

A portal to information about medical genetics. MedGen includes term lists from multiple sources and organizes them into concept groupings and hierarchies. Links are also provided to information related to those concepts in the NIH Genetic Testing Registry (GTR), ClinVarGene, OMIM, PubMed, and other sources.

A database of  human genes and genetic disorders. NCBI maintains current content and continues to support its searching and integration with other NCBI databases.  However, OMIM now has a new home at omim.org, and users are directed to this site for full record displays.

A database of citations and abstracts for biomedical literature from MEDLINE and additional life science journals. Links are provided when full text versions of the articles are available via PubMed Central (described below) or other websites.

A digital archive of full-text biomedical and life sciences journal literature, including clinical medicine and public health.

A collection of clinical effectiveness reviews and other resources to help consumers and clinicians use and understand clinical research results. These are drawn from the NCBI Bookshelf and PubMed, including published systematic reviews from organizations such as the Agency for Health Care Research and Quality, The Cochrane Collaboration, and others (see complete listing). Links to full text articles are provided when available.

A collection of human gene-specific reference genomic sequences. RefSeq gene is a subset of  NCBI’s RefSeq database, and are defined based on review from curators of locus-specific databases and the genetic testing community. They form a stable foundation for reporting mutations, for establishing consistent intron and exon numbering conventions, and for defining the coordinates of other biologically significant variation. RefSeqGene is a part of the Locus Reference Genomic ( LRG) Collaboration.
Retrovirus Resources

A collection of resources specifically designed to support the research of retroviruses, including a genotyping tool that uses the BLAST algorithm to identify the genotype of a query sequence; an alignment tool for global alignment of multiple sequences; an HIV-1 automatic sequence annotation tool; and annotated maps of numerous retroviruses viewable in GenBank, FASTA, and graphic formats, with links to associated sequence records.

SARS CoV

A summary of data for the SARS coronavirus (CoV), including links to the most recent sequence data and publications, links to other SARS related resources, and a pre-computed alignment of genome sequences from various isolates.

Virus Variation

An extension of the Influenza Virus Resource to other organisms, providing an interface to download sequence sets of selected viruses, analysis tools, including virus-specific BLAST pages, and genome annotation pipelines.

Downloads

FTP: ClinVar Data

This site provides full data extractions in XML and summary data in VCF format. It contains files with information about standard terms used in ClinVarMedGen, and GTR.

FTP: SKY/M-Fish and CGH Data

This site contains SKY-CGH data in ASN.1, XML and EasySKYCGH formats. See the skycghreadme.txt file for more information.

FTP: dbGAP Open-Access Data

Open-access data generally include summaries of genotype/phenotype association studies, descriptions of the measured variables, and study documents, such as the protocol and questionnaires. Access to individual-level data, including phenotypic data tables and genotypes, requires varying levels of authorization.

FTP: dbMHC Data

This site contains data in separate directories for the various projects and resources within the database of human major histocompatibility (dbMHC).

Submissions

Database of Genotype and Phenotype (dbGaP) Data Submission Policies

Guidelines and requirements for submitting genotype and phenotype association data to dbGaP.

Database of Major Histocompatibility Complex (dbMHC) Microsatellite Markers Submission Template

Guidelines and template for submitting MHC region microsatellite data to dbMHC.

Submission Portal

A single entry point for submitters to link to and find information about all of the data submission processes at NCBI. Currently, this serves as an interface for the registration of BioProjects and BioSamples and submission of data for WGS and GTR. Future additions to this site are planned.

Tools

1000 Genomes Browser

An interactive graphical viewer that allows users to explore variant calls, genotype calls and supporting evidence (such as aligned sequence reads) that have been produced by the 1000 Genomes Project.

BLAST Microbial Genomes

Performs a BLAST search for similar sequences from selected complete eukaryotic and prokaryotic genomes.

BLAST RefSeqGene

Performs a BLAST search of the genomic sequences in the RefSeqGene/LRG set. The default display provides ready navigation to review alignments in the Graphics display.

Provides special browsing capabilities of maps and assembled sequences for a subset of organisms. You can view and search an organism's complete genome, display maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest.

Phenotype-Genotype Integrator (PheGenI)

Supports finding human phenotype/genotype relationships with queries by phenotype, chromosome location, gene, and SNP identifiers. Currently includes information from dbGaP, the NHGRI GWAS Catalog, and GTeX. Displays results on the genome, on sequence, or in tables for download.

A specialized PubMed search form targeted to clinicians and health services researchers. The page simplifies searching by clinical study category, finding systematic reviews and searching the medical genetics literature.

Sequence Viewer

Provides a configurable graphical display of a nucleotide or protein sequence and features that have been annotated on that sequence. In addition to use on NCBI sequence database pages, this viewer is available as an embeddable webpage component. Detailed documentation including an API Reference guide is available for developers wishing to embed the viewer in their own pages.

Variation Reporter

A tool designed to search for and report human sequence variation data from dbSNP and dbVar. Individual variations or batch files can be submitted in HGVS, GVF or BED formats. Related information will be retrieved and reported in a downloadable table containing variation identifiers, nucleotide and cytogenetic band locations on various genomic assemblies, allele type and minor allele frequencies, predicted functional consequences (missense, nonsense, frameshift, splice site, etc.), reported clinical significance, and relevant citations.