Variant-disease association databases | Genome annotation
The invention of high throughput sequencing technologies has led to the discoveries of hundreds of thousands of genetic variants associated with thousands of human diseases. Many of these genetic variants are located outside the protein coding regions, and as such, it is challenging to interpret the function of these genetic variants by traditional genetic approaches.
Offers an online catalog of human genes and genetic disorders. OMIM integrates genomic coordinate searches of the gene map, views of genetic heterogeneity of phenotypes, and side-by-side comparisons of clinical synopses. It focuses on the molecular relationship between genetic variation and phenotypic expression. This database is based on the published peer-reviewed biomedical literature. It is useful for clinicians, molecular biologists and genome scientists.
Compiles information related to disease-related functional genetic variation in the germline. HGMD includes more than 200000 mutation entries, manually curated, obtained from the scientific literature. The database can be consulted in two formats: a public and a commercial version providing additional features. It can be used for supporting the pathological authenticity and/or novelty of detected gene lesions, establishing an overview of the mutational spectra for specific genes.
A permanent archive that promotes the distribution and sharing of genetic and phenotypic data consented for specific approved uses but not fully open, public distribution. The EGA follows strict protocols for information management, data storage, security and dissemination. Authorized access to the data is managed in partnership with the data-providing organizations. The EGA includes major reference data collections for human genetics research.
An accessible online repository of genetic variation with associated phenotypes that facilitates the identification and interpretation of pathogenic genetic variation in patients with rare disorders. Contributing to DECIPHER is an international consortium of >200 academic clinical centres of genetic medicine and ≥1600 clinical geneticists and diagnostic laboratory scientists. Information integrated from a variety of bioinformatics resources, coupled with visualization tools, provides a comprehensive set of tools to identify other patients with similar genotype-phenotype characteristics and highlights potentially pathogenic genes.
Provides germline and somatic variants of any size, type or genomic location. ClinVar gathers interpretations of clinical significance of variants for reported conditions. It accepts submissions from clinical testing labs, researchers, locus-specific databases, other databases, expert panels and groups establishing professional guidelines from all countries. This database offers general and advanced query interfaces.
Permits the identification of active long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), messenger RNA (mRNA) interactions. LncACTdb can also be used for dissecting the competing endogenous RNAs (ceRNAs) regulation in various cancers and identifying novel cancer biomarkers. Moreover, this resource provides confidential resources for researchers. Furthermore, it can supply illustration of survival, network and cancer hallmark information.
Provides a collection of millions of methylation quantitative trait loci (meQTLs) across more than 20 cancer types. Pancan-meQTL can serve for the identification of single nucleotide polymorphisms (SNPs) that significantly affect DNA methylation levels. It allows the assessment of the effects of genetic variants on DNA methylation across diverse cancer types. This tool is useful in the fields of cancer and epigenetic research.
Hosts information dealing with single nucleotide polymorphisms (SNPs) and multiple protein post-translational modifications (PTMs). AWESOME provides a repository of more than 1,000,000 coding SNPs encompassing common and rare variants, about 18,000 proteins and 6 PTM types. Users can submit queries by gene, rsID or chromosome location and can also download files of interest in format including TSV, CSV or Excel.
Gathers information about reference sequences designed for the reporting of diagnostically relevant variants. Locus Reference Genomic (LRG) is a manually curated database which provides for each record a stable reference sequence including genomic DNA, transcript and protein sequences and an updated section accompanied by the most recent biological information about LRG.
Increases the usage of existing genome-wide association study (GWAS) results. DistiLD database performs three important tasks: (i) published GWAS are collected from several sources and linked to standardized, international disease codes; (ii) data from the International HapMap program are analyzed to define linkage disequilibrium (LD) blocks onto which single nucleotide polymorphisms (SNPs) and genes are mapped; (iii) a web interface makes it easy to query and visualize disease-associated SNPs and genes within LD blocks. Users can query DistiLD in three different ways, starting from either a disease, a list of SNPs or a list of genes.
Provide a flexible, freely available tool for Gene-centered collection and display of DNA variations. LOVD 3.0 extends this idea to also provide patient-centered data storage and storage of NGS data, even of variants outside of genes. LOVD allows users to link large numbers of DNA variants in one or more genes to an individual (multi-gene disorders or large scale next-generation sequencing). You can even use LOVD on your personal computer to browse through the variants in your own exome/genome. To maintain a high quality of the data stored, LOVD connects with various resources, like HGNC, NCBI, EBI and Mutalyzer.
Gathers genetic, genomic, and clinical knowledge of coding variants in the human genome. VarCards accelerates the prioritization of candidate variations and genes. It offers a web interface to search, browse and annotate the variant and gene-level implications of any given coding variants. This database is composed of about 110 155 000 single nucleotide variants (SNVs) and 1 223 000 insertions and deletions (INDELs) in coding regions or splicing sites.
A robust, useful database for collection, storage, and analysis of phenotypic data, especially in the context of whole exome/genome sequencing approaches to identify the responsible gene and variant. The phenotypic features are organized hierarchically according to the major headings and subheadings of the Online Mendelian Inheritance in Man (OMIM) clinical synopses, with further subdivisions according to structure and function. Every string allows for a free-text entry. All of the approximately 2,900 features use the preferred term from Elements of Morphology and are fully searchable and mapped to the Human Phenotype Ontology and Elements of Morphology. The PhenoDB allows for ascertainment of relevant information from a case in a family or cohort, which is then searchable by family, OMIM number, phenotypic feature, mode of inheritance, genes screened, and so on.
Classifies and catalogs the predicted functionality of nonsynonymous coding SNPs (nsSNPs) in human genes to facilitate sequence-based association studies. PolyDoms contains a central table, “Gene”, that has an up-to-date list of all human RefSeq genes and is linked to several other master tables. Users can query the database with sequence accession numbers, gene symbols, Entrez Gene IDs, rsSNP IDs, description or probeset IDs (Illumina; Affymetrix). They can also retrieve a list of genes and associated coding regions (cSNPs).
Provides a resource for researchers and clinicians to conduct studies and practice in rare diseases. eRAM is an online resource that includes (i) collected phenotypes and symptoms of rare diseases from published medical literatures and clinical data, (ii) standardized and classified extracted information via different patterns and approaches and (iii) enriched clinical and molecular annotations for most rare diseases.
Provides unified broad annotation and flexible filtering strategies. VariantDB can retrieve annotation or filtering data from multiple sources in parallel. It can provide family and experimental relations which can be reused to formulate inheritance patterns for variant filtering. The platform also provides a tool to automate the conversion between genome builds from the web interface. It offers an all-in-one solution for annotation and filtering of variants obtained from next generation sequencing (NGS) experiments.
Allows users to search and list gene expression values from a selected cell line. TCLP integrates a catalog of cancer cell line annotations integrating human leukocyte antigen (HLA) type, HLA expression, predicted HLA Class I and Class II neo-epitopes, virus, and gene expression. It enables users to filter via the gene name or to define reads per kilobase of exon per million mapped reads (RPKM) value range.
Facilitates searches for drug therapies clinically associated with genetic biomarkers. DEPO is a database of clinically relevant genomic variants and their respective drug therapies. It contains observed and validated, druggable genomic events: single nucleotide polymorphisms (missense, frameshift, and nonsense mutation single nucleotide polymorphisms), in-frame insertions and deletions, fusions, copy number alterations (amplification and loss), and expression changes. Users can query the resource using standard gene names and, optionally, a cancer type, variant type or position.
Provides information on genetic variants observed in various disease populations. We have gathered several large studies, including GERA and GRU, and computed population- and disease-specific genetic variant frequencies. In total, our portal provides fast access to genetic variants observed in 84,928 individuals from 39 disease populations. We also include 66,335 controls, such as the 1000 Genomes and Scripps Wellderly. Combining multiple studies helps validate disease-associated variants in each underlying data set, detect potential false positives using frequencies of control populations, and identify novel candidate disease-causing alterations in known or suspected genes. Users can quickly obtain frequencies, functional annotations, and known disease annotations by performing simple queries.