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.
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.
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.
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.
Offers a portal through which families with rare genetic conditions who are interested in sharing their health and genetic information can connect with other families, clinicians, and researchers. By sharing information through MyGene2, a family can help and even participate in the discovery of new genetic conditions and the genes underlying these conditions. Families have the option to make the information they submit to MyGene2 available to anyone visiting the site (i.e., public) or available to only registered users who have also contributed data to MyGene2. Families also have the choice of whether or not they want to be contacted by clinicians and researchers or other families.
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.
Informs about copy number variation (CNV) association. CNV association DB is an online resource that puts in storage CNV region data, or results of one research laboratory. The database can be browse by informing CNV keyword search, whole genome, or region.
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.