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Integrates multiple regulatory networks and human disease-associated mutations for the generation of mechanistic insights into pathogenesis. iRegNet3D can be used for understanding the mechanisms by which both coding and non-coding mutations lead to disease. It may facilitate the future discovery of hitherto unknown disease genes and mutations. The software is the only tool that integrates transcription factor (TF)-TF interactions, TF-DNA interactions and chromatin-chromatin interactions as well as topologically associating domains (TADs) to study mutation/gene-phenotype relationships and provide mechanistic insights of disease-associated mutations in both coding and non-coding regions.
A freely accessible web-based tool developed as part of the Baylor-Hopkins Center for Mendelian Genomics. The goal of GeneMatcher is to identify additional individuals with rare phenotypes who had variants in the same candidate disease gene. It also facilitates connections to basic scientists working on orthologous genes in model systems with the goal of connecting their work to human Mendelian phenotypes. GeneMatcher is also part of the Matchmaker Exchange with an application programing interface enabling submitters to query other databases of genetic variants and phenotypes without having to create accounts and data entries in multiple systems.
A tool aimed at the rational design of cancer gene panels. OncoPaD estimates the cost-effectiveness of the designed panel on a cohort of tumors and provides reports on the importance of individual mutations for tumorigenesis or therapy. With a friendly interface and intuitive input, OncoPaD suggests researchers relevant sets of genes to be included in the panel, because prior knowledge or analyses indicate that their mutations either drive tumorigenesis or function as biomarkers of drug response. OncoPaD will help clinicians and researchers design tailored next-generating sequencing (NGS) panels to detect circulating tumor DNA or biopsy specimens, thereby facilitating early and accurate detection of tumors, genomics informed therapeutic decisions, patient follow-up and timely identification of resistance mechanisms to targeted agents.
MME API / Matchmaker Exchange Application Programming Interface
A protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms.
PRO-MINE / PROtein Mutations In NEurodegeneration
Contains data from the literature regarding all TDP-43/TDP43/TARDBP gene disease-associated mutations identified to date. PRO-MINE provides a web interface to query the database and to provide tools for the analysis of already reported or novel TDP-43 gene mutations. It provides simultaneous access to several prediction tools and by displaying the results into a single output. The tool simplifies and enhances the time-consuming task of assessing the potential effects of mutations on protein function by providing simultaneous retrieval and display of predictions from separate web tools for a set of submitted mutations.
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OMIM / Online Mendelian Inheritance in Man
A comprehensive, authoritative and timely research resource of curated descriptions of human genes and phenotypes and the relationships between them. OMIM® is based on the published peer-reviewed biomedical literature and is used by overlapping and diverse communities of clinicians, molecular biologists and genome scientists, as well as by students and teachers of these disciplines. Genes and phenotypes are described in separate entries and are given unique, stable six-digit identifiers (MIM numbers). OMIM® entries have a structured free-text format that provides the flexibility necessary to describe the complex and nuanced relationships between genes and genetic phenotypes in an efficient manner.
HGMD / Human Gene Mutation Database
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.
DECIPHER / DatabasE of Genomic variants and Phenotype in Humans Using Ensembl Resources
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.
LOVD / Leiden Open Variation Database
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.
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).
DistiLD Database / DistiLinkage Disequilibrium Database
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.
eRAM / encyclopedia of Rare disease Annotations for Precision Medicine
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.
DIVAS / Disease Variant Store
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.
dbDSM / database of Deleterious Synonymous Mutation
Collects, curates and manages available human disease-related SM data obtained from published literature. In the current release, dbDSM collects 1936 SM-disease association entries, including 1289 SMs and 443 human diseases from ClinVar, GRASP, GWAS Catalog, GWASdb, PolymiRTS database, PubMed database and Web of Knowledge. Additionally, we provided users a link to download all the data in the dbDSM and a link to submit novel data into the database.
HGDP / Human Genome Diversity Project
Allows to genetic diversity in human populations. HGDP has collected genomic DNA from 1,043 individuals from around the world and has determined their genotypes at more than 650,000 single nucleotide polymorphism (SNP) loci. It represents 51 different populations from Africa, Europe, the Middle East, South and Central Asia, East Asia, Oceania and the Americas. The database shares ancestry and admixture, relationships between haplotype heterozygosity and geography, and population differences in copy number variation (CNV) throughout the human genome in the 1,043 individuals.
A benchmark database suite comprising variation datasets for testing and training methods for variation effect prediction. VariBench contains information for experimentally verified effects and datasets that have been used for developing and testing the performance of prediction tools. VariBench contains datasets for disease-causing missense variations, neutral high frequency SNPs, protein stability affecting missense variations, variations affecting transcription factor binding sites and variations affecting splice sites.
Cancer GAMAdb / Genome-wide Association and Meta Analyses database
Contains key descriptive characteristics of each genetic association extracted from published genome-wide association studies (GWAS) and meta-analyses relevant to cancer risk. Cancer GAMAdb is a userful tool to find many novel genetic associations. Cancer GAMAdb also provides analytic functionalities. Filter features by nine key elements on the retrieved records allow users to perform quick descriptive analyses on the associations of interest while undergoing the dataset search.
Allows the study of genetic variation in disease. Diseasome is a database constructed using an automatic integration pipeline system. It contains information on more than 124,000 diseases, 12,000,000 single nucleotide polymorphism (SNP) markers, and about 38,500 genes, as well as more than 14,000 SNP records and 109,000 gene records associated with human diseases. This database-pipeline system can economically facilitate disease-association studies by identifying candidate genes associated with disease, and genetic variation.
Skeleton Genetics
The first comprehensive and annotated genetic skeletal disorders database, which contains information about all genetic skeletal disorders-related knowledge. SkeletonGenetics includes 8225 mutations in 357 genes, with detailed information associated with 481 clinical diseases (2260 clinical phenotype) classified in 42 groups defined by molecular, biochemical and/or radiographic criteria from 1698 publications. The SkeletonGenetics database could serve as a reclassified reference tool and valuable resource for unveiling the genetic and pathway basis of genetic skeletal disorders.
Provides allele and genotype frequency data generated in the Indian Genome Variation Consortium (IGVC) project. The database harbors 4,229 SNPs from more than 900 candidate genes in contrasting Indian populations. Analysis shows that most of the markers are from genic regions. Further, a large fraction of genes are implicated in cardiovascular, metabolic, cancer and immune system-related diseases. Thus, the IGVC data provide a basal level variation data in Indian population to study genetic diseases and pharmacology.
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.
Genome Trax
A comprehensive compilation of variant knowledge that is made available for download for easy integration into your own custom variant analysis pipeline for human whole genome, exome and targeted sequences. With Genome Trax™ content you can confidently identify known pathogenic variants or explore novel, as-yet-uncharacterized variants found within your sequence samples that are predicted to have a deleterious effect by virtue of a change in amino acid, disruption of a regulatory motif, or the disease-, drug-, or pathway-association of the affected gene. The database includes the world’s most comprehensive collection of inherited disease causing mutations from HGMD® Professional and pharmacogenomic variants from PGMD™, as well as regulatory sites from TRANSFAC®, and disease genes, drug targets and pathways from PROTEOME™. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations.
Helps to determine functionally-characterized genetic variants role in disease development and treatment. Ranomics is a comprehensive database that founded on one core principle: to improve understanding of human genetics for the betterment of patient health and wellness. It provides a cloud-based catalog of information on the functional impact of missense variants in cancer genes. This server reduces the time spend searching for literature with comprehensive functional evidence on every missense variant in hereditary cancer genes.
Annotates mutated positions both in protein sequences and their associated X-ray and solution nuclear magnetic resonance (NMR) structures. SNP2Structure allows users to inspect protein mutations that may affect the interaction with other macromolecules. It permits exploration of potential structural and functional impact of missense mutations in various human diseases. The database allows users to download the structural models for further structural and functional analysis.
HGVbase / Human Genome Variation database
Provides a non-redundant collection of all known and suspected human DNA variants of any type, emphasizing high data quality and active data collection from a broad range of sources. HGVbase is a central depository for mutation collection efforts undertaken in allegiance with the inaugurated Human Genome Variation Society (HGVS). Online search tools facilitate data interrogation of all information fields, comprising five major categories: (i) sequence location, (ii) predicted functional importance, (iii) validation status, (iv) allele frequencies in populations and (v) data sources.
CNVD / Copy Number Variation in Disease
A systematic and comprehensive database for copy number variations and related diseases, in which all the records were manually extracted from experimental data published in CNV-related articles. Hence, CNVD database is a reliable and comprehensive resource for studying diseases associated copy number variations. Users can search the database in several ways: by gene name, disease name, chromosome location, or copy number variation region. In query results, each record contains such information: species, chromosomes, the start and end locations of the CNV, related disease, genes in the CNV region and PubMed ID of the source article. The results can be downloaded in batches or single, according to the users' need.
dbWGFP / a database and web server of human whole-genome single nucleotide variants and their functional predictions
A database and web server of human whole-genome single nucleotide variants and their functional predictions. dbWGFP collects nearly 8.58 billion possible SNVs across the whole human genome, with each SNV described by 48 functional prediction scores and 44 valuable annotations. dbWGFP is a large-scale comprehensive database for functional predictions and annotations of human whole-genome SNVs. This database can not only be helpful in the capture of causative variants from massive candidates derived from whole-genome or exome sequencing data, but also provide a valuable resource in the study of human genetic variants. dbWGFP offers a user-friendly web interface to facilitate the access of the database. The web interface provides two main components: a query service for retrieving functional prediction scores and annotations of SNVs in different data formats and a download service for setting up a local version of this database. In the step-by-step mode of the query service, users can upload a file containing query variants and retrieve results online. In the batch query mode, users can upload a file containing query variants and an email address.
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