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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.
ClinGen / Clinical Genome Resource
A National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genomic variants for use in precision medicine and research. ClinGen will engage the genomics community in data sharing efforts, develop the infrastructure and standards to support curation activities, and incorporate machine-learning approaches to speed the identification of clinically relevant variants.
CGD / Clinical Genomic Database
A manually curated database of conditions with known genetic causes, focusing on medically significant genetic data with available interventions. All conditions with identified genetic causes are included in the CGD. For each entry, the database includes the gene symbol, condition(s), allelic conditions, inheritance, age (pediatric or adult) in which interventions are indicated, clinical categorization, and a general description of interventions/rationale. The contents are not intended to serve as nor substitute for comprehensive clinical guidelines, but are rather intended to briefly describe the types of interventions that might be considered.
COL7A1 mutation database
Provides a registry for clinicians, genetic counselors, and researchers about dystrophic epidermolysis bullosa DEB patients and their associated COL7A1 mutations. The international dystrophic epidermolysis bullosa patient registry also collects data about the genotypes (i.e., the combinations of mutations in RDEB), patients, and clinical and molecular phenotypes in which they are involved. Lists contains all the phenotypes ever found in combination with a certain genotype including the reported exceptions to that most likely outcome.
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.
UMD-CFTR
Combines a relational database with various functions that can be directly queried online and shared by users. UMD-CFTR is a database designed for extensive collection and analysis of disease-causing mutations, polymorphisms, and unclassified variants. This resource offers, for patients who have been explored for all Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) coding/flanking sequences, the possibility to record and analyze any variations that have been found for each allele in cis and in trans.
JG-SNP / Japanese Single Nucleotide Polymorphism for Geriatric Research
Collects information about genetic polymorphisms topic. JG-SNP is an online resource that informs about allele frequencies of single nucleotide polymorphisms (SNPs) of candidate genes and associations between SNPs and geriatric diseases. It provides an explanation on the significance of genetic polymorphisms and brief explanations on each geriatric disease. Comparison can be made between researchers’ data on SNPs of the candidate genes to obtain the allele frequencies in the elderly population.
OncoLnc
A tool for interactively exploring survival correlations, and for downloading clinical data coupled to expression data for mRNAs, miRNAs, or lncRNAs. OncoLnc contains survival data for 8,647 patients from 21 cancer studies performed by The Cancer Genome Atlas (TCGA), along with RNA-seq expression for mRNAs and miRNAs from TCGA, and lncRNA expression from MiTranscriptome beta. Storing this data gives users the ability to separate patients by gene expression, and then create publication-quality Kaplan-Meier plots or download the data for further analyses. OncoLnc also stores precomputed survival analyses, allowing users to quickly explore survival correlations for up to 21 cancers in a single click.
PMKB / Precision Medicine Knowledge Base
Provides information about clinical cancer variants and interpretations in a structured way. PMKB is an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations. The database contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. The interpretations are accessed either directly via the Web interface or programmatically via the existing application programming interface (API).
CIViC / Clinical Interpretations of Variants in Cancer
Describes the therapeutic, prognostic, and diagnostic relevance of inherited and somatic variants of all types. CIViC is committed to open source code, open access content, public application programming interfaces (APIs), and provenance of supporting evidence to allow for the transparent creation of current and accurate variant interpretations for use in cancer precision medicine. It contains 1,411 curated interpretations of clinical relevance for 560 variants affecting 235 genes. These interpretations were curated from 918 published studies by 37 CIViC curators. CIViC evidence records are currently biased towards somatic alterations, supporting positive associations with treatment response and supported by a wide range of evidence levels and trust ratings. At least one evidence records has been created for 144 cancer subtypes and 271 drugs, with some bias towards lung, breast, leukemia, colorectal and skin cancer, and associated targeted therapies.
KDD / Kawasaki Disease Database
Facilitates the usage of clinical and genetic data collected by the Korean Kawasaki Disease Genetics Consortium (KKDGC). KDD was built by collecting clinical data of kawasaki disease (KD) patients using 51 variables of which the main are: (1) personal information, (2) clinical signs and symptoms, (3) echocardiogram finding, (4) treatment, (5) family history and recurrence and (6) laboratory test data. It can be used to find a potential disease cause, a treatment, and a prevention method.
OncoKB
Contains information about the effects and treatment implications of specific cancer gene alterations. OncoKB is a precision oncology knowledge base that offers oncologists detailed information about individual mutations found in cancer and enables them to make treatment decisions. This resource currently contains treatment information for Level 1, Level 2, and Level 3 variants, i.e. those variants for which an FDA-approved or standard of care treatment is available (Levels 1 and 2), and those for which there is clinically proven sensitivity to drugs that are currently in clinical trials (Level 3).
Personalized Cancer Therapy
Allows physicians and patients to assess potential therapy options based on specific tumor biomarkers. Personalized Cancer Therapy integrates information about tumor DNA, RNA, protein and metabolomic profiles with predicted therapy response. The approach used for the generation of this resource is: (i) association of a detected genomic alteration with tumor development and growth, (ii) association of genomic alteration to increased or decreased response to therapy, (iii) availability of relevant Food and Drug Administration (FDA)-approved therapies or investigational agents in clinical trials. Personalized Cancer Therapy provides scientific support and rationale for all cancer patients and physicians to use as a resource in guiding potential therapy options. The information presented is not intended to provide direct treatment recommendations, but rather to discuss what is known about cancer-related genes and their implications for cancer treatment.
MExDB / Melanoma Exome Database
Obsolete
Provides valuable biological tool to improve the genetic comprehension of complex cancer disease. MExDB is an extensive genomic characterization for coding mutations and DNA copy number alterations of six melanoma cell lines derived from metastatic lesions of stage. It also studies functional relevance of individual mutational events, and these findings could provide insights potentially useful for identification of novel therapeutic targets for cutaneous malignant melanoma.
Database of cattle candidate genes and genetic markers for milk production and mastitis
Obsolete
Provides an integrated research tool that incorporates different types of information supporting a genomic approach to study lactation, udder development and health. The Database of cattle candidate genes and genetic markers for milk production and mastitis is only downloadable in Excel format. This resource contains almost 950 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies.
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