Genepanel.iobio is a web app to compile disease and phenotype associated gene lists. It has three main components: Genentic testing registry (GTR), Phenolyzer, HPO with ClinPhen. Genepanel is developed by iobio in MarthLab at University of Utah.
The Genetic Testing Registry (GTR®) is an NCBI resource that compiles genetic test information that has been voluntarily submitted by multiple providers.
Genepanel.iobio allows you to search for one or more disorders, and generates a list of all of genes appearing on gene panels associated with these disorders. The list is sorted with genes appearing on the most panels at the top. The list can then be filtered based on your own specific requirements.
How To Use Genetic Testing Registry
Example: Gene list for suspected condition such as "Treacher collins syndrome"
Phenolyzer is a tool from the Wang Genomics lab , that converts discrete phenotype terms into a list of candidate genes.
This is achieved by interpreting the phenotype term into a set of disease names. Then, all genes having a reported association with these diseases are found, then expands this list by considering gene-gene relation databases. Finally, all this information is integrated to generate a weighted score for each gene.
How To Use Phenolyzer
Example: Gene list for suspected Phenotype such as "Lactic acidosis"
genes from all the sources: Genetic Testing Registry, phenolyzer and HPO are combined to produce a comprehensive gene list. The list can be exported by copying it to the clipboard or by saving it to a file. genepanel.iobio is available both as a standalone app, and as part of our integrated clinical diagnostic analysis tool clin.iobio
A gene panel is a test that analyzes multiple genes at once for a patient's condition. Gene panel contains a set of genes that are known to have been associated with a particular disease or phenotypes.
A comprehensive list of candidate genes that correctly describe the phenotypic feature of a condition is very critical when ordering genetic gene panel testing as well as finding variants in whole genome sequencing (WGS) or whole exome sequencing (WES).
Gene panel test is a technique in which a number of specific genes linked to a particular genetic condition or a disease are examined at the same time. Genepanel.iobio helps by providing number of genes that are usually associated with a particular genetic conditions and this list of genes can be used for gene panel tests.
Finding out the cause of a genetic condition by ordering gene panel tests help health professionals to give the patient information about the progress of the condition, possible preventive actions or treatment.
Precision medicine, the use of genetic information to inform clinical diagnosis, continues to provide significant clinical benefits to patients. The time spent on the diagnostic variant analysis can be significantly reduced by focussing the analysis only on those genes that are already known to be relevant to the patient’s condition or phenotype(s). To this end, a number of other tools and databases exist to provide this information. However, current tools are time-consuming and tedious often require computational expertise with command line interface. Diagnostic clinicians have limited time and currently rely on consolidating disparate data sources into one comprehensive list of genes that may be associated with the disease. To address these challenges, we have developed, genepanel.iobio (https://genepanel.iobio.io/), an intuitive web app that allows diagnostic clinicians to refine and prioritize disease-relevant genes from a comprehensive set of resources. We hope our readily-accessible application will continue to bolster the work of bioinformaticians, diagnostic clinicians and others and lead to increased precision medicine diagnoses. The app is also useful when analyzing rare and undiagnosed diseases.
Gene list can be used to order a panel test as well as used to find variants or for powering variant interrogation in apps such as gene.iobio
The first step in the diagnostic variant analysis process usually involves the identification of variants in genes related to the patient’s condition or phenotypes. Compiling a comprehensive list of genes using currently available tools is not straightforward. Additionally, these tools currently have little utility for the physicians or diagnostic clinicians who currently have to rely on the experts to compile such a gene list.