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Exploring Genes and Phenotypes Within Chromosomal Regions Using OMIM's GeneScout.
Carolyn D Applegate1, François Schiettecatte2, Ada Hamosh1
1Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Current Protocols
|September 21, 2022
Summary
GeneScout is a web tool for identifying genes and phenotypes within genomic regions, aiding in the study of structural variations like copy number variants (CNVs) and regions of homozygosity (ROH). It facilitates phenotype-gene discovery by filtering and comparing genetic data.
Area of Science:
- Genomics
- Bioinformatics
- Human Genetics
Background:
- Genomic structural variations, including copy number variants (CNVs) and regions of homozygosity (ROH), play a role in phenotypic variation and evolution.
- Identifying genes and associated phenotypes within these genomic regions is crucial for understanding their functional and evolutionary impact.
- The presence of multiple CNVs and ROHs per individual complicates the identification of phenotypically significant genomic regions.
Purpose of the Study:
- To introduce GeneScout, a web-based tool designed to facilitate the search and analysis of genes and phenotypes within specific genomic regions.
- To enable researchers to filter genes and phenotypes based on inheritance patterns and clinical features.
- To provide comparative analysis of phenotypes and genomic regions, including overlap and unique region identification.
Main Methods:
- GeneScout allows users to input genomic coordinates and search for associated genes and phenotypes.
- The tool offers filtering options based on phenotype inheritance patterns and clinical features.
- Comparative analysis of two coordinate sets for overlap or unique regions is supported, with results displayed interactively.
- Supports genomic assemblies GRCh37 (hg19) and GRCh38 (hg38), with liftover functionality between them.
Main Results:
- GeneScout displays genes and phenotypes within specified genomic regions, with filtering capabilities.
- Users can compare clinical synopses of selected phenotypes via OMIM®.
- Interactive results tables provide links to external databases (ClinVar, ClinGen, gnomAD) and highlight genes spanning coordinate ranges.
- Search coordinates and results are downloadable in tab-delimited or Excel formats.
Conclusions:
- GeneScout is a valuable resource for phenotype-gene discovery within genomic regions of interest.
- The tool simplifies the analysis of complex genomic variations like CNVs and ROHs.
- GeneScout enhances genomic research by providing integrated data access and comparative analysis functionalities.
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