C12199: Mutation Position Imaging Toolbox (muPIT) Interactive
Novelty:
The current invention is a browser-based application for single nucleotide variants and mutations, designed to map genomic positions onto 3D protein structures.
Value Proposition:
The vast amount of available sequencing data is evidence that the limiting factor of research is shifting from data acquisition towards data analysis. As part of this effort, computational methods have been developed to identify putatively relevant genetic variants, but results are sometimes difficult to interpret. For example, many popular methods use machine learning algorithms. While these methods provide a means to score the putative importance of genetic variants, the biological meaning of a score may be difficult to interpret. The current invention allows the researcher to explore the biological function of genetic variants and has the following advantages:
• Functional annotations are incorporated into the 3D display, allowing for rapid interactive visualization of the structural and functional relevance of mutations.
• MuPIT currently accepts up to 2500 mutations in a single upload.
• Visualizations updated from trusted databases.
• Compatible with common web browsers.
Technical Details:
Johns Hopkins researchers have developed MuPIT Interactive to complement existing computational tools by visualization with an interactive three-dimensional protein structure taken from the Protein Data Bank (PDB). Users can view variation in the context of position-specific annotations, such as binding sites, experimental mutagenesis results, and both polymorphic and disease-associated variants that have been previously documented. A software pipeline creates mappings between genomic positions and PDB structure positions. Genomic positions are first mapped to RefSeq transcripts, which are subsequently mapped to SwissProt protein sequences, and then finally mapped to PDB sequence. Alignments are calculated on a high-performance computing (HPC) cluster. The resulting annotations and alignments are stored in a MySQL database. The database is updated on a weekly basis to stay in sync with PDB and bi-monthly to stay in sync with UniProt and RefSeq. Queries take from one second to one minute, depending on the number of variants submitted, up to a maximum of 2500.
Looking for Partners:
To develop and commercialize the technology as a tool for genomic visualization.
Stage of Development:
Pre-Clinical
Data Availability:
Under CDA/NDA
Publications/Associated Cases:
Niknafs et al. MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. Hum Genet. 2013 Nov;132(11):1235-43
